Jurnal AgroBiogen

cover jurnal agrobiogenJurnal AgroBiogen merupakan jurnal ilmiah yang menerbitkan artikel hasil penelitian primer maupun ulasan di bidang bioteknologi dan sumber daya genetis pertanian. Jurnal AgroBiogen merupakan pengganti atau kelanjutan dari Jurnal AgroBio sejak tahun 2005. Berikut adalah daftar artikel yang telah diterbitkan dalam Jurnal AgroBiogen.

2015

  1. Chaerani and R. E. Voorrips. 2015. Segregation Analysis of SSR, SNP, and AFLP Markers in F2 Population of Solanum lycopersicum × S. Arcanum. Jurnal agrobiogen 11 (1):1-6.
    [BibTeX] [Abstract] [PDF: Segregation Analysis of SSR, SNP, and AFLP Markers in F2 Population of Solanum lycopersicum × S. Arcanum ]
    Distorted marker segregation is a common phenomenon in interspecific cross of various crops. Previous mapping study of early blight fungus (Alternaria solani) resistance loci showed 52% marker distortion in the genetic linkage map of 176 F2 progenies derived from Solanum lycopersicum cv. Solentos × S. arcanum LA2157. The objectives of this study were to analyze in detail the marker segregation in the map and to determine the cause of segregation distortion by calculating the allele and genotype frequencies of each marker. Out of 371 mapped markers, 192 markers deviated from the expected Mendelian ratio of 1 : 2 : 1. Distorted markers occurred in all chromosomes, ranging from 1% to 92%. Surplus of S. arcanum homozygotes contributed most to the skewness (40%), followed by heterozygotes (18%), and S. lycopersicum homozygotes (5%). The allele frequencies of 152 markers deviated from the expected allele homogeneity frequency, indicating that their segregation might be affected by gamethophytic selection. Sixty-one markers deviated from the expected F2 genotype frequency distribution, indicating that their segregation might be influenced by zygotic selection. Thirty-seven of the distorted markers showed deviation from expected frequencies of allele homogeneity and F2 genotype frequency distribution. Distorted markers can be retained in linkage analysis since chromosomal regions containing distorted markers showed linkage with early blight fungus resistance loci. Further identification of the mechanism contributing segregation distortion requires detailed and extensive mapping studies.
    @article{Chaerani14p1,
    title = {{Segregation Analysis of SSR, SNP, and AFLP Markers in F2 Population of Solanum lycopersicum × S. Arcanum}},
    author = {Chaerani and R. E. Voorrips},
    journal = {Jurnal AgroBiogen},
    pages = {1 - 6},
    volume = {11},
    number = {1},
    year = {2015},
    abstract = {Distorted marker segregation is a common phenomenon in interspecific cross of various crops. Previous mapping study of early blight fungus (Alternaria solani) resistance loci showed 52% marker distortion in the genetic linkage map of 176 F2 progenies derived from Solanum lycopersicum cv. Solentos × S. arcanum LA2157. The objectives of this study were to analyze in detail the marker segregation in the map and to determine the cause of segregation distortion by calculating the allele and genotype frequencies of each marker. Out of 371 mapped markers, 192 markers deviated from the expected Mendelian ratio of 1 : 2 : 1. Distorted markers occurred in all chromosomes, ranging from 1% to 92%. Surplus of S. arcanum homozygotes contributed most to the skewness (40%), followed by heterozygotes (18%), and S. lycopersicum homozygotes (5%). The allele frequencies of 152 markers deviated from the expected allele homogeneity frequency, indicating that their segregation might be affected by gamethophytic selection. Sixty-one markers deviated from the expected F2 genotype frequency distribution, indicating that their segregation might be influenced by zygotic selection. Thirty-seven of the distorted markers showed deviation from expected frequencies of allele homogeneity and F2 genotype frequency distribution. Distorted markers can be retained in linkage analysis since chromosomal regions containing distorted markers showed linkage with early blight fungus resistance loci. Further identification of the mechanism contributing segregation distortion requires detailed and extensive mapping studies.},
    keywords = {tomato, solanum arcanum, marker segregation distortion},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Jurnal Agrobiogen 11-1/Chaerani.pdf}
    }
  2. Ambarwati, A. D., E. Listanto, Slamet, Umar, Sustiprijatno, and Sutoro. 2015. Induksi dan Regenerasi Kalus Jagung yang Ditransformasi dengan Gen CsNitr1-L melalui Penembakan Partikel. Jurnal agrobiogen 11 (1):25-32.
    [BibTeX] [Abstract] [PDF: Induksi dan Regenerasi Kalus Jagung yang Ditransformasi dengan Gen CsNitr1-L melalui Penembakan Partikel ]
    The success in development of transgenic plants is influenced by the regeneration system. The objective of the study was to assess the response of maize genotypes to regeneration system of organogenesis and embryogenesis, after transformed with CsNitr1-L gene through particle bombardment. Induction and callus regeneration of maize immature embryos of inbred lines Ult:cm.1#, ARC 178-123-112-XB3, and AZ2 were conducted through organogenesis, whereas those inbred lines AZ1, AZ2, P4G19(S)C2.59.3.3.1.3 and P4S3.29.4.4.1 were conducted through embryogenesis somatic. Transformation of CsNitr1-L gene was done with the distance of bombardment of 7 cm and 9 cm and calli were then selected using 10 mg/l hygromycin. All explants (100%) of inbred lines Ult:cm.1# formed organogenic callus, while callus formation of ARC 178-123-112-XB3 was 94.3% and AZ2 was 60.5%. Ult:cm.1# was the most responsive line to the regeneration of organogenesis and produced 24 green shoots, compared with ARC 178-123-112-XB3 which produced one green shoot and AZ2 that did not produce green shoots. The highest percentage of embryogenic calli formed through somatic embryogenesis was obtained on inbred lines AZ1 (85.4%) and the lowest was on P4S3.29.4.4.1 (18.9%). Inbred lines AZ1 had the highest percentage of regeneration (50.7%) and produced 62 plants, followed by P4G19(S)C2.59.3.3.1.3 that produced 17 plants (2.8%) and P4S3.29.4.4.1 which produced two plants. Preliminary identification on 31 putative transgenic plants through PCR analysis produced 22 plants (70.96%) that contained nptII gene. Keywords: Zea mays, organogenesis, somatic embryogenesis, transformant identification.
    @article{Ambarwati15p25,
    title = {{Induksi dan Regenerasi Kalus Jagung yang Ditransformasi dengan Gen CsNitr1-L melalui Penembakan Partikel}},
    author = {A. D. Ambarwati and E. Listanto and Slamet and Umar and Sustiprijatno and Sutoro},
    journal = {Jurnal AgroBiogen},
    pages = {25 - 32},
    volume = {11},
    number = {1},
    year = {2015},
    abstract = {The success in development of transgenic plants is influenced by the regeneration system. The objective of the study was to assess the response of maize genotypes to regeneration system of organogenesis and embryogenesis, after transformed with CsNitr1-L gene through particle bombardment. Induction and callus regeneration of maize immature embryos of inbred lines Ult:cm.1#, ARC 178-123-112-XB3, and AZ2 were conducted through organogenesis, whereas those inbred lines AZ1, AZ2, P4G19(S)C2.59.3.3.1.3 and P4S3.29.4.4.1 were conducted through embryogenesis somatic. Transformation of CsNitr1-L gene was done with the distance of bombardment of 7 cm and 9 cm and calli were then selected using 10 mg/l hygromycin. All explants (100%) of inbred lines Ult:cm.1# formed organogenic callus, while callus formation of ARC 178-123-112-XB3 was 94.3% and AZ2 was 60.5%. Ult:cm.1# was the most responsive line to the regeneration of organogenesis and produced 24 green shoots, compared with ARC 178-123-112-XB3 which produced one green shoot and AZ2 that did not produce green shoots. The highest percentage of embryogenic calli formed through somatic embryogenesis was obtained on inbred lines AZ1 (85.4%) and the lowest was on P4S3.29.4.4.1 (18.9%). Inbred lines AZ1 had the highest percentage of regeneration (50.7%) and produced 62 plants, followed by P4G19(S)C2.59.3.3.1.3 that produced 17 plants (2.8%) and P4S3.29.4.4.1 which produced two plants. Preliminary identification on 31 putative transgenic plants through PCR analysis produced 22 plants (70.96%) that contained nptII gene. Keywords: Zea mays, organogenesis, somatic embryogenesis, transformant identification.},
    keywords = {zea mays, organogenesis, somatic embryogenesis, transformant identification},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Jurnal Agrobiogen 11-1/Dinar Ambarwati.pdf}
    }
  3. Tasma, I. M., D. Satyawan, and H. Rijzaani. 2015. Pembentukan Pustaka Genom, Resekuensing, dan Identifikasi SNP Berdasarkan Sekuen Genom Total Genotipe Kedelai Indonesia. Jurnal agrobiogen 11 (1):7-16.
    [BibTeX] [Abstract] [PDF: Pembentukan Pustaka Genom, Resekuensing, dan Identifikasi SNP Berdasarkan Sekuen Genom Total Genotipe Kedelai Indonesia ]
    Resequencing of the soybean genome facilitates SNP marker discoveries useful for supporting the national soybean breeding programs. The objectives of the present study were to construct soybean genomic libraries, to resequence the whole genome of five Indonesian soybean genotypes, and to identify SNPs based on the resequence data. The studies consisted of genomic library construction and quality analysis, resequencing the whole-genome of five soybean genotypes, and genome-wide SNP identification based on alignment of the resequence data with reference sequence, Williams 82. The five Indonesian soybean genotypes were Tambora, Grobogan, B3293, Malabar, and Davros. The results showed that soybean genomic library was successfully constructed having the size of 400 bp with library concentrations range from 21.2-64.5 ng/µl. Resequencing of the libraries resulted in 50.1 x 109 bp total genomic sequence. The quality of genomic library and sequence data resulted from this study was high as indicated by Q score of 88.6% with low sequencing error of only 0.97%. Bioinformatic analysis resulted in a total of 2,597,286 SNPs, 257,598 insertions, and 202,157 deletions. Of the total SNPs identified, only 95,207 SNPs (2.15%) were located within exons. Among those, 49,926 SNPs caused missense mutation and 1,535 SNPs caused nonsense mutation. SNPs resulted from this study upon verification will be very useful for genome-wide SNP chip development of the soybean genome to accelerate breeding program of the soybean.
    @article{Tasma15p7,
    title = {{Pembentukan Pustaka Genom, Resekuensing, dan Identifikasi SNP Berdasarkan Sekuen Genom Total Genotipe Kedelai Indonesia}},
    author = {I. M. Tasma and D. Satyawan and H. Rijzaani},
    journal = {Jurnal AgroBiogen},
    pages = {7 - 16},
    volume = {11},
    number = {1},
    year = {2015},
    abstract = {Resequencing of the soybean genome facilitates SNP marker discoveries useful for supporting the national soybean breeding programs. The objectives of the present study were to construct soybean genomic libraries, to resequence the whole genome of five Indonesian soybean genotypes, and to identify SNPs based on the resequence data. The studies consisted of genomic library construction and quality analysis, resequencing the whole-genome of five soybean genotypes, and genome-wide SNP identification based on alignment of the resequence data with reference sequence, Williams 82. The five Indonesian soybean genotypes were Tambora, Grobogan, B3293, Malabar, and Davros. The results showed that soybean genomic library was successfully constructed having the size of 400 bp with library concentrations range from 21.2-64.5 ng/µl. Resequencing of the libraries resulted in 50.1 x 109 bp total genomic sequence. The quality of genomic library and sequence data resulted from this study was high as indicated by Q score of 88.6% with low sequencing error of only 0.97%. Bioinformatic analysis resulted in a total of 2,597,286 SNPs, 257,598 insertions, and 202,157 deletions. Of the total SNPs identified, only 95,207 SNPs (2.15%) were located within exons. Among those, 49,926 SNPs caused missense mutation and 1,535 SNPs caused nonsense mutation. SNPs resulted from this study upon verification will be very useful for genome-wide SNP chip development of the soybean genome to accelerate breeding program of the soybean.},
    keywords = {soybean, genomic library, ngs, snp, genome variation},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Jurnal Agrobiogen 11-1/I Made Tasma.pdf}
    }
  4. Pardal, S. J., Slamet, R. Purnamaningsih, E. G. Lestari, and Sutini. 2015. Analisis Molekuler Gen Partenokarpi DefH9-RI-iaaM pada Progeni Tomat Transgenik. Jurnal agrobiogen 11 (1):33-40.
    [BibTeX] [Abstract] [PDF: Analisis Molekuler Gen Partenokarpi DefH9-RI-iaaM pada Progeni Tomat Transgenik ]
    The development of seedless tomato fruits will be more attractive to both consumers and industries. Seedless tomatoes can be produced through parthenocarpy technology. Artificial parthenocarpy can be induced by conventional crossing, hormone application, or genetic engineering. The development of parthenocarpic tomatoes through genetic engineering has been carried out by inserting DefH9-iaaM parthenocarpic geneinto tomato genome via Agrobacterium tumefaciens mediated transformation. Sixty putative transgenic tomato lines were produced and three events (OvR1#14-4, OvM2#10-1, and OvM2#6-2) were selected as the best events. The background of the tomato lines was Oval variety, and based on PCR results, the three selected lines contained DefH9-RI-iaaM in their genome. The objective of this research was to determine the integration of DefH9-RI-iaaM gene in the progenies of three transgenic tomatoes lines using PCR technique. The research was conducted in the laboratory and Biosafety Containment Facility of Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD). Parental variety, Oval (neither transgenic nor in vitro cultured), and elite line of CL 6046 were used as control plants. The results indicated that the progenies (T1, T2, and T3) of the three tomato lines contained the insert DefH9-RIiaaM gene.
    @article{Pardal15p33,
    title = {{Analisis Molekuler Gen Partenokarpi DefH9-RI-iaaM pada Progeni Tomat Transgenik}},
    author = {S. J. Pardal and Slamet and R. Purnamaningsih and E. G. Lestari and Sutini},
    journal = {Jurnal AgroBiogen},
    pages = {33 - 40},
    volume = {11},
    number = {1},
    year = {2015},
    abstract = {The development of seedless tomato fruits will be more attractive to both consumers and industries. Seedless tomatoes can be produced through parthenocarpy technology. Artificial parthenocarpy can be induced by conventional crossing, hormone application, or genetic engineering. The development of parthenocarpic tomatoes through genetic engineering has been carried out by inserting DefH9-iaaM parthenocarpic geneinto tomato genome via Agrobacterium tumefaciens mediated transformation. Sixty putative transgenic tomato lines were produced and three events (OvR1#14-4, OvM2#10-1, and OvM2#6-2) were selected as the best events. The background of the tomato lines was Oval variety, and based on PCR results, the three selected lines contained DefH9-RI-iaaM in their genome. The objective of this research was to determine the integration of DefH9-RI-iaaM gene in the progenies of three transgenic tomatoes lines using PCR technique. The research was conducted in the laboratory and Biosafety Containment Facility of Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD). Parental variety, Oval (neither transgenic nor in vitro cultured), and elite line of CL 6046 were used as control plants. The results indicated that the progenies (T1, T2, and T3) of the three tomato lines contained the insert DefH9-RIiaaM gene.},
    keywords = {molecular analysis, transgenic tomato lines, parthenocarpic gene, genetic engineering},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Jurnal Agrobiogen 11-1/Saptowo J Pardal.pdf}
    }
  5. Tasliah, Ma’sumah, K. R. Trijatmiko, and J. Prasetiyono. 2015. Analisis Molekuler dan Keragaan Agronomis Galur-galur Padi BC1F1 Persilangan Code x qTSN4 dan Code x qDTH. Jurnal agrobiogen 11 (1):17-24.
    [BibTeX] [Abstract] [PDF: Analisis Molekuler dan Keragaan Agronomis Galur-galur Padi BC1F1 Persilangan Code x qTSN4 dan Code x qDTH ]
    Breeding based on molecular marker has become a routine activity in the current rice research. The development of an early maturity of rice variety with high yield is needed to increase national rice production. This study aimed to determine the pattern of alleles for loci controlling total spikelet number and number of days to heading, as well as agronomic performances of the BC1F1 Code x qTSN4 and Code x qDTH8 populations. The study was conducted at the Indonesian Center for Biotechnology and Genetic Resources Research and Development from January to August 2014. The plant materials used were Code (a national variety with bacterial blight resistance gene [Xa7]), IR64-Nils-qTSN4[YP9] (qTSN4 that contains a locus controlling the number of spikelet), IR64-Nils-qDTH8[YP1] (qDTH8 that contains a locus controlling the number of days to heading), BC1F1 Code x qTSN4, and BC1F1 Code x qDTH8. A total of 250 BC1F1 plants of each crosses were selected using molecular markers of RM20582 for Xa7 gene, RM17483 and RM6909 for QTL position of qTSN4, RM5556 and RM6838 for QTL position of qDTH8. Based on molecular analysis, there were 63 BC1F1-qTSN4 lines and 65 BC1F1-qDTH8 lines showing heterozygote alleles for qTSN4 or qDTH8 loci and were homozygote for Xa7 locus (HHA pattern). Five plants from each locus target were backcrossed to the recurrent parent, Code, to obtain BC2F1 seeds. The remaining BC1F1 plants were self-pollinated to obtain BC1F2 seeds. Observations on some agronomic characters demontrated that the BC1F1 plants showed higher yield potential than Code and the flowering time of the BC1F1 progenis were also earlier than Code. These results indicated that the yield potential of Code could be improved by introgression of qTSN4 and qDTH8 loci into the Code genome.
    @article{Tasliah15p17,
    title = {{Analisis Molekuler dan Keragaan Agronomis Galur-galur Padi BC1F1 Persilangan Code x qTSN4 dan Code x qDTH}},
    author = {Tasliah and Ma'sumah and K. R. Trijatmiko and J. Prasetiyono},
    journal = {Jurnal AgroBiogen},
    pages = {17 - 24},
    volume = {11},
    number = {1},
    year = {2015},
    abstract = {Breeding based on molecular marker has become a routine activity in the current rice research. The development of an early maturity of rice variety with high yield is needed to increase national rice production. This study aimed to determine the pattern of alleles for loci controlling total spikelet number and number of days to heading, as well as agronomic performances of the BC1F1 Code x qTSN4 and Code x qDTH8 populations. The study was conducted at the Indonesian Center for Biotechnology and Genetic Resources Research and Development from January to August 2014. The plant materials used were Code (a national variety with bacterial blight resistance gene [Xa7]), IR64-Nils-qTSN4[YP9] (qTSN4 that contains a locus controlling the number of spikelet), IR64-Nils-qDTH8[YP1] (qDTH8 that contains a locus controlling the number of days to heading), BC1F1 Code x qTSN4, and BC1F1 Code x qDTH8. A total of 250 BC1F1 plants of each crosses were selected using molecular markers of RM20582 for Xa7 gene, RM17483 and RM6909 for QTL position of qTSN4, RM5556 and RM6838 for QTL position of qDTH8. Based on molecular analysis, there were 63 BC1F1-qTSN4 lines and 65 BC1F1-qDTH8 lines showing heterozygote alleles for qTSN4 or qDTH8 loci and were homozygote for Xa7 locus (HHA pattern). Five plants from each locus target were backcrossed to the recurrent parent, Code, to obtain BC2F1 seeds. The remaining BC1F1 plants were self-pollinated to obtain BC1F2 seeds. Observations on some agronomic characters demontrated that the BC1F1 plants showed higher yield potential than Code and the flowering time of the BC1F1 progenis were also earlier than Code. These results indicated that the yield potential of Code could be improved by introgression of qTSN4 and qDTH8 loci into the Code genome.},
    keywords = {molecular analysis, agronomic performance, bc1f1 code x qtsn4, bc1f1 code x qdth},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Jurnal Agrobiogen 11-1/Tasliah.pdf}
    }
  6. Nugroho, K., Reflinur, P. Lestari, I. Rosdianti, R. T. Terryana, Kusmana, and I. M. Tasma. 2015. Keragaman Genetika Empat Belas Aksesi Kentang (Solanum tuberosum L.) Berdasarkan Marka SSR dan STS. Jurnal agrobiogen 11 (2):41-48.
    [BibTeX] [Abstract] [PDF: Keragaman Genetika Empat Belas Aksesi Kentang (Solanum tuberosum L.) Berdasarkan Marka SSR dan STS ]
    Kentang (Solanum tuberosum L.) merupakan salah satu tanaman hortikultura yang memiliki nilai ekonomis tinggi. Meningkatnya kebutuhan konsumsi kentang nasional menjadi tantangan bagi pemulia kentang. Tersedianya sumber keragaman genetika merupakan prasyarat keberhasilan program pemuliaan suatu varietas. Penelitian ini bertujuan menganalisis keragaman genetika empat belas aksesi kentang menggunakan marka simple sequence repeats (SSR) dan sequence-tagged sites (STS). Hasil analisis polymerase chain reaction (PCR) diberi skor sebagai data biner. Analisis data dilakukan menggunakan perangkat lunak NTSYS dan PowerMarker. Hasil penelitian menunjukkan dari 19 marka yang digunakan terdapat 12 marka (63%) yang bersifat polimorfik. Sebanyak 60 alel berukuran antara 200-500 bp dengan kisaran 2-9 alel per lokus berhasil dideteksi. Nilai polymorphic information content (PIC) menunjukkan rerata sebesar 0,59 dengan nilai tertinggi 0,74 (RGH-SSR 21) dan nilai terendah 0,36 (RGH-SSR 30). Rerata frekuensi alel utama adalah 49,42% dengan nilai terendah 35,71% (STG-0016) dan nilai tertinggi 63,64% (RGH-SSR 40). Terdapat 9 marka dengan nilai PIC >0,5 yang dapat digunakan untuk mendeteksi keragaman genetika aksesi kentang. Keragaman aksesi kentang tersebut cukup tinggi, seperti yang direfleksikan oleh nilai rerata diversitas gen, yaitu 0,65. Hasil analisis klaster menunjukkan bahwa keempat belas aksesi kentang tersebut mengelompok menjadi dua kelompok utama pada koefisien 0,70. Kelompok pertama terdiri atas varietas Atlantik, GM 05, Granola Kembang, dan Merbabu 17, sedangkan kelompok kedua terdiri atas varietas Repita, Maglia, Medians, CIP 397078.7, CIP 392781.1, Margahayu, Granola, CIP 394613.139, Amabile, dan Tenggo. Informasi keragaman genetika plasma nutfah tersebut dapat menjadi dasar awal untuk pemilihan tetua persilangan dalam pemuliaan kentang di Indonesia.
    @article{Nugroho15p41,
    title = {{Keragaman Genetika Empat Belas Aksesi Kentang (Solanum tuberosum L.) Berdasarkan Marka SSR dan STS}},
    author = {K. Nugroho and Reflinur and P. Lestari and I. Rosdianti and R. T. Terryana and Kusmana and I. M. Tasma},
    journal = {Jurnal AgroBiogen},
    pages = {41 - 48},
    volume = {11},
    number = {2},
    year = {2015},
    abstract = {Kentang (Solanum tuberosum L.) merupakan salah satu tanaman hortikultura yang memiliki nilai ekonomis tinggi. Meningkatnya kebutuhan konsumsi kentang nasional menjadi tantangan bagi pemulia kentang. Tersedianya sumber keragaman genetika merupakan prasyarat keberhasilan program pemuliaan suatu varietas. Penelitian ini bertujuan menganalisis keragaman genetika empat belas aksesi kentang menggunakan marka simple sequence repeats (SSR) dan sequence-tagged sites (STS). Hasil analisis polymerase chain reaction (PCR) diberi skor sebagai data biner. Analisis data dilakukan menggunakan perangkat lunak NTSYS dan PowerMarker. Hasil penelitian menunjukkan dari 19 marka yang digunakan terdapat 12 marka (63%) yang bersifat polimorfik. Sebanyak 60 alel berukuran antara 200-500 bp dengan kisaran 2-9 alel per lokus berhasil dideteksi. Nilai polymorphic information content (PIC) menunjukkan rerata sebesar 0,59 dengan nilai tertinggi 0,74 (RGH-SSR 21) dan nilai terendah 0,36 (RGH-SSR 30). Rerata frekuensi alel utama adalah 49,42% dengan nilai terendah 35,71% (STG-0016) dan nilai tertinggi 63,64% (RGH-SSR 40). Terdapat 9 marka dengan nilai PIC >0,5 yang dapat digunakan untuk mendeteksi keragaman genetika aksesi kentang. Keragaman aksesi kentang tersebut cukup tinggi, seperti yang direfleksikan oleh nilai rerata diversitas gen, yaitu 0,65. Hasil analisis klaster menunjukkan bahwa keempat belas aksesi kentang tersebut mengelompok menjadi dua kelompok utama pada koefisien 0,70. Kelompok pertama terdiri atas varietas Atlantik, GM 05, Granola Kembang, dan Merbabu 17, sedangkan kelompok kedua terdiri atas varietas Repita, Maglia, Medians, CIP 397078.7, CIP 392781.1, Margahayu, Granola, CIP 394613.139, Amabile, dan Tenggo. Informasi keragaman genetika plasma nutfah tersebut dapat menjadi dasar awal untuk pemilihan tetua persilangan dalam pemuliaan kentang di Indonesia.},
    keywords = {kentang, solanum tuberosum l, ssr, sts, keragaman genetika},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Jurnal Agrobiogen 11-2/Kristianto.pdf}
    }
  7. Risliawati, A., E. I. Riyanti, P. Lestari, D. W. Utami, and T. S. Silitonga. 2015. Development of SSR Marker Set to Identify Fourty Two Indonesian Soybean Varieties. Jurnal agrobiogen 11 (2):49-58.
    [BibTeX] [Abstract] [PDF: Development of SSR Marker Set to Identify Fourty Two Indonesian Soybean Varieties ]
    Profile of molecular marker can be used for variety identification, genetic purity monitoring of germplasm and additional requirement in proposing intellectual property protection. DNA fingerprinting of soybean had been applied at the ICABIOGRADIAARD since 2004 using simple sequence repeat (SSR) markers which were run automatically by CEQ 8000 Genetic Analyzer platform based on capillary electrophoresis system. This method had produced unique DNA fingerprints of the varieties tested, but the marker set to efficiently identify the varieties had not yet been developed. This study aimed to develop a set of SSR markers as a tool to identify the Indonesian soybean varieties. Fourty two soybean varieties were analyzed using 14 random SSR markersA total of 168 alleles that were obtained from the polymorphism analysis. The average of polymorphic information content (PIC) value observed was 0.7337 per SSR locus. Based on marker reproducibility rate, PIC value, number of rare alleles, frequency of dominant alleles, and percentage of SSR fragment detected by genetic analyzer, we identified five SSR markers i.e. Satt414, Satt147, Satt308, Satt009, and Satt516 as a SSR marker set to be used for soybean variety identification purposes. This marker set was used to develop the identity (ID) of the 42 Indonesian soybean varieties.
    @article{Risliawati15p49,
    title = {{Development of SSR Marker Set to Identify Fourty Two Indonesian Soybean Varieties}},
    author = {A. Risliawati and E. I. Riyanti and P. Lestari and D. W. Utami and T. S. Silitonga},
    journal = {Jurnal AgroBiogen},
    pages = {49 - 58},
    volume = {11},
    number = {2},
    year = {2015},
    abstract = {Profile of molecular marker can be used for variety identification, genetic purity monitoring of germplasm and additional requirement in proposing intellectual property protection. DNA fingerprinting of soybean had been applied at the ICABIOGRADIAARD since 2004 using simple sequence repeat (SSR) markers which were run automatically by CEQ 8000 Genetic Analyzer platform based on capillary electrophoresis system. This method had produced unique DNA fingerprints of the varieties tested, but the marker set to efficiently identify the varieties had not yet been developed. This study aimed to develop a set of SSR markers as a tool to identify the Indonesian soybean varieties. Fourty two soybean varieties were analyzed using 14 random SSR markersA total of 168 alleles that were obtained from the polymorphism analysis. The average of polymorphic information content (PIC) value observed was 0.7337 per SSR locus. Based on marker reproducibility rate, PIC value, number of rare alleles, frequency of dominant alleles, and percentage of SSR fragment detected by genetic analyzer, we identified five SSR markers i.e. Satt414, Satt147, Satt308, Satt009, and Satt516 as a SSR marker set to be used for soybean variety identification purposes. This marker set was used to develop the identity (ID) of the 42 Indonesian soybean varieties.},
    keywords = {dna fingerprinting, marker set for identification, soybean, ssr},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Jurnal Agrobiogen 11-2/Andari.pdf}
    }
  8. Hadiarto, T., E. Listanto, and E. I. Riyanti. 2015. Identifikasi cDNA Gen RB pada Tanaman Kentang Produk Rekayasa Genetika Katahdin SP951. Jurnal agrobiogen 11 (2):59-64.
    [BibTeX] [Abstract] [PDF: Identifikasi cDNA Gen RB pada Tanaman Kentang Produk Rekayasa Genetika Katahdin SP951 ]
    Penanaman kentang transgenik dapat mengurangi penggunaan fungisida. Gen RB, yang merupakan gen ketahanan terhadap patogen penyakit hawar daun (Phytophthora infestans), telah berhasil diisolasi dari tanaman kentang liar S. bulbocastanum dan disisipkan ke dalam genom tanaman kentang varietas Katahdin, yang kemudian dinamai klon Katahdin SP951. Penelitian ini bertujuan mengonfirmasi keberadaan gen RB dalam genom tanaman kentang transgenik Katahdin SP951 dengan cara menyekuen gen tersebut dari tanaman kentang Katahdin SP951, dan kemudian membandingkannya dengan sekuen gen RB dari plasmid pCLD04541 yang digunakan untuk mentransformasi Katahdin dan mengandung gen RB. Katahdin nontransgenik dan S. bulbocastanum secara berurutan digunakan sebagai kontrol negatif dan positif. Hasil PCR mendapatkan tujuh primer yang spesifik terhadap gen RB dan kemudian digunakan untuk sekuensing. Hasil sekuensing berupa urutan DNA sepanjang 2.913 basa yang memiliki kesamaan 100% dengan urutan gen RB pada plasmid pCLD04541. Dapat disimpulkan bahwa gen RB tidak mengalami mutasi, baik dalam proses transformasi maupun pada waktu integrasi ke dalam genom kentang varietas Katahdin.
    @article{Hadiarto15p59,
    title = {{Identifikasi cDNA Gen RB pada Tanaman Kentang Produk Rekayasa Genetika Katahdin SP951}},
    author = {T. Hadiarto and E. Listanto and E. I. Riyanti},
    journal = {Jurnal AgroBiogen},
    pages = {59 - 64},
    volume = {11},
    number = {2},
    year = {2015},
    publisher = {BB Biogen},
    abstract = {Penanaman kentang transgenik dapat mengurangi penggunaan fungisida. Gen RB, yang merupakan gen ketahanan terhadap patogen penyakit hawar daun (Phytophthora infestans), telah berhasil diisolasi dari tanaman kentang liar S. bulbocastanum dan disisipkan ke dalam genom tanaman kentang varietas Katahdin, yang kemudian dinamai klon Katahdin SP951. Penelitian ini bertujuan mengonfirmasi keberadaan gen RB dalam genom tanaman kentang transgenik Katahdin SP951 dengan cara menyekuen gen tersebut dari tanaman kentang Katahdin SP951, dan kemudian membandingkannya dengan sekuen gen RB dari plasmid pCLD04541 yang digunakan untuk mentransformasi Katahdin dan mengandung gen RB. Katahdin nontransgenik dan S. bulbocastanum secara berurutan digunakan sebagai kontrol negatif dan positif. Hasil PCR mendapatkan tujuh primer yang spesifik terhadap gen RB dan kemudian digunakan untuk sekuensing. Hasil sekuensing berupa urutan DNA sepanjang 2.913 basa yang memiliki kesamaan 100% dengan urutan gen RB pada plasmid pCLD04541. Dapat disimpulkan bahwa gen RB tidak mengalami mutasi, baik dalam proses transformasi maupun pada waktu integrasi ke dalam genom kentang varietas Katahdin.},
    keywords = {gen rb, kentang, konfirmasi sekuen},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Jurnal Agrobiogen 11-2/Toto Hadiarto.pdf}
    }
  9. Bahagiawati, Reflinur, and T. J. Santoso. 2015. Teknik PCR Kualitatif untuk Deteksi Produk Rekayasa Genetika Jagung Event BT11 dan GA21. Jurnal agrobiogen 11 (2):65-72.
    [BibTeX] [Abstract] [PDF: Teknik PCR Kualitatif untuk Deteksi Produk Rekayasa Genetika Jagung Event BT11 dan GA21 ]
    Pelabelan produk hasil rekayasa genetika (PRG) di beberapa negara, termasuk Indonesia, merupakan mandat yang memberikan kesempatan kepada konsumen untuk mendapatkan informasi produk yang akan dibeli atau digunakan. Untuk itu, diperlukan perangkat teknologi yang dapat mendeteksi keberadaan produk PRG tersebut, baik dalam bentuk bahan dasar (bijibijian) maupun produk turunannya. Penelitian ini bertujuan membandingkan dan mendapatkan teknik yang akurat dan efisien untuk deteksi tanaman jagung BT11 dan GA21 berdasarkan teknik PCR, baik secara tunggal (simpleks) maupun ganda (dupleks). Jagung produk PRG, yaitu BT11 dan GA21, dan non-PRG, yaitu Nk11, digunakan sebagai sampel dalam pengembangan metode deteksi PRG pada kedua event tersebut. Setiap sampel diamplifikasi secara simpleks menggunakan primer spesifik untuk mendeteksi keberadaan gen target pada event PRG dan sepasang primer spesifik sebagai internal kontrol untuk tanaman jagung. Selanjutnya, pada metode dupleks, sampel DNA kedua event diamplifikasi dengan primer-primer tersebut secara bersamaan dalam suatu reaksi PCR. Hasil penelitian menunjukkan bahwa teknik deteksi yang didapatkan dari penelitian ini dapat digunakan untuk skrining PRG dan identifikasi spesifik BT11 dan GA21, baik secara simpleks maupun dupleks. Kemampuan metode dupleks untuk mendeteksi PRG akan sangat bermanfaat dalam kegiatan skrining PRG dalam jumlah sampel yang besar karena metode ini lebih efisien dibanding dengan metode simpleks.
    @article{Bahagiawati15p65,
    title = {{Teknik PCR Kualitatif untuk Deteksi Produk Rekayasa Genetika Jagung Event BT11 dan GA21}},
    author = {Bahagiawati and Reflinur and T. J. Santoso},
    journal = {Jurnal AgroBiogen},
    pages = {65 - 72},
    volume = {11},
    number = {2},
    year = {2015},
    publisher = {BB Biogen},
    abstract = {Pelabelan produk hasil rekayasa genetika (PRG) di beberapa negara, termasuk Indonesia, merupakan mandat yang memberikan kesempatan kepada konsumen untuk mendapatkan informasi produk yang akan dibeli atau digunakan. Untuk itu, diperlukan perangkat teknologi yang dapat mendeteksi keberadaan produk PRG tersebut, baik dalam bentuk bahan dasar (bijibijian) maupun produk turunannya. Penelitian ini bertujuan membandingkan dan mendapatkan teknik yang akurat dan efisien untuk deteksi tanaman jagung BT11 dan GA21 berdasarkan teknik PCR, baik secara tunggal (simpleks) maupun ganda (dupleks). Jagung produk PRG, yaitu BT11 dan GA21, dan non-PRG, yaitu Nk11, digunakan sebagai sampel dalam pengembangan metode deteksi PRG pada kedua event tersebut. Setiap sampel diamplifikasi secara simpleks menggunakan primer spesifik untuk mendeteksi keberadaan gen target pada event PRG dan sepasang primer spesifik sebagai internal kontrol untuk tanaman jagung. Selanjutnya, pada metode dupleks, sampel DNA kedua event diamplifikasi dengan primer-primer tersebut secara bersamaan dalam suatu reaksi PCR. Hasil penelitian menunjukkan bahwa teknik deteksi yang didapatkan dari penelitian ini dapat digunakan untuk skrining PRG dan identifikasi spesifik BT11 dan GA21, baik secara simpleks maupun dupleks. Kemampuan metode dupleks untuk mendeteksi PRG akan sangat bermanfaat dalam kegiatan skrining PRG dalam jumlah sampel yang besar karena metode ini lebih efisien dibanding dengan metode simpleks.},
    keywords = {deteksi prg, skrining prg, jagung, bt11, ga21},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Jurnal Agrobiogen 11-2/Bahagiawati.pdf}
    }
  10. Manzila, I., N. Gunaeni, Y. Kusandriani, and T. P. Priyatno. 2015. Ketahanan dan Karakter Fenotipe Galur Mutan (M2) Cabai terhadap Chilli Veinal Mottle Virus. Jurnal agrobiogen 11 (1):73-80.
    [BibTeX] [Abstract] [PDF: Ketahanan dan Karakter Fenotipe Galur Mutan (M2) Cabai terhadap Chilli Veinal Mottle Virus ]
    Infeksi Chilli veinal mottle virus (ChiVMV) menurunkan kualitas dan kuantitas cabai serta kehilangan hasil mencapai 60-100%. Di antara varietas cabai yang dilepas, belum ada yang tahan terhadap serangan ChiVMV. Hal ini terutama disebabkan oleh variasi strain ChiVMV yang sangat tinggi di lapangan dan belum terpetakan dengan baik. Oleh sebab itu, pencarian sumbersumber gen tahan ChiVMV perlu dilakukan. Pendekatan melalui teknik induksi mutasi in vitro menggunakan mutagen ethyl methanesulfonate (EMS) merupakan salah satu upaya untuk meningkatkan keragaman genetik. Dari hasil penelitian sebelumnya melalui induksi kalus cabai varietas Gelora dengan mutagen EMS telah berhasil diperoleh 800 galur M2. Tujuan penelitian ini adalah memperoleh sejumlah galur M2 hasil induksi mutasi kimia varietas Gelora yang tahan ChiVMV dan berpenampilan agronomis baik. Sebanyak 800 galur M2 cabai yang berasal dari mutasi menggunakan mutagen EMS telah diuji ketahanannya terhadap ChiVMV dan dipelajari karakter fenotipenya di rumah kaca. Hasil penelitian ini menunjukkan bahwa dari 800 galur yang diuji diperoleh 28 galur yang menunjukkan respons toleran dan tahan terhadap ChiVMV. Delapan galur di antaranya memiliki karakter agronomis baik. Galur-galur tersebut adalah M2.100, M2.108, M2.200, M2. 122, M2.238, M2.353, M2.420, dan M2.517. Delapan galur ini perlu diseleksi dan diobservasi lebih lanjut hingga diperoleh galur-galur harapan cabai yang tahan terhadap ChiVMV dan berdaya hasil tinggi.
    @article{Manzila15p73,
    title = {{Ketahanan dan Karakter Fenotipe Galur Mutan (M2) Cabai terhadap Chilli Veinal Mottle Virus}},
    author = {I. Manzila and N. Gunaeni and Y. Kusandriani and T. P. Priyatno},
    journal = {Jurnal AgroBiogen},
    pages = {73 - 80},
    volume = {11},
    number = {1},
    year = {2015},
    publisher = {BB Biogen},
    abstract = {Infeksi Chilli veinal mottle virus (ChiVMV) menurunkan kualitas dan kuantitas cabai serta kehilangan hasil mencapai 60-100%. Di antara varietas cabai yang dilepas, belum ada yang tahan terhadap serangan ChiVMV. Hal ini terutama disebabkan oleh variasi strain ChiVMV yang sangat tinggi di lapangan dan belum terpetakan dengan baik. Oleh sebab itu, pencarian sumbersumber gen tahan ChiVMV perlu dilakukan. Pendekatan melalui teknik induksi mutasi in vitro menggunakan mutagen ethyl methanesulfonate (EMS) merupakan salah satu upaya untuk meningkatkan keragaman genetik. Dari hasil penelitian sebelumnya melalui induksi kalus cabai varietas Gelora dengan mutagen EMS telah berhasil diperoleh 800 galur M2. Tujuan penelitian ini adalah memperoleh sejumlah galur M2 hasil induksi mutasi kimia varietas Gelora yang tahan ChiVMV dan berpenampilan agronomis baik. Sebanyak 800 galur M2 cabai yang berasal dari mutasi menggunakan mutagen EMS telah diuji ketahanannya terhadap ChiVMV dan dipelajari karakter fenotipenya di rumah kaca. Hasil penelitian ini menunjukkan bahwa dari 800 galur yang diuji diperoleh 28 galur yang menunjukkan respons toleran dan tahan terhadap ChiVMV. Delapan galur di antaranya memiliki karakter agronomis baik. Galur-galur tersebut adalah M2.100, M2.108, M2.200, M2. 122, M2.238, M2.353, M2.420, dan M2.517. Delapan galur ini perlu diseleksi dan diobservasi lebih lanjut hingga diperoleh galur-galur harapan cabai yang tahan terhadap ChiVMV dan berdaya hasil tinggi.},
    keywords = {cabai, capsicum annuum l, induksi mutasi, ketahanan, chivmv},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Jurnal Agrobiogen 11-2/Ifa Manzila.pdf}
    }

2014

  1. Apriana, A., A. Sisharmini, Fitriyani, and Sustiprijatno. 2014. Regenerasi Empat Genotipe Gandum (Triticum aestivum L.) Pasca Transformasi Melalui Agrobacterium tumefaciens. Jurnal agrobiogen 10 (1):18-25.
    [BibTeX] [Abstract] [PDF: Regenerasi Empat Genotipe Gandum (Triticum aestivum L.) Pasca Transformasi Melalui Agrobacterium tumefaciens ]
    Genetic transformation of wheat mediated by Agrobacterium tumefaciens has not been established yet. This research aimed to obtain the most responsive wheat genotype to be transformed, to select the most effective combination of growth regulator for regenerating transforman calli, and to determine the transformation efficiency. Transformation mediated by A. tumefaciens was performed on four genotypes of wheat, namely Combi, Fasan, Perdix, and Naxos-Wew. Transformed calli with green spots in selection media were transferred to regeneration media containing 25 mg/l hygromycin, i.e. R1H25 and R2H25. The obtained plantlets were analyzed by PCR using specific primers for hygromycin phosphotransferase gene. The results showed that Fasan was the most responsive genotype in callus formation (95.47%) and regeneration both in R1H25 (27%) and R2H25 (28.6%) media. Fourteen plantlets were succesfully acclimatized and PCR analysis showed that there were four positive transformants containing the hpt gene. The results are expected to provide information on the development of transgenic wheat in Indonesia, specifically in the success of callus formation and regeneration of wheat after transformation using A. tumefaciens.
    @article{Apriana14p18,
    title = {{Regenerasi Empat Genotipe Gandum (Triticum aestivum L.) Pasca Transformasi Melalui Agrobacterium tumefaciens}},
    author = {A. Apriana and A. Sisharmini and Fitriyani and Sustiprijatno},
    journal = {Jurnal AgroBiogen},
    pages = {18 - 25},
    volume = {10},
    number = {1},
    year = {2014},
    abstract = {Genetic transformation of wheat mediated by Agrobacterium tumefaciens has not been established yet. This research aimed to obtain the most responsive wheat genotype to be transformed, to select the most effective combination of growth regulator for regenerating transforman calli, and to determine the transformation efficiency. Transformation mediated by A. tumefaciens was performed on four genotypes of wheat, namely Combi, Fasan, Perdix, and Naxos-Wew. Transformed calli with green spots in selection media were transferred to regeneration media containing 25 mg/l hygromycin, i.e. R1H25 and R2H25. The obtained plantlets were analyzed by PCR using specific primers for hygromycin phosphotransferase gene. The results showed that Fasan was the most responsive genotype in callus formation (95.47%) and regeneration both in R1H25 (27%) and R2H25 (28.6%) media. Fourteen plantlets were succesfully acclimatized and PCR analysis showed that there were four positive transformants containing the hpt gene. The results are expected to provide information on the development of transgenic wheat in Indonesia, specifically in the success of callus formation and regeneration of wheat after transformation using A. tumefaciens. },
    keywords = {wheat, transformation study, agrobacterium},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Jurnal Agrobiogen 10-1/Aniversari A.pdf}
    }
  2. D.Damayanti and D. W. Utami. 2014. Pendugaan gen Bph1, bph2, Bph3, dan bph4 pada Galur-galur Padi Terpilih Tahan Hama Wereng Batang Coklat(Nilaparvatalugens [Stal]).. Jurnal agrobiogen 10 (1):1-8.
    [BibTeX] [Abstract] [PDF: Pendugaan gen Bph1, bph2, Bph3, dan bph4 pada Galur-galur Padi Terpilih Tahan Hama Wereng Batang Coklat(Nilaparvatalugens [Stal]). ]
    Pests are major constraints to increasing rice production and brown planthoppers/BPH (Nilaparvata lugens [St{å{}}l]) is one of the major pests of rice plant. Resistance cultivar is one of the strategies for BPH management. The objective of this research was to analyze the Bph1, bph2, Bph3, and bph4 gene existence on the selected rice lines using the molecular markers. The phenotype of the rice lines were tested based on their response to BPH population collected from West Java and Cental Java. Molecular markers linked to Bph1, bph2, Bph3, and bph4 were used to characterize the genotypic profile based on PCR analysis. The results showed that there are six genotypes resistant to one of the BPH populations from West Java or Central Java. The six rice varieties were detected to have not only allele of Bph3 gene, but also other different allele genes. B12344-2D-PN-42-1 and Inpari 13 were detected to have the alleles of Bph3 dan Bph1 genes. B12512-18-SI-3-3-MR-3-PN-1, B12512-18-SI-3-3-MR-3-PN-1, BMIP46-4-1, and PTB33 were detected to have the alleles of Bph3 and bph2 genes. Meanwhile, B11007E-MR-3-2-PN-2-1MR-1-2 was detected to have alleles of three genes: Bph3, bph2, and bph4. Nevertheless, this last line had medium resistance to both BPH populations invested. There is a possibility that the interaction between two genes, Bph3 and bph4, occured which may affect the resistance responses of rice varieties tested to BPH.
    @article{Damayanti14p1,
    title = {{Pendugaan gen Bph1, bph2, Bph3, dan bph4 pada Galur-galur Padi Terpilih Tahan Hama Wereng Batang Coklat(Nilaparvatalugens [Stal]).}},
    author = {D.Damayanti and D. W. Utami},
    journal = {Jurnal AgroBiogen},
    pages = {1 - 8},
    volume = {10},
    number = {1},
    year = {2014},
    abstract = {Pests are major constraints to increasing rice production and brown planthoppers/BPH (Nilaparvata lugens [St{\aa{}}l]) is one of the major pests of rice plant. Resistance cultivar is one of the strategies for BPH management. The objective of this research was to analyze the Bph1, bph2, Bph3, and bph4 gene existence on the selected rice lines using the molecular markers. The phenotype of the rice lines were tested based on their response to BPH population collected from West Java and Cental Java. Molecular markers linked to Bph1, bph2, Bph3, and bph4 were used to characterize the genotypic profile based on PCR analysis. The results showed that there are six genotypes resistant to one of the BPH populations from West Java or Central Java. The six rice varieties were detected to have not only allele of Bph3 gene, but also other different allele genes. B12344-2D-PN-42-1 and Inpari 13 were detected to have the alleles of Bph3 dan Bph1 genes. B12512-18-SI-3-3-MR-3-PN-1, B12512-18-SI-3-3-MR-3-PN-1, BMIP46-4-1, and PTB33 were detected to have the alleles of Bph3 and bph2 genes. Meanwhile, B11007E-MR-3-2-PN-2-1MR-1-2 was detected to have alleles of three genes: Bph3, bph2, and bph4. Nevertheless, this last line had medium resistance to both BPH populations invested. There is a possibility that the interaction between two genes, Bph3 and bph4, occured which may affect the resistance responses of rice varieties tested to BPH.},
    keywords = {bph resistance gene marker, promising rice line, gene estimation},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Jurnal Agrobiogen 10-1/Diani Damayanti.pdf}
    }
  3. Utami, D. W. and I. Hanarida. 2014. Evaluasi Lapang dan Identifikasi Molekuler Plasma Nutfah Padi terhadap Keracunan Fe. Jurnal agrobiogen 10 (1):9-17.
    [BibTeX] [Abstract] [PDF: Evaluasi Lapang dan Identifikasi Molekuler Plasma Nutfah Padi terhadap Keracunan Fe ]
    Fe toxicity is one of the abiotic constraints that can significantly decrease rice production, especially in marginal wetlands. The use of tolerant varieties can reduce the cost of soil processing and fertilizing. Many accessions of rice germplasm have potential alleles that can be utilized to create new varieties tolerant to Fe toxicity. The objectives of this research were to evaluate the Fe toxicity tolerance of rice germplasm and to analyze the genotype diversity using SNP markers for OsIRT, Fe toxicity tolerant gene(s). Fe toxicity tolerant rice germplasms were screened in acid marginal wetlands of Taman Bogo Experimental Station, Indonesian Soil Research Insitute, Lampung Province. Meanwhile, the genotypes performance analysis was conducted on SNP genotyping analysis using SNP markers for OsIRT gene(s). Based on phenotypic data of 97 accessions, which were clustered into six groups, two of them (group 2 and group 5) consisted of the tolerant accessions at both vegetative and generative stages. The results of grouping analysis of genotyping based on SNP markers were obtained that there were five genotype groups: AGT, AAT, GAT, AAC, and GAC. The AGT genotype cluster was dominated by the accessions included in group 1. Meanwhile, the GAT genotype cluster consisted of mixed tolerant and untolerant accessions to Fe toxicity. The GAC genotype cluster was dominated by the accessions included in group 2. The accessions which were included in the best tolerant group, group 5, were separated in different genotype cluster. Based on association analysis, among the three SNP markers, OsIRT1 was the most significant SNP marker (P value = 0.01) which correlated to Fe toxicity tolerant on vegetative stage. Some of the selected accessions that were tolerant to Fe toxicity and had good agronomic performance on acid soil with high Fe content were Ketan Alay, Markuti, Arias Halus, Komas a, Lantiak, and Utri Deli. These local rice accessions have the potential alleles of OsIRT genes.
    @article{Utami13p9,
    title = {{Evaluasi Lapang dan Identifikasi Molekuler Plasma Nutfah Padi terhadap Keracunan Fe}},
    author = {D. W. Utami and I. Hanarida},
    journal = {Jurnal AgroBiogen},
    pages = {9 - 17},
    volume = {10},
    number = {1},
    year = {2014},
    abstract = {Fe toxicity is one of the abiotic constraints that can significantly decrease rice production, especially in marginal wetlands. The use of tolerant varieties can reduce the cost of soil processing and fertilizing. Many accessions of rice germplasm have potential alleles that can be utilized to create new varieties tolerant to Fe toxicity. The objectives of this research were to evaluate the Fe toxicity tolerance of rice germplasm and to analyze the genotype diversity using SNP markers for OsIRT, Fe toxicity tolerant gene(s). Fe toxicity tolerant rice germplasms were screened in acid marginal wetlands of Taman Bogo Experimental Station, Indonesian Soil Research Insitute, Lampung Province. Meanwhile, the genotypes performance analysis was conducted on SNP genotyping analysis using SNP markers for OsIRT gene(s). Based on phenotypic data of 97 accessions, which were clustered into six groups, two of them (group 2 and group 5) consisted of the tolerant accessions at both vegetative and generative stages. The results of grouping analysis of genotyping based on SNP markers were obtained that there were five genotype groups: AGT, AAT, GAT, AAC, and GAC. The AGT genotype cluster was dominated by the accessions included in group 1. Meanwhile, the GAT genotype cluster consisted of mixed tolerant and untolerant accessions to Fe toxicity. The GAC genotype cluster was dominated by the accessions included in group 2. The accessions which were included in the best tolerant group, group 5, were separated in different genotype cluster. Based on association analysis, among the three SNP markers, OsIRT1 was the most significant SNP marker (P value = 0.01) which correlated to Fe toxicity tolerant on vegetative stage. Some of the selected accessions that were tolerant to Fe toxicity and had good agronomic performance on acid soil with high Fe content were Ketan Alay, Markuti, Arias Halus, Komas a, Lantiak, and Utri Deli. These local rice accessions have the potential alleles of OsIRT genes.},
    keywords = {rice germplasm, phenotype, genotype, fe toxicity, osirt},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Jurnal Agrobiogen 10-1/Dwinita W Utami.pdf}
    }
  4. N. Dewi, Dewi I. S. and I. Roostika. 2014. Pemanfaatan Teknik Kultur In Vitro untuk Konservasi Plasma Nutfah Ubi-ubian.. Jurnal agrobiogen 10 (1):34-44.
    [BibTeX] [Abstract] [PDF: Pemanfaatan Teknik Kultur In Vitro untuk Konservasi Plasma Nutfah Ubi-ubian. ]
    Except for potato, sweet potato, taro, yam, and cassava, most of tuber crops are considered as underutilized crops. However, tuber crops are potential as alternative carbohydrate sources, so they can be used as food reserves to face global climate change that affects food security in certain area throughout the world, including Indonesia. Having high diversity in tuber crops germplasm, Indonesia must be able to conserve those germplasm to ensure their availability in the future. In the future, without ignoring all the probable constraints, the prospect in utilization of in vitro culture technique will be higher for improvement of conservation and management of genetic resources in the form of active and base collections. In this paper, strategy in developing in vitro collection of tuber crops germplasm, i.e. slow growth technique for medium term storage and cryopreservation technique for long term storage, is discussed including how to analyze genetic stability of the collections. Several national and international research centers dealing with research and development of in vitro conservation technique are presented.
    @article{Dewi96p34,
    title = {{Pemanfaatan Teknik Kultur In Vitro untuk Konservasi Plasma Nutfah Ubi-ubian.}},
    author = {N. Dewi , I. S. Dewi and I. Roostika},
    journal = {Jurnal AgroBiogen},
    pages = {34 - 44},
    volume = {10},
    number = {1},
    year = {2014},
    abstract = {Except for potato, sweet potato, taro, yam, and cassava, most of tuber crops are considered as underutilized crops. However, tuber crops are potential as alternative carbohydrate sources, so they can be used as food reserves to face global climate change that affects food security in certain area throughout the world, including Indonesia. Having high diversity in tuber crops germplasm, Indonesia must be able to conserve those germplasm to ensure their availability in the future. In the future, without ignoring all the probable constraints, the prospect in utilization of in vitro culture technique will be higher for improvement of conservation and management of genetic resources in the form of active and base collections. In this paper, strategy in developing in vitro collection of tuber crops germplasm, i.e. slow growth technique for medium term storage and cryopreservation technique for long term storage, is discussed including how to analyze genetic stability of the collections. Several national and international research centers dealing with research and development of in vitro conservation technique are presented.},
    keywords = {in vitro culture, conservation, tuber crops},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Jurnal Agrobiogen 10-1/Nurwita Dewi.pdf}
    }
  5. Koerniati, S. and A. R. Heritiera. 2014. Construction of Cry1Ac Plasmid Vector and Its Transformation into Agrobacterium tumefaciens. Jurnal agrobiogen 10 (1):26-33.
    [BibTeX] [Abstract] [PDF: Construction of Cry1Ac Plasmid Vector and Its Transformation into Agrobacterium tumefaciens ]
    Introducing cry genes into rice genome is reported able to produce rice plant resistant to stemborer. DNA sequence encodes cry1Ac gene has been inserted into pGEM4Z, but this construct does not have a selectable marker gene for selection of transformed plant cells. The research aims were to construct a plasmid vector expressing a cry1Ac gene that has a transformation selectable gene and to transform it into Agrobacterium tumefaciens. Materials used were pAY560325 binary plasmid vector, pGEM4Z-cry1Ac vector, Escherichia coli strain DH5-$\alpha$ and A. tumefaciens strain LBA4404 competent cells. The methods consisted of plasmid DNA digestion using HindIII and EcoRI, electrophoresis, DNA (backbone and insert) dissection from the gel, purification, and ligation using T4 DNA ligase. Transformation of ligated DNA into E. coli by heat shock followed by cell plating onto selection medium, colony cultured, DNA isolation, and identification using restriction enzymes. Reconfirmation was done by cutting using restriction enzyme and PCR using F3 and R3, cry1Ac gene specific primers. Research result were DNA fragments of 3.8 kb ubiquitin::cry1Ac insert and pAY560325, the backbone vector, that after ligated and transformed into E. coli produced colonies. One of ten colonies containing plasmid DNA was evidently confirmed and named pAY560325-cry1Ac. Subsequently, it was transformed into A. tumefaciens by electrophoration method. Plasmid DNA was isolated from Agrobacterium that after digested with HindIII and EcoRI produced DNA fragments of 9.44 kb (pAY560325) and 3.814 kb (ubiquitin::cry1Ac). While by PCR, plasmid produced DNA fragment of about 711 bp. Thus, cry1Ac plasmid vector (pAY560325-cry1Ac) was successfully constructed and transformed into A. tumefaciens and is ready to be transformed into rice genome.
    @article{Koerniati13p26,
    title = {{Construction of Cry1Ac Plasmid Vector and Its Transformation into Agrobacterium tumefaciens}},
    author = {S. Koerniati and A. R. Heritiera},
    journal = {Jurnal AgroBiogen},
    pages = {26 - 33},
    volume = {10},
    number = {1},
    year = {2014},
    abstract = {Introducing cry genes into rice genome is reported able to produce rice plant resistant to stemborer. DNA sequence encodes cry1Ac gene has been inserted into pGEM4Z, but this construct does not have a selectable marker gene for selection of transformed plant cells. The research aims were to construct a plasmid vector expressing a cry1Ac gene that has a transformation selectable gene and to transform it into Agrobacterium tumefaciens. Materials used were pAY560325 binary plasmid vector, pGEM4Z-cry1Ac vector, Escherichia coli strain DH5-$\alpha$ and A. tumefaciens strain LBA4404 competent cells. The methods consisted of plasmid DNA digestion using HindIII and EcoRI, electrophoresis, DNA (backbone and insert) dissection from the gel, purification, and ligation using T4 DNA ligase. Transformation of ligated DNA into E. coli by heat shock followed by cell plating onto selection medium, colony cultured, DNA isolation, and identification using restriction enzymes. Reconfirmation was done by cutting using restriction enzyme and PCR using F3 and R3, cry1Ac gene specific primers. Research result were DNA fragments of 3.8 kb ubiquitin::cry1Ac insert and pAY560325, the backbone vector, that after ligated and transformed into E. coli produced colonies. One of ten colonies containing plasmid DNA was evidently confirmed and named pAY560325-cry1Ac. Subsequently, it was transformed into A. tumefaciens by electrophoration method. Plasmid DNA was isolated from Agrobacterium that after digested with HindIII and EcoRI produced DNA fragments of 9.44 kb (pAY560325) and 3.814 kb (ubiquitin::cry1Ac). While by PCR, plasmid produced DNA fragment of about 711 bp. Thus, cry1Ac plasmid vector (pAY560325-cry1Ac) was successfully constructed and transformed into A. tumefaciens and is ready to be transformed into rice genome.},
    keywords = {construction of expression vector, cry1ac gene, agrobacterium tumefaciens, rice stemborer},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Jurnal Agrobiogen 10-1/Sri Koerniati.pdf}
    }
  6. D. Sukmadjaja, Supriati Y. and S. J. Pardal. 2014. Kultur Apeks untuk Penyediaan Bibit Unggul Tebu Varietas PS864 dan PS881. Jurnal agrobiogen 10 (2):45-52.
    [BibTeX] [Abstract] [PDF: Kultur Apeks untuk Penyediaan Bibit Unggul Tebu Varietas PS864 dan PS881 ]
    In vitro culture techniques have become alternative to help overcome the problems those are often encountered in the provision of seeds through conventional means. Micropropagation through apex culture in sugarcane has several advantages, such as the produced plants have higher genetic stability, high multiplication rate, and more healthy seeds (especially virus-free)., The aims of the the research were to produce seeds of two varieties of sugarcane, namely PS864 and PS881, through apex culture. Laboratory-scale research was conducted at the Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD), Bogor, while sowing seeds nursery was done in the Experimental Station of Gowa, South Sulawesi Assessment Institute for Agricultural Technology. The experiments consisted of initiation and regeneration of apexes, shoots multiplication, rooting induction, and acclimatization of plantlets. Research results showed the initiation and regeneration of PS864 and PS881 through apex culture could be done on MS basic medium containing 0.5 mg/l BAP. Shoot proliferation of both varieties increased in the second subculture. Addition of 1 mg/l BAP into medium in the second subculture resulted in higher average number of shoots than that of 5 mg/l BAP, both for PS864 and PS881. Addition of 1 mg/l and 5 mg/l kinetin showed no significant differences for shoot numbers compared to that of PS864 in medium containing 1 mg/l BAP. The average number of PS881 shoots in multiplication media containing 5 mg/l kinetin was higher than that of 1 mg/l kinetin. Increased concentrations of NAA and IBA from 0.1 mg/l to 0.5 mg/l in the MS medium were correlated to the increased number of roots in PS864 shoots. Meanwhile, only increased concentration of NAA that affected rooting percentage of PS881. Acclimatization showed the percentage of the plantlets grown in polybags was higher than that directly grown in planting bed. The primary seeds (G0) produced in these experiments were ready to be reproduced again to obtain further stages.
    @article{Supriati14p45,
    title = {{Kultur Apeks untuk Penyediaan Bibit Unggul Tebu Varietas PS864 dan PS881}},
    author = {D. Sukmadjaja , Y. Supriati and S. J. Pardal},
    journal = {Jurnal AgroBiogen},
    pages = {45 - 52},
    volume = {10},
    number = {2},
    year = {2014},
    abstract = {In vitro culture techniques have become alternative to help overcome the problems those are often encountered in the provision of seeds through conventional means. Micropropagation through apex culture in sugarcane has several advantages, such as the produced plants have higher genetic stability, high multiplication rate, and more healthy seeds (especially virus-free)., The aims of the the research were to produce seeds of two varieties of sugarcane, namely PS864 and PS881, through apex culture. Laboratory-scale research was conducted at the Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD), Bogor, while sowing seeds nursery was done in the Experimental Station of Gowa, South Sulawesi Assessment Institute for Agricultural Technology. The experiments consisted of initiation and regeneration of apexes, shoots multiplication, rooting induction, and acclimatization of plantlets. Research results showed the initiation and regeneration of PS864 and PS881 through apex culture could be done on MS basic medium containing 0.5 mg/l BAP. Shoot proliferation of both varieties increased in the second subculture. Addition of 1 mg/l BAP into medium in the second subculture resulted in higher average number of shoots than that of 5 mg/l BAP, both for PS864 and PS881. Addition of 1 mg/l and 5 mg/l kinetin showed no significant differences for shoot numbers compared to that of PS864 in medium containing 1 mg/l BAP. The average number of PS881 shoots in multiplication media containing 5 mg/l kinetin was higher than that of 1 mg/l kinetin. Increased concentrations of NAA and IBA from 0.1 mg/l to 0.5 mg/l in the MS medium were correlated to the increased number of roots in PS864 shoots. Meanwhile, only increased concentration of NAA that affected rooting percentage of PS881. Acclimatization showed the percentage of the plantlets grown in polybags was higher than that directly grown in planting bed. The primary seeds (G0) produced in these experiments were ready to be reproduced again to obtain further stages.},
    keywords = {sugarcane, saccharum spp, apex culture, ps864, ps881},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Jurnal Agrobiogen 10-2/Deden Sukmadjaja.pdf}
    }
  7. Manzila, I., T. P. Priyatno, R. Herlis, I. Rusmana, I. M. Samudra, and Y. Suryadi. 2014. Pengaruh Media terhadap Produksi Prodigiosin Isolat Bakteri Entomopatogen Serratia marcescens Asal Wereng Batang Cokelat. Jurnal agrobiogen 10 (2):77-84.
    [BibTeX] [Abstract] [PDF: Pengaruh Media terhadap Produksi Prodigiosin Isolat Bakteri Entomopatogen Serratia marcescens Asal Wereng Batang Cokelat ]
    Prodigiosin, the red pigment produced by the bacterium Serratia marcescens, is a secondary metabolite of the family tripyrrole that has been widely used as an antibiotic in the multifunction treatment of antibacterial as well as antifungal. This study was aimed to study the effect of Luria-Bertani (LB) broth and nutrient broth (NB) media suplemented with several concentrations of FeSO4 and CaCO3 on the production and characteristic of prodigiosin derived from S. marcescens. The study was arranged in a completely randomized factorial design with four replications. The LB and NB media were supplemented with 0, 2.5, 5, and 10 mM CaCO3 and 0, 0.25, 0.5, and 1 mM FeSO4. Results showed a red pigment produced by S. marcescens when cultured on both LB and NB media. Redlike pigmentation was varied when supplemented with different concentration of Fe2+ and Ca2+. The higher the concentration of Fe2+, the more intense the red color, conversely, the higher the concentration of Ca2+, the lighter the red color. The interaction was found between the media and concentrations of CaCO3 and FeSO4 on the production of prodigiosin. The highest prodigiosin production was obtained on NB media supplemented with FeSO4. Meanwhile, the addition of CaCO3 did not affect the prodigiosin production. An addition of 1 mM FeSO4 to LB and NB media produced crude prodigiosin of 486.0 mg/ml and 489.0 mg/ml, respectively. Based on purification by column chromatography using silica gel, the prodigiosin production on LB and NB media was 378 mg/ml and 450 mg/ml, with the purity level of 77.8% and 92%, respectively. Detection of prodigiosin by thin-layer chromatography using silica gel showed the red pigment had Rf value of 0.83 and bioautography assay showed there was an antibacterial activity against Xanthomanas oryzae pv. oryzae.
    @article{Manzila14p77,
    title = {{Pengaruh Media terhadap Produksi Prodigiosin Isolat Bakteri Entomopatogen Serratia marcescens Asal Wereng Batang Cokelat}},
    author = {I. Manzila and T. P. Priyatno and R. Herlis and I. Rusmana and I. M. Samudra and Y. Suryadi},
    journal = {Jurnal AgroBiogen},
    pages = {77 - 84},
    volume = {10},
    number = {2},
    year = {2014},
    abstract = {Prodigiosin, the red pigment produced by the bacterium Serratia marcescens, is a secondary metabolite of the family tripyrrole that has been widely used as an antibiotic in the multifunction treatment of antibacterial as well as antifungal. This study was aimed to study the effect of Luria-Bertani (LB) broth and nutrient broth (NB) media suplemented with several concentrations of FeSO4 and CaCO3 on the production and characteristic of prodigiosin derived from S. marcescens. The study was arranged in a completely randomized factorial design with four replications. The LB and NB media were supplemented with 0, 2.5, 5, and 10 mM CaCO3 and 0, 0.25, 0.5, and 1 mM FeSO4. Results showed a red pigment produced by S. marcescens when cultured on both LB and NB media. Redlike pigmentation was varied when supplemented with different concentration of Fe2+ and Ca2+. The higher the concentration of Fe2+, the more intense the red color, conversely, the higher the concentration of Ca2+, the lighter the red color. The interaction was found between the media and concentrations of CaCO3 and FeSO4 on the production of prodigiosin. The highest prodigiosin production was obtained on NB media supplemented with FeSO4. Meanwhile, the addition of CaCO3 did not affect the prodigiosin production. An addition of 1 mM FeSO4 to LB and NB media produced crude prodigiosin of 486.0 mg/ml and 489.0 mg/ml, respectively. Based on purification by column chromatography using silica gel, the prodigiosin production on LB and NB media was 378 mg/ml and 450 mg/ml, with the purity level of 77.8% and 92%, respectively. Detection of prodigiosin by thin-layer chromatography using silica gel showed the red pigment had Rf value of 0.83 and bioautography assay showed there was an antibacterial activity against Xanthomanas oryzae pv. oryzae.},
    keywords = {prodigiosin, serratia marcescens, lb, nb, caco3, feso4},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Jurnal Agrobiogen 10-2/Ifa Manzila.pdf}
    }
  8. Kristamtini, Taryono, P. Basunanda, and R. H. Murti. 2014. Keragaman Genetik Kultivar Padi Beras Hitam Lokal Berdasarkan Penanda Mikrosatelit. Jurnal agrobiogen 10 (2):69-76.
    [BibTeX] [Abstract] [PDF: Keragaman Genetik Kultivar Padi Beras Hitam Lokal Berdasarkan Penanda Mikrosatelit ]
    {Genetic Diversity of Local Black Rice Cultivars Based on Microsatellite Markers. Kristamtini, Taryono, Panjisakti Basunanda, and Rudi H. Murti. Indonesia has diverse accessions of local black rice, which are important sources of germplasm. However, some of the local black rice cultivars have different names, leading a need to be identified to determine their genetic diversity using molecular marker. This study aimed to identify genetic diversity of eleven cultivars of local black rice, collection of the Assessment Institute for Agricultural Technology, Yogyakarta and compared them with two white rice varieties using four microsatellite markers. Detection of microsatellite alleles polymorphism was carried out by visualization of PCR amplicons by electrophoresis on agarose gel. To estimate their genetic diversity, phylogenetic tree and principal coordinate analysis were performed using binary data of SSR alleles. The results revealed that total markers enabled to differentiate black rice cultivars as reflected by high value of polymorphic information content (PIC) mean (0.695). This value was consistent with the high genetic diversity of black rice (genetic diversity index
    @article{Kristamtini14p69,
    title = {{Keragaman Genetik Kultivar Padi Beras Hitam Lokal Berdasarkan Penanda Mikrosatelit}},
    author = {Kristamtini and Taryono and P. Basunanda and R. H. Murti},
    journal = {Jurnal AgroBiogen},
    pages = {69 - 76},
    volume = {10},
    number = {2},
    year = {2014},
    abstract = {Genetic Diversity of Local Black Rice Cultivars Based on Microsatellite Markers. Kristamtini, Taryono, Panjisakti Basunanda, and Rudi H. Murti. Indonesia has diverse accessions of local black rice, which are important sources of germplasm. However, some of the local black rice cultivars have different names, leading a need to be identified to determine their genetic diversity using molecular marker. This study aimed to identify genetic diversity of eleven cultivars of local black rice, collection of the Assessment Institute for Agricultural Technology, Yogyakarta and compared them with two white rice varieties using four microsatellite markers. Detection of microsatellite alleles polymorphism was carried out by visualization of PCR amplicons by electrophoresis on agarose gel. To estimate their genetic diversity, phylogenetic tree and principal coordinate analysis were performed using binary data of SSR alleles. The results revealed that total markers enabled to differentiate black rice cultivars as reflected by high value of polymorphic information content (PIC) mean (0.695). This value was consistent with the high genetic diversity of black rice (genetic diversity index, h = 0.283) in comparison with white rice cultivars (h = 0.020). The phylogenetic and main coordinate analyses suggested that black rice cultivars genetically differed from white rice. The local black rice cultivars were preferentially grouped based on their genetic those were distributed in three coordinates and did not represent their local geographic origin. Genetic diversity analysis in this study will be useful as an initial basis for proper identification and selection for appropriate parents to assist breeding program of black rice in Indonesia.},
    keywords = {genetic diversity, local cultivar, black rice, microsatellite markers},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Jurnal Agrobiogen 10-2/Kristamtini.pdf}
    }
  9. Hutami, S., R. Purnamaningsih, I. Mariska, and S. Diantina. 2014. Multiplikasi Tunas dan Induksi Perakaran pada Ubi Kelapa (Dioscorea alata L.) Dan Gembili (Dioscorea esculenta L.) Secara In Vitro. Jurnal agrobiogen 10 (2):53-60.
    [BibTeX] [Abstract] [PDF: Multiplikasi Tunas dan Induksi Perakaran pada Ubi Kelapa (Dioscorea alata L.) Dan Gembili (Dioscorea esculenta L.) Secara In Vitro ]
    Dioscorea sp. (yam) is one of the minor tuber crops which grows wildly in the forest and only a few of its species are cultivated and used as main or secondary food. Conservation is needed to preserve plant genetic material. The objective of this research was to obtain methods of plantlets propagation of D. alata L. and D. esculenta L. through in vitro culture. The research was conducted at Tissue Culture Laboratory of ICABIOGRAD in 2012. The research consisted of three stages. First, shoot emergence. In this experiment, young shoots were planted in MS basic medium combined with benzyl adenine (BA) (0, 1, 3, and 5 mg/l) and gibberelic acid (GA) (0 and 5 mg/l). Second, shoot multiplication. Shoots of Dioscorea which were planted in the best medium of the first experiment were subcultured in MS medium combined with thidiazuron (0, 0.1, 0.5, 1, 2, and 3 mg/l). Third, root initiation. Shoots of Dioscorea which were planted in the best medium of the second experiment were subcultured in MS medium (½ MS and 1 MS) combined with indole-3-butyric acid (IBA) (0, 1, 3, and 5 mg/l). Result of these experiments showed that shoot emergence of D. alata L. and D. esculenta L. began at 2 weeks after planting in MS medium. More plantlets of D. alata L. and D. esculenta L. were obtained by shoot multiplication in MS media. Root initiation of the Dioscorea began at 4 weeks after planting in MS media. The addition of IBA (3-5 mg/l) on D. esculenta L. could not stimulate rooting but led to the formation of callus at the base of the stem buds.
    @article{Hutami14p53,
    title = {{Multiplikasi Tunas dan Induksi Perakaran pada Ubi Kelapa (Dioscorea alata L.) Dan Gembili (Dioscorea esculenta L.) Secara In Vitro}},
    author = {S. Hutami and R. Purnamaningsih and I. Mariska and S. Diantina},
    journal = {Jurnal AgroBiogen},
    pages = {53 - 60},
    volume = {10},
    number = {2},
    year = {2014},
    abstract = {Dioscorea sp. (yam) is one of the minor tuber crops which grows wildly in the forest and only a few of its species are cultivated and used as main or secondary food. Conservation is needed to preserve plant genetic material. The objective of this research was to obtain methods of plantlets propagation of D. alata L. and D. esculenta L. through in vitro culture. The research was conducted at Tissue Culture Laboratory of ICABIOGRAD in 2012. The research consisted of three stages. First, shoot emergence. In this experiment, young shoots were planted in MS basic medium combined with benzyl adenine (BA) (0, 1, 3, and 5 mg/l) and gibberelic acid (GA) (0 and 5 mg/l). Second, shoot multiplication. Shoots of Dioscorea which were planted in the best medium of the first experiment were subcultured in MS medium combined with thidiazuron (0, 0.1, 0.5, 1, 2, and 3 mg/l). Third, root initiation. Shoots of Dioscorea which were planted in the best medium of the second experiment were subcultured in MS medium (½ MS and 1 MS) combined with indole-3-butyric acid (IBA) (0, 1, 3, and 5 mg/l). Result of these experiments showed that shoot emergence of D. alata L. and D. esculenta L. began at 2 weeks after planting in MS medium. More plantlets of D. alata L. and D. esculenta L. were obtained by shoot multiplication in MS media. Root initiation of the Dioscorea began at 4 weeks after planting in MS media. The addition of IBA (3-5 mg/l) on D. esculenta L. could not stimulate rooting but led to the formation of callus at the base of the stem buds.},
    keywords = {dioscorea alata l, dioscorea esculenta l, shoots multiplication, root induction, in vitro culture},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Jurnal Agrobiogen 10-2/Sri Hutami.pdf}
    }
  10. Wardoyo, S. H., Miftahudin, S. Moeljopawiro, and J. Prasetiyono. 2014. Konstitusi Genetik dan Karakter Fenotipik Galur-galur Padi Pup1 Turunan Varietas Situ Bagendit. Jurnal agrobiogen 10 (2):61-68.
    [BibTeX] [Abstract] [PDF: Konstitusi Genetik dan Karakter Fenotipik Galur-galur Padi Pup1 Turunan Varietas Situ Bagendit ]
    Acidity, phosphorus deficiency, and drought stress are major problems in Indonesia’s Ultisol rice farming. Development of rice lines tolerant to those stresses is expected to be able to reduce the consumption of P fertilizer. The objectives of the research were to evaluate genetic constitutive of rice lines (BC2F6 population) derived from Situ Bagendit x Kasalath and Situ Bagendit x NIL-C433 crossings, and to evaluate responses of those lines to Yoshida nutrient solution under P deficiency and Al stress condition. The research was conducted at Molecular Biology Laboratory and Greenhouse of ICABIOGRAD, from November 2011 to May 2013. The result of foreground analysis showed that Pup1 locus has been integrated into the genome of BC2F6 rice lines, eventhough some lines (SK5, SK6, SK7, SK8, SK9, SK10, SK19, and SK20) showed incomplete integration. Background analysis indicated that majority (95.7%) of the Situ Bagendit background has been recovered in BC2F6 rice lines. Al stress evaluation showed SN lines were more tolerant to P deficiency and Al stress than that of SK lines. Pup1 locus showed good expression under low P and no Al stress. Based on genome proportion and Yoshida nutrient solution experiments, a total of three lines, namely SK13, SN2, and SN9, have potential good characteristics. Molecular analysis within a marker-assisted backcrossing (MAB) experiment should be carried out at each generation of lines for gaining fully gene segment in advanced generations.
    @article{Wardoyo14p61,
    title = {{Konstitusi Genetik dan Karakter Fenotipik Galur-galur Padi Pup1 Turunan Varietas Situ Bagendit}},
    author = {S. H. Wardoyo and Miftahudin and S. Moeljopawiro and J. Prasetiyono},
    journal = {Jurnal AgroBiogen},
    pages = {61 - 68},
    volume = {10},
    number = {2},
    year = {2014},
    abstract = {Acidity, phosphorus deficiency, and drought stress are major problems in Indonesia's Ultisol rice farming. Development of rice lines tolerant to those stresses is expected to be able to reduce the consumption of P fertilizer. The objectives of the research were to evaluate genetic constitutive of rice lines (BC2F6 population) derived from Situ Bagendit x Kasalath and Situ Bagendit x NIL-C433 crossings, and to evaluate responses of those lines to Yoshida nutrient solution under P deficiency and Al stress condition. The research was conducted at Molecular Biology Laboratory and Greenhouse of ICABIOGRAD, from November 2011 to May 2013. The result of foreground analysis showed that Pup1 locus has been integrated into the genome of BC2F6 rice lines, eventhough some lines (SK5, SK6, SK7, SK8, SK9, SK10, SK19, and SK20) showed incomplete integration. Background analysis indicated that majority (95.7%) of the Situ Bagendit background has been recovered in BC2F6 rice lines. Al stress evaluation showed SN lines were more tolerant to P deficiency and Al stress than that of SK lines. Pup1 locus showed good expression under low P and no Al stress. Based on genome proportion and Yoshida nutrient solution experiments, a total of three lines, namely SK13, SN2, and SN9, have potential good characteristics. Molecular analysis within a marker-assisted backcrossing (MAB) experiment should be carried out at each generation of lines for gaining fully gene segment in advanced generations.},
    keywords = {rice, pup1, foreground, background, yoshida nutrient solution},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Jurnal Agrobiogen 10-2/Suwaji.pdf}
    }
  11. Nur, A., M. Azrai, and Trikoesoemaningtyas. 2014. Interaksi Genetik x Lingkungan dan Variabilitas Genetik Galur Gandum Introduksi (Triticum aestivum L.) Di Agroekosistem Tropika. Jurnal agrobiogen 10 (3):93-100.
    [BibTeX] [Abstract] [PDF: Interaksi Genetik x Lingkungan dan Variabilitas Genetik Galur Gandum Introduksi (Triticum aestivum L.) Di Agroekosistem Tropika ]
    The focus of wheat research in Indonesia is to obtained new potential wheat lines that are adapted to low-mid elevation and heat tolerant. This study was aimed to obtain information on the effect of interaction of season x line x location and genetic variability of wheat lines in tropical agroecosystem. This study was conducted at the SeameoBiotrop (<400 masl) and Indonesian Ornamental Crops Research Institute-Cipanas (>1,000 masl) experimental field for two seasons. The results showed that there was an effect of interaction of season x line x location on plant height, days to flowering, number of spikelet and floret, seed/head weight, rate of grain filling, yield, flag leaf width, stomata density, chlorophyll b, and leaf greenness. Meanwhile several characters were only influenced by the interaction of line x location, they were yield component characters, ie. empty floret percentage, number of seed/ head, 1,000 seed weight, number of head/m2 and seed/plant weight. Seven characters were not influenced by interaction of neither season x line x environment nor line x location, they were number of productive tillers, head length, number of seed/head, chlorophyll a, ratio of chlorophyll a/b, total chlorophyll, and leaf thickness. The characters that have high heritability and wide genetic variability for the two analysis models were the number of spikelet.
    @article{Nur14p93,
    title = {{Interaksi Genetik x Lingkungan dan Variabilitas Genetik Galur Gandum Introduksi (Triticum aestivum L.) Di Agroekosistem Tropika}},
    author = {A. Nur and M. Azrai and Trikoesoemaningtyas},
    journal = {Jurnal AgroBiogen},
    pages = {93 - 100},
    volume = {10},
    number = {3},
    year = {2014},
    abstract = {The focus of wheat research in Indonesia is to obtained new potential wheat lines that are adapted to low-mid elevation and heat tolerant. This study was aimed to obtain information on the effect of interaction of season x line x location and genetic variability of wheat lines in tropical agroecosystem. This study was conducted at the SeameoBiotrop (<400 masl) and Indonesian Ornamental Crops Research Institute-Cipanas (>1,000 masl) experimental field for two seasons. The results showed that there was an effect of interaction of season x line x location on plant height, days to flowering, number of spikelet and floret, seed/head weight, rate of grain filling, yield, flag leaf width, stomata density, chlorophyll b, and leaf greenness. Meanwhile several characters were only influenced by the interaction of line x location, they were yield component characters, ie. empty floret percentage, number of seed/ head, 1,000 seed weight, number of head/m2 and seed/plant weight. Seven characters were not influenced by interaction of neither season x line x environment nor line x location, they were number of productive tillers, head length, number of seed/head, chlorophyll a, ratio of chlorophyll a/b, total chlorophyll, and leaf thickness. The characters that have high heritability and wide genetic variability for the two analysis models were the number of spikelet.},
    keywords = {genetic-environment interaction, heat tolerant, genetic variability, tropical agroecosystems},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Jurnal Agrobiogen 10-3/Amin Nur.pdf}
    }
  12. M. Susilowati P. Basunanda, Enggarini Ma’sumah W. and K. R. Trijatmiko. 2014. Survei Polimorfisme Tetua untuk Pengembangan Panel CSSL Padi (Oryza sativa L.) Dan Identifikasi Tanaman F1. Jurnal agrobiogen 10 (3):85-92.
    [BibTeX] [Abstract] [PDF: Survei Polimorfisme Tetua untuk Pengembangan Panel CSSL Padi (Oryza sativa L.) Dan Identifikasi Tanaman F1 ]
    Raising yield potential of modern indica varieties is essential to meet the increased demand of rice production. This is due to increased human population, threats of climate change and degradation of agricultural resources. The use of chromosome segment substitution lines (CSSL) is more effective for identification of genes those are useful for improvement of yield potential. The aims of this study were to observe the morphological trait differences between recipient parent (var. Ciherang) and three candidates of donor parent (var. Fatmawati and new plant type lines, i.e. B12743 and B11143D), to identify polymorphic SSR markers among them and to verify F1 individuals. Ciherang and B11143D showed significant differences on flowering time, plant height, flag leaf area, tiller number, productive tiller number, panicle length, spikelet number per panicle and 1,000 grain weight. The rate of SSR marker polymorphisms between Ciherang and B11143D was the highest, where 155 of 513 markers (30.2%) were polymorphic. Marker genotyping using three polymorphic markers showed that 26 of 27 plants resulted from the cross of Ciherang х B11143D were F1. These F1 plants could become the basis of CSSL panel that facilitate the mapping of genes responsible for increasing the yield potential.
    @article{Masumah14p85,
    title = {{Survei Polimorfisme Tetua untuk Pengembangan Panel CSSL Padi (Oryza sativa L.) Dan Identifikasi Tanaman F1}},
    author = {M. Susilowati, P. Basunanda, W. Enggarini, Ma'sumah and K. R. Trijatmiko},
    journal = {Jurnal AgroBiogen},
    pages = {85 - 92},
    volume = {10},
    number = {3},
    year = {2014},
    abstract = {Raising yield potential of modern indica varieties is essential to meet the increased demand of rice production. This is due to increased human population, threats of climate change and degradation of agricultural resources. The use of chromosome segment substitution lines (CSSL) is more effective for identification of genes those are useful for improvement of yield potential. The aims of this study were to observe the morphological trait differences between recipient parent (var. Ciherang) and three candidates of donor parent (var. Fatmawati and new plant type lines, i.e. B12743 and B11143D), to identify polymorphic SSR markers among them and to verify F1 individuals. Ciherang and B11143D showed significant differences on flowering time, plant height, flag leaf area, tiller number, productive tiller number, panicle length, spikelet number per panicle and 1,000 grain weight. The rate of SSR marker polymorphisms between Ciherang and B11143D was the highest, where 155 of 513 markers (30.2%) were polymorphic. Marker genotyping using three polymorphic markers showed that 26 of 27 plants resulted from the cross of Ciherang х B11143D were F1. These F1 plants could become the basis of CSSL panel that facilitate the mapping of genes responsible for increasing the yield potential.},
    keywords = {cssl, ciherang, new plant type, oryza sativa, ssr markers},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Jurnal Agrobiogen 10-3/Mariana.pdf}
    }
  13. Lestari, P., Sutrisno, and I. M. Tasma. 2014. QTL Study to Reveal Soybean Response on Abiotic and Biotic Stresses. Jurnal agrobiogen 10 (3):109-114.
    [BibTeX] [Abstract] [PDF: QTL Study to Reveal Soybean Response on Abiotic and Biotic Stresses ] [PDF: QTL Study to Reveal Soybean Response on Abiotic and Biotic Stresses ]
    abiotic and biotic stresses, current progress of quantitative trait loci (QTL) for abiotic and biotic stresses and flowering and related genomic resources could be accessed at SoyBase (http://www.soybase.org) and Phytozome (http://www.phytozome.net). As the involvement of abiotic and biotic stresses modulating flowering in soybean, genes linked to QTL for abiotic/biotic stress and flowering/maturity were also potential for resisting the environmental changes. By mapping QTLs for flowering using one population in different locations (Korea and China) with distinctive longitude, latitude, and altitude, syntenic correlation between these two QTLs on soybean chromosomes 6 and 13 indicates the environmental specific role of syntenic regions. The information on QTL and related candidate genes may assist marker-assisted breeding and enact soybean as a model of adaptive legume crop under abiotic/ biotic stress.
    @article{Lestari14p109,
    title = {{QTL Study to Reveal Soybean Response on Abiotic and Biotic Stresses}},
    author = {P. Lestari and Sutrisno and I. M. Tasma},
    journal = {Jurnal AgroBiogen},
    pages = {109 - 114},
    volume = {10},
    number = {3},
    year = {2014},
    abstract = {abiotic and biotic stresses, current progress of quantitative trait loci (QTL) for abiotic and biotic stresses and flowering and related genomic resources could be accessed at SoyBase (http://www.soybase.org) and Phytozome (http://www.phytozome.net). As the involvement of abiotic and biotic stresses modulating flowering in soybean, genes linked to QTL for abiotic/biotic stress and flowering/maturity were also potential for resisting the environmental changes. By mapping QTLs for flowering using one population in different locations (Korea and China) with distinctive longitude, latitude, and altitude, syntenic correlation between these two QTLs on soybean chromosomes 6 and 13 indicates the environmental specific role of syntenic regions. The information on QTL and related candidate genes may assist marker-assisted breeding and enact soybean as a model of adaptive legume crop under abiotic/ biotic stress.},
    keywords = {abiotic stress, biotic stress, climate change, qtl, soybean},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Jurnal Agrobiogen 10-3/Puji Lestari.pdf},
    url = {http://www.}
    }
  14. Yunita, R., N. Khumaida, D. Sopandie, and I. Mariska. 2014. Pengaruh Iradiasi Sinar Gama terhadap Pertumbuhan dan Regenerasi Kalus Padi Varietas Ciherang dan Inpari. Jurnal agrobiogen 10 (3):101-108.
    [BibTeX] [Abstract] [PDF: Pengaruh Iradiasi Sinar Gama terhadap Pertumbuhan dan Regenerasi Kalus Padi Varietas Ciherang dan Inpari ]
    Effect of gamma irradiation on rice callus depends on the irradiation dose used. Irradiation dose is one of the factors that affect the genetic changes in the cells of plants. High doses can result in tissue death, meanwhile low doses will result in abnormal changes in plant phenotype. The level of sensitivity of a plant tissue against gamma irradiation is different. This study aimed to evaluate the growth and regeneration of callus in various irradiation doses of gamma ray. The plant materials used were mature embryos of rice var. Ciherang and Inpari 13. This study used a completely randomized design with gamma irradiation treatment at doses of 10, 20, 30, 40, 50, 60, 70, 80, 90, and 100 Gy. Each treatment consisted of 10 replicates with 5 embryogenic calli per bottle. The results showed that the increasing doses of gamma irradiation increased the percentage of dead callus, inhibited callus growth, and its ability to regenerate. The high percentages of callus of Ciherang and Inpari 13 that formed green spots and adventitious shoots were mostly obtained from controls. The percentages decreased at irradiation doses of 10, 20, 30, and 40 Gy. Moreover, the calli of Ciherang and Inpari 13 were not able to form adventitious shoots at irradiation doses higher than 40 Gy and 30 Gy, respectively.
    @article{Yunita14p101,
    title = {{Pengaruh Iradiasi Sinar Gama terhadap Pertumbuhan dan Regenerasi Kalus Padi Varietas Ciherang dan Inpari}},
    author = {R. Yunita and N. Khumaida and D. Sopandie and I. Mariska},
    journal = {Jurnal AgroBiogen},
    pages = {101 - 108},
    volume = {10},
    number = {3},
    year = {2014},
    abstract = {Effect of gamma irradiation on rice callus depends on the irradiation dose used. Irradiation dose is one of the factors that affect the genetic changes in the cells of plants. High doses can result in tissue death, meanwhile low doses will result in abnormal changes in plant phenotype. The level of sensitivity of a plant tissue against gamma irradiation is different. This study aimed to evaluate the growth and regeneration of callus in various irradiation doses of gamma ray. The plant materials used were mature embryos of rice var. Ciherang and Inpari 13. This study used a completely randomized design with gamma irradiation treatment at doses of 10, 20, 30, 40, 50, 60, 70, 80, 90, and 100 Gy. Each treatment consisted of 10 replicates with 5 embryogenic calli per bottle. The results showed that the increasing doses of gamma irradiation increased the percentage of dead callus, inhibited callus growth, and its ability to regenerate. The high percentages of callus of Ciherang and Inpari 13 that formed green spots and adventitious shoots were mostly obtained from controls. The percentages decreased at irradiation doses of 10, 20, 30, and 40 Gy. Moreover, the calli of Ciherang and Inpari 13 were not able to form adventitious shoots at irradiation doses higher than 40 Gy and 30 Gy, respectively.},
    keywords = {irradiation dose, lethal dose irradiation, rice callus, gamma ray},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Jurnal Agrobiogen 10-3/Rossa.pdf}
    }
  15. Sutrisno. 2014. Resistensi Wereng Batang Cokelat Padi, Nilaparvata lugens Stål terhadap Insektisida di Indonesia. Jurnal agrobiogen 10 (3):115-124.
    [BibTeX] [Abstract] [PDF: Resistensi Wereng Batang Cokelat Padi, Nilaparvata lugens Stål terhadap Insektisida di Indonesia ]
    The rice brown planthopper (BPH), Nilaparvata lugens (St{å{}}l) is a major insect pest of rice and their infestations occur every year in several locations in Indonesia. The use of insecticides often fails to control the BPH so their populations are still high that cause rice crops show hopperburn and the farmer loses the yields. The development of insecticide resistant in BPH population is one of the factors to contribute to the failure of insecticides control. We have detected the development of field population BPH resistance to BPMC, carbofuran, MIPC, and imidacloprid, but we do not know yet the development of resistance to other insecticides to control BPH in Indonesia. This paper will review several cases on BPH resistance to insecticides in Indonesia and other countries that include aspects of the development of resistance in the field and in the laboratory, the mechanism of resistance, inheritance of resistance, genomics of resistance, and resistance management. A policy and further study is also suggested for insecticide resistance management in Indonesia.
    @article{Sutrisno14p115,
    title = {{Resistensi Wereng Batang Cokelat Padi, Nilaparvata lugens St{\aa{}}l terhadap Insektisida di Indonesia}},
    author = {Sutrisno},
    journal = {Jurnal AgroBiogen},
    pages = {115 - 124},
    volume = {10},
    number = {3},
    year = {2014},
    abstract = {The rice brown planthopper (BPH), Nilaparvata lugens (St{\aa{}}l) is a major insect pest of rice and their infestations occur every year in several locations in Indonesia. The use of insecticides often fails to control the BPH so their populations are still high that cause rice crops show hopperburn and the farmer loses the yields. The development of insecticide resistant in BPH population is one of the factors to contribute to the failure of insecticides control. We have detected the development of field population BPH resistance to BPMC, carbofuran, MIPC, and imidacloprid, but we do not know yet the development of resistance to other insecticides to control BPH in Indonesia. This paper will review several cases on BPH resistance to insecticides in Indonesia and other countries that include aspects of the development of resistance in the field and in the laboratory, the mechanism of resistance, inheritance of resistance, genomics of resistance, and resistance management. A policy and further study is also suggested for insecticide resistance management in Indonesia.},
    keywords = {insecticides, resistance, rice brown planthopper, nilaparvata lugens},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Jurnal Agrobiogen 10-3/Sutrisno.pdf}
    }

2013

  1. Apriana, Aniversari, Toto Hadiarto, and Ahmad Dadang. 2013. Optimasi Sistem Regenerasi dan Transformasi Padi Varietas Elit Indonesia. Jurnal agrobiogen 9 (1):11-18.
    [BibTeX] [Abstract] [PDF: Optimasi Sistem Regenerasi dan Transformasi Padi Varietas Elit Indonesia ]
    Optimization of Regeneration and Transformation System of Indonesian Elite Rice Variety. Aniversari Apriana, Toto Hadiarto, and Ahmad Dadang. New rice variety can be generated by means of transgenic approach. Transgenic rice researches have been conducted in many institutions worldwide using Japonica, Indica, and Javanica varieties. The most cultivated rice in Indonesia is Indica. Indica type is known to have low responsive tissues in culture and transformation media when compared to Japonica rice. This research activity is aimed to optimize regeneration and transformation systems of the Indonesian elite rice varieties, so that good method can be achieved to be used in the generation of transgenic elite rice varieties of Indica type. The research consisted of two activities: regeneration and transformation optimizations in varieties of Dodokan (upland rice) and Inpari 6 (irrigated rice). Immature embryo was used as the explant in this research. The optimization studies used 2 types of media, NBH (N6 salts and vitamins, cassamino acid 0.5 g/l, L-proline 0.5 g/l, sucrose 20 g/l, D-glucose 10 g/l, 2.4-D 2 mg/l, NAA 1 mg/l, BA 1 mg/l, agarose Type I 5.5 g/l) and NBH-M (N6 macro salts, B5 micro salts, and vitamins, 0.3 g/l cassamino acid, 3 g/l Lproline, 20 g/l sucrose, 3 mg/l 2.4-D, 1 mg/l NAA, 1 mg/l BAP, 5.5 agarose Type I), 2 types of regeneration media, R1 (MS base media and vitamis, 0.3 g/l glutamine, 30 g/l sucrose, 2 mg/l kinetin, 1 mg/l NAA, 3 g/l phytagel) and R2 (MS base media and vitamins, 2 g/l cassamino acid, 20 g/l sucrose, 30 mg/l sorbitol, 2.5 mg/l kinetin, 0.25 mg/l NAA, 3 g/l phytagel). Optimization transformation of Indonesian elite rice varieties used developed an empty plasmid pCAMBIA 1301 containing hpt gene. The transformation was conducted using two types of co-cultivation media, K1 (N6 macro salts, B5 micro salts, and vitamins, 0.5 g/l cassamino acid, 0.5 g/l L-proline, 20 g/l sucrose, 10 g/l glucose, 2 mg/l 2.4-D, 1 mg/l NAA, 1 mg/l BAP, 0.1 mM acetosyringone) and K2 (N6 macro salts, B5 micro salts, and vitamins, 0.5 g/l cassamino acid, 0.5 g/l Lproline, 20 g/l sucrose, 10 g/l glucose, 2 mg/l 2.4-D, 1 mg/l NAA, 1 mg/l BAP, 0.2 mM acetosyringone). The results showed that Inpari 6 could form embryonic calli in NBH media and further regenerated well in R1 media (13.8%). The co-cultivation media K1 generated more selected calli which then generated green plant of young embryo compared to K2. Inpari 6 showed higher regeneration rates after transformation (3.6%) compared to Dodokan (0%). Molecular analysis showed that all 11 transformants (Inpari 6) tested contained the hpt gene. These results are expected to support the development of transgenic Indica rice generation in Indonesia.
    @article{AniversariApriana13p11,
    title = {{Optimasi Sistem Regenerasi dan Transformasi Padi Varietas Elit Indonesia}},
    author = {Aniversari Apriana and Toto Hadiarto and Ahmad Dadang},
    journal = {Jurnal AgroBiogen},
    pages = {11 - 18},
    volume = {9},
    number = {1},
    year = {2013},
    abstract = {Optimization of Regeneration and Transformation System of Indonesian Elite Rice Variety. Aniversari Apriana, Toto Hadiarto, and Ahmad Dadang. New rice variety can be generated by means of transgenic approach. Transgenic rice researches have been conducted in many institutions worldwide using Japonica, Indica, and Javanica varieties. The most cultivated rice in Indonesia is Indica. Indica type is known to have low responsive tissues in culture and transformation media when compared to Japonica rice. This research activity is aimed to optimize regeneration and transformation systems of the Indonesian elite rice varieties, so that good method can be achieved to be used in the generation of transgenic elite rice varieties of Indica type. The research consisted of two activities: regeneration and transformation optimizations in varieties of Dodokan (upland rice) and Inpari 6 (irrigated rice). Immature embryo was used as the explant in this research. The optimization studies used 2 types of media, NBH (N6 salts and vitamins, cassamino acid 0.5 g/l, L-proline 0.5 g/l, sucrose 20 g/l, D-glucose 10 g/l, 2.4-D 2 mg/l, NAA 1 mg/l, BA 1 mg/l, agarose Type I 5.5 g/l) and NBH-M (N6 macro salts, B5 micro salts, and vitamins, 0.3 g/l cassamino acid, 3 g/l Lproline, 20 g/l sucrose, 3 mg/l 2.4-D, 1 mg/l NAA, 1 mg/l BAP, 5.5 agarose Type I), 2 types of regeneration media, R1 (MS base media and vitamis, 0.3 g/l glutamine, 30 g/l sucrose, 2 mg/l kinetin, 1 mg/l NAA, 3 g/l phytagel) and R2 (MS base media and vitamins, 2 g/l cassamino acid, 20 g/l sucrose, 30 mg/l sorbitol, 2.5 mg/l kinetin, 0.25 mg/l NAA, 3 g/l phytagel). Optimization transformation of Indonesian elite rice varieties used developed an empty plasmid pCAMBIA 1301 containing hpt gene. The transformation was conducted using two types of co-cultivation media, K1 (N6 macro salts, B5 micro salts, and vitamins, 0.5 g/l cassamino acid, 0.5 g/l L-proline, 20 g/l sucrose, 10 g/l glucose, 2 mg/l 2.4-D, 1 mg/l NAA, 1 mg/l BAP, 0.1 mM acetosyringone) and K2 (N6 macro salts, B5 micro salts, and vitamins, 0.5 g/l cassamino acid, 0.5 g/l Lproline, 20 g/l sucrose, 10 g/l glucose, 2 mg/l 2.4-D, 1 mg/l NAA, 1 mg/l BAP, 0.2 mM acetosyringone). The results showed that Inpari 6 could form embryonic calli in NBH media and further regenerated well in R1 media (13.8%). The co-cultivation media K1 generated more selected calli which then generated green plant of young embryo compared to K2. Inpari 6 showed higher regeneration rates after transformation (3.6%) compared to Dodokan (0%). Molecular analysis showed that all 11 transformants (Inpari 6) tested contained the hpt gene. These results are expected to support the development of transgenic Indica rice generation in Indonesia.},
    keywords = {Rice, indica, regeneration, transformation},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_9_1_2013_11-18.pdf}
    }
  2. Tasma, Made I., Ahmad Warsun, Dani Satyawan, Syafaruddin, and Budi Martono. 2013. Analisis Kekerabatan 50 Aksesi Kelapa Sawit (Elaeis guineensis Jacq.) Asal Kamerun Berdasarkan Marka Mikrosatelit. Jurnal agrobiogen 9 (1):19-27.
    [BibTeX] [Abstract] [PDF: Analisis Kekerabatan 50 Aksesi Kelapa Sawit (Elaeis guineensis Jacq.) Asal Kamerun Berdasarkan Marka Mikrosatelit ]
    Phylogenetic Analysis of 50 Cameroonian-Originated Oil Palm Accessions Assessed with Microsatelitte Markers. I Made Tasma, Ahmad Warsun, Dani Satyawan, Syafaruddin, and Budi Martono. Genetic diversity of the Indonesian oil palm collection remains low and collection enrichness through exploration activities from the center of origins is required. In 2009, 103 oil palm accessions from Cameroon were collected at the National Oil Palm Genetic Resources Collection located at the District of Sijunjung, West Sumatera. The objectives of the present study were to analayze the 50 Cameroon-originated oil palm accessions in order to: (1) determine polymorphism levels of the SSR markers used; (2) understand diversity levels of the oil palm accessions tested; and (3) analyze accessions potentially used for germ plasm collection. Fifty oil palm accessions were used in this study. DNA was isolated from leaves of the selected individual plants representing each of the accessions. DNA was analyzed with 12 SSR markers. A dendrogram was constructed using the UPGMA through Numerical Taxonomy and Multivariate System program version 2.1-pc. Results showed that SSR markers used demonstrated the average number of alleles per locus of 3.6 (2-6). The polymorphism level was 0.53 (0.21-0.73). The phylogenetic analysis resulted nine clusters with genetic diversity between two accessions ranged from 4-82%. Ten accessions (20%) showed low genetic diversity (<10%) but the accessions demonstrated high diversity in flowering time. Eleven accessions showed medium diversity level (2742%). Five accessions demonstrated high genetic diversity level (45-82%). A confirmation study using more SSR markers is recommended. This study finding may be useful in planning the oil palm germ plasm collection activities.
    @article{MadeTasma13p19,
    title = {{Analisis Kekerabatan 50 Aksesi Kelapa Sawit (Elaeis guineensis Jacq.) Asal Kamerun Berdasarkan Marka Mikrosatelit}},
    author = {I. Made Tasma and Ahmad Warsun and Dani Satyawan and Syafaruddin and Budi Martono},
    journal = {Jurnal AgroBiogen},
    pages = {19 -27},
    volume = {9},
    number = {1},
    year = {2013},
    abstract = {Phylogenetic Analysis of 50 Cameroonian-Originated Oil Palm Accessions Assessed with Microsatelitte Markers. I Made Tasma, Ahmad Warsun, Dani Satyawan, Syafaruddin, and Budi Martono. Genetic diversity of the Indonesian oil palm collection remains low and collection enrichness through exploration activities from the center of origins is required. In 2009, 103 oil palm accessions from Cameroon were collected at the National Oil Palm Genetic Resources Collection located at the District of Sijunjung, West Sumatera. The objectives of the present study were to analayze the 50 Cameroon-originated oil palm accessions in order to: (1) determine polymorphism levels of the SSR markers used; (2) understand diversity levels of the oil palm accessions tested; and (3) analyze accessions potentially used for germ plasm collection. Fifty oil palm accessions were used in this study. DNA was isolated from leaves of the selected individual plants representing each of the accessions. DNA was analyzed with 12 SSR markers. A dendrogram was constructed using the UPGMA through Numerical Taxonomy and Multivariate System program version 2.1-pc. Results showed that SSR markers used demonstrated the average number of alleles per locus of 3.6 (2-6). The polymorphism level was 0.53 (0.21-0.73). The phylogenetic analysis resulted nine clusters with genetic diversity between two accessions ranged from 4-82%. Ten accessions (20%) showed low genetic diversity (<10%) but the accessions demonstrated high diversity in flowering time. Eleven accessions showed medium diversity level (2742%). Five accessions demonstrated high genetic diversity level (45-82%). A confirmation study using more SSR markers is recommended. This study finding may be useful in planning the oil palm germ plasm collection activities.},
    keywords = {Genetic diversity, resources, oil palm, ssr marker, genetic},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_9_1_2013_19-27.pdf}
    }
  3. Dewi, Iswari S., Yusie Arisanti, Bambang S. Purwoko, Hariyadi, and M. Syukur. 2013. Keragaman Genetik Beberapa Genotipe Jarak Pagar (Jatropha curcas L.) Berdaya Hasil Tinggi Berdasarkan Karakter Morfologi, Agronomi, dan Isozim. Jurnal agrobiogen 9 (1):28-38.
    [BibTeX] [Abstract] [PDF: Keragaman Genetik Beberapa Genotipe Jarak Pagar (Jatropha curcas L.) Berdaya Hasil Tinggi Berdasarkan Karakter Morfologi, Agronomi, dan Isozim ]
    Genetic Variation of Several Genotypes of High Yielding Physic Nut (Jatropha curcas L.) Based on Morphology, Agronomy and Isozymes Characters. Iswari S. Dewi, Yusie Arisanti, Bambang S. Purwoko, Hariyadi, and M. Syukur. The interest in using Jatropha curcas L. from the family Euphorbiaceae for the production of biofuel is rapidly growing. The research objective was to determine genetic variation of several high yielding physic nuts based on their morphology, agronomy, and isozyme characters. The research used Completely Randomized Design with three replications. The treatment was consisted of 8 genotypes i.e. IP-1A, IP-1M, IP-2P, Lombok Timur, Lombok Tengah, Lombok Barat, Sumbawa, and Bima. Analysis of isozyme of the eight genotypes was also conducted according to 5 enzyme systems, i.e. peroksidase, esterase, aspartat aminotransferase, malat dehidrogenase, and alcohol dehidrogenase. Observation was done on qualitative and quantitative characters as well as banding pattern derivedisozymes. The results showed that genetic variation was low when based on qualitative characters and isozyme (0-25%) but relatively high when based on selected quantitative characters analysis (17-81%). Analysis of combined qualitative, quantitative, and isozyme characters still gave low genetic variation (6-33%). Based on the quantitative characters at similarity coefficient of 46% the genotypes can be devided into three clusters. Improved population genotypes, i.e. IP-1A, IP-1M, and IP-2P were placed in 3 different clusters, while other genotypes from NTB area were grouped in the same cluster. Therefore, selection among population of the same ecotype based on agronomic characters such as yield components, yield and oil content was suitable in Jatropha improvement, especially when genetic variation was low. Furthermore, introduction, mutation and crossing are suggested to increase genetic variation of current Jatropha collection.
    @article{Dewi13p28,
    title = {{Keragaman Genetik Beberapa Genotipe Jarak Pagar (Jatropha curcas L.) Berdaya Hasil Tinggi Berdasarkan Karakter Morfologi, Agronomi, dan Isozim}},
    author = {Iswari S. Dewi and Yusie Arisanti and Bambang S. Purwoko and Hariyadi and M. Syukur},
    journal = {Jurnal AgroBiogen},
    pages = {28 - 38},
    volume = {9},
    number = {1},
    year = {2013},
    abstract = {Genetic Variation of Several Genotypes of High Yielding Physic Nut (Jatropha curcas L.) Based on Morphology, Agronomy and Isozymes Characters. Iswari S. Dewi, Yusie Arisanti, Bambang S. Purwoko, Hariyadi, and M. Syukur. The interest in using Jatropha curcas L. from the family Euphorbiaceae for the production of biofuel is rapidly growing. The research objective was to determine genetic variation of several high yielding physic nuts based on their morphology, agronomy, and isozyme characters. The research used Completely Randomized Design with three replications. The treatment was consisted of 8 genotypes i.e. IP-1A, IP-1M, IP-2P, Lombok Timur, Lombok Tengah, Lombok Barat, Sumbawa, and Bima. Analysis of isozyme of the eight genotypes was also conducted according to 5 enzyme systems, i.e. peroksidase, esterase, aspartat aminotransferase, malat dehidrogenase, and alcohol dehidrogenase. Observation was done on qualitative and quantitative characters as well as banding pattern derivedisozymes. The results showed that genetic variation was low when based on qualitative characters and isozyme (0-25%) but relatively high when based on selected quantitative characters analysis (17-81%). Analysis of combined qualitative, quantitative, and isozyme characters still gave low genetic variation (6-33%). Based on the quantitative characters at similarity coefficient of 46% the genotypes can be devided into three clusters. Improved population genotypes, i.e. IP-1A, IP-1M, and IP-2P were placed in 3 different clusters, while other genotypes from NTB area were grouped in the same cluster. Therefore, selection among population of the same ecotype based on agronomic characters such as yield components, yield and oil content was suitable in Jatropha improvement, especially when genetic variation was low. Furthermore, introduction, mutation and crossing are suggested to increase genetic variation of current Jatropha collection.},
    keywords = {Jatropha curcas l, morphology, agronomy, isozymes, genetic variation},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_9_1_2013_28-38.pdf}
    }
  4. Roostika, Ika. 2013. Perkembangan Aplikasi Teknik Kriopreservasi untuk Konservasi dan Mendukung Program Pemuliaan Tanaman. Jurnal agrobiogen 9 (1):39-48.
    [BibTeX] [Abstract] [PDF: Perkembangan Aplikasi Teknik Kriopreservasi untuk Konservasi dan Mendukung Program Pemuliaan Tanaman ]
    Development of the Application of Cryopreservation Techniques for Conservation and Supporting Plant Breeding Program. Ika Roostika. In the beginning, cryopreservation technique was primarily used for germplasms long-term storage as passive collection because cell division and metabolism process can be stopped at super low temperature, commonly in liquid nitrogen. The technique is suitable for vegetative propagated plants and recalcitrant seeds. Recently, its application is extending for storing many species and orthodox seeds. In this paper, the development of cryopreservation application is discussed. In Indonesia, cryopreservation is being studied but the application of cryopreservation has been significantly developed abroad. The application of cryopreservation technique is not only for preserving passive collections but also for storing active collections, including to provide plant materials for hybridization, cellular engineering, genetic transformation, as well as pathogens eradication or cryotherapy. It is concluded that cryopreservation plays an important role in conventional and modern plant breeding program.
    @article{IkaRoostika13p39,
    title = {{Perkembangan Aplikasi Teknik Kriopreservasi untuk Konservasi dan Mendukung Program Pemuliaan Tanaman}},
    author = {Ika Roostika},
    journal = {Jurnal AgroBiogen},
    pages = {39 - 48},
    volume = {9},
    number = {1},
    year = {2013},
    abstract = {Development of the Application of Cryopreservation Techniques for Conservation and Supporting Plant Breeding Program. Ika Roostika. In the beginning, cryopreservation technique was primarily used for germplasms long-term storage as passive collection because cell division and metabolism process can be stopped at super low temperature, commonly in liquid nitrogen. The technique is suitable for vegetative propagated plants and recalcitrant seeds. Recently, its application is extending for storing many species and orthodox seeds. In this paper, the development of cryopreservation application is discussed. In Indonesia, cryopreservation is being studied but the application of cryopreservation has been significantly developed abroad. The application of cryopreservation technique is not only for preserving passive collections but also for storing active collections, including to provide plant materials for hybridization, cellular engineering, genetic transformation, as well as pathogens eradication or cryotherapy. It is concluded that cryopreservation plays an important role in conventional and modern plant breeding program.},
    keywords = {Cryopreservation, passive collection, collection, cryotherapy, plant breeding, active},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_9_1_2013_39-48.pdf}
    }
  5. Dadang, Ahmad, Tasliah, and Joko Prasetiyono. 2013. Seleksi dan Konfirmasi Alel Gen-gen Hd pada Padi Berumur Genjah dan Produktivitas Tinggi Persilangan Code x Nipponbare. Jurnal agrobiogen 9 (1):1-10.
    [BibTeX] [Abstract] [PDF: Seleksi dan Konfirmasi Alel Gen-gen Hd pada Padi Berumur Genjah dan Produktivitas Tinggi Persilangan Code x Nipponbare ]
    Selection and Confirmation Allele of Hd Genes on Rice with Early Maturity and High Productivity on Code x Nipponbare Crossed. Ahmad Dadang, Tasliah, and Joko Prasetiyono. To support the IP 300 program rice varieties with both early maturity and high productivity are needed. The objective of the research was to improve those traits in Code variety using RIL (recombinant inbreed line) methods. The research was conducted in the year 2009-2011 at the greenhouse and laboratory of Molecular Biology, Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development. Materials consisted of 600 individuals of F2 derived from one of F1 Code x Nipponbare crossed plants and they were planted up to F4 with seed-to-seed, then confirmed by 8 microsatelite markers linked to loci of Hd genes. The molecular analysis showed that 84 of 600 F2 plants produced. The F4 plants have 50% of flowering time shorter than F2 and F3 plants. Two lines (CdNb_388 and CdNb_270) have higher productivity compared to Code by the number of productive tillers (20) and the number of tiller grains (2240 and 1740) and have closely 50% of 60 days flowering time of Nipponbare. Three lines of F4 plants (CdNb_270, 364, and 388) were predicted to have allele of Hd7 gene, and CdNb_472 was predicted to have alelle of Hd14 gene.
    @article{AhmadDadang13p1,
    title = {{Seleksi dan Konfirmasi Alel Gen-gen Hd pada Padi Berumur Genjah dan Produktivitas Tinggi Persilangan Code x Nipponbare}},
    author = {Ahmad Dadang and Tasliah and Joko Prasetiyono},
    journal = {Jurnal AgroBiogen},
    pages = {1 - 10},
    volume = {9},
    number = {1},
    year = {2013},
    abstract = {Selection and Confirmation Allele of Hd Genes on Rice with Early Maturity and High Productivity on Code x Nipponbare Crossed. Ahmad Dadang, Tasliah, and Joko Prasetiyono. To support the IP 300 program rice varieties with both early maturity and high productivity are needed. The objective of the research was to improve those traits in Code variety using RIL (recombinant inbreed line) methods. The research was conducted in the year 2009-2011 at the greenhouse and laboratory of Molecular Biology, Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development. Materials consisted of 600 individuals of F2 derived from one of F1 Code x Nipponbare crossed plants and they were planted up to F4 with seed-to-seed, then confirmed by 8 microsatelite markers linked to loci of Hd genes. The molecular analysis showed that 84 of 600 F2 plants produced. The F4 plants have 50% of flowering time shorter than F2 and F3 plants. Two lines (CdNb_388 and CdNb_270) have higher productivity compared to Code by the number of productive tillers (20) and the number of tiller grains (2240 and 1740) and have closely 50% of 60 days flowering time of Nipponbare. Three lines of F4 plants (CdNb_270, 364, and 388) were predicted to have allele of Hd7 gene, and CdNb_472 was predicted to have alelle of Hd14 gene.},
    keywords = {Rice, early maturity, microsatellite, hd gene.},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_9_1_2013_1-10.pdf}
    }
  6. Tasliah, Mahrup, and J. Prasetiyono. 2013. Identifikasi Molekuler Hawar Daun Bakteri (Xanthomonas oryzae pv. Oryzae) dan Uji Patogenisitasnya pada Galur-galur Padi Isogenik. Jurnal agrobiogen 9 (2):49-57.
    [BibTeX] [Abstract] [PDF: Identifikasi Molekuler Hawar Daun Bakteri (Xanthomonas oryzae pv. Oryzae) dan Uji Patogenisitasnya pada Galur-galur Padi Isogenik ]
    Identifikasi bakteri Xanthomonas oryzae pv. oryzae (Xoo) berdasarkan analisis molekuler telah diperkenalkan beberapa tahun yang lalu. Metode ini menggunakan beberapa primer spesifik untuk bakteri hawar daun khusus patovar oryzae dan dapat dikerjakan secara cepat. Tujuan penelitian ini adalah untuk mengidentifikasi isolat Xoo dari lima wilayah di Indonesia dan mengetahui tingkat patogenisitas bakteri tersebut. Isolat bakteri diambil dari tanaman padi yang terserang bakteri hawar daun dari lima wilayah diIndonesia, yakni Sumatera Barat, Jawa Barat, Jawa Tengah, Sulawesi Selatan, dan Kalimantan Barat. Primer spesifik untuk Xoo adalah primer Xoo2967, Xoo80, dan Xoo. Hasil penelitian menunjukkan bahwa sebanyak 216 isolat berhasil ditumbuhkan membentuk koloni berwarna kuning, yaitu suatu kriteria bagi Xoo dan berdasarkan analisis molekuler sebanyak 189 isolat adalah positif Xoo, dan 27 isolat bukan Xoo. Amplifikasi DNA isolat-isolat HDB tersebut menghasilkan produk berukuran 337 pb untuk primer Xoo2976, 700 pb untuk primer Xoo80, dan 534 pb untuk primer Xoo. Uji patogenisitas dari isolat-isolat Xoo menunjukkan bahwa gen resisten pada tanaman xa5, Xa7, dan Xa21 masih cukup efektif menangkal serangan penyakit hawar daun bakteri padi dari lima wilayah pertanaman padi yang menjadi target penelitian ini, dengan persentase ketahanan berturut-turut sebesar 93,57; 77,49; dan 85,37%.
    @article{Tasliah13p49,
    title = {{Identifikasi Molekuler Hawar Daun Bakteri (Xanthomonas oryzae pv. Oryzae) dan Uji Patogenisitasnya pada Galur-galur Padi Isogenik}},
    author = {Tasliah and Mahrup and J. Prasetiyono},
    journal = {Jurnal AgroBiogen},
    pages = {49 - 57},
    volume = {9},
    number = {2},
    year = {2013},
    abstract = {Identifikasi bakteri Xanthomonas oryzae pv. oryzae (Xoo) berdasarkan analisis molekuler telah diperkenalkan beberapa tahun yang lalu. Metode ini menggunakan beberapa primer spesifik untuk bakteri hawar daun khusus patovar oryzae dan dapat dikerjakan secara cepat. Tujuan penelitian ini adalah untuk mengidentifikasi isolat Xoo dari lima wilayah di Indonesia dan mengetahui tingkat patogenisitas bakteri tersebut. Isolat bakteri diambil dari tanaman padi yang terserang bakteri hawar daun dari lima wilayah diIndonesia, yakni Sumatera Barat, Jawa Barat, Jawa Tengah, Sulawesi Selatan, dan Kalimantan Barat. Primer spesifik untuk Xoo adalah primer Xoo2967, Xoo80, dan Xoo. Hasil penelitian menunjukkan bahwa sebanyak 216 isolat berhasil ditumbuhkan membentuk koloni berwarna kuning, yaitu suatu kriteria bagi Xoo dan berdasarkan analisis molekuler sebanyak 189 isolat adalah positif Xoo, dan 27 isolat bukan Xoo. Amplifikasi DNA isolat-isolat HDB tersebut menghasilkan produk berukuran 337 pb untuk primer Xoo2976, 700 pb untuk primer Xoo80, dan 534 pb untuk primer Xoo. Uji patogenisitas dari isolat-isolat Xoo menunjukkan bahwa gen resisten pada tanaman xa5, Xa7, dan Xa21 masih cukup efektif menangkal serangan penyakit hawar daun bakteri padi dari lima wilayah pertanaman padi yang menjadi target penelitian ini, dengan persentase ketahanan berturut-turut sebesar 93,57; 77,49; dan 85,37%.},
    keywords = {padi, xanthomonas oryzae pv, oryzae, primer spesifik, uji patogenisitas},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Agrobiogen_9_2_2013_49-57.pdf}
    }
  7. Waluyo, S., Sustiprijatno, and Suharsono. 2013. Transformasi Genetik Tembakau dengan Gen Cold Shock Protein melalui Perantara Agrobacterium tumefaciens. Jurnal agrobiogen 9 (2):58-65.
    [BibTeX] [Abstract] [PDF: Transformasi Genetik Tembakau dengan Gen Cold Shock Protein melalui Perantara Agrobacterium tumefaciens ]
    Cold shock protein (Csp) merupakan komponen penting dalam organisme untuk ketahanan terhadap kondisi cekaman abiotik. Gen ini telah disisipkan ke dalam promotor ubiquitin di daerah T-DNA dari pCambia 1300int, dan diintroduksikan ke dalam Agrobacte-rium tumefaciens LBA 4404. Penelitian ini bertujuan untuk melakukan transformasi genetik Nicotiana tabacum L. cv. Samsun dengan gen CspB di bawah kendali promotor pUbiquitin dan terminator NOS yang diperantarai A. tumefaciens. Potongan daun dikokultivasikan dengan A. tumefaciens LBA 4404. Hasil ketahanan kalus terhadap higromisin menghasilkan efisiensi transformasi sebesar 57,5%. Pada media seleksi yang mengandung 50 mg/l higromisin, dihasilkan efisiensi regenerasi tunascalon transgenik sebesar 82,6%. Analisis PCR menggunakan primer yang menempel pada promotor ubiquitin dan gen Csp menunjukkan 18 tembakau putatif transgenik mengandung gen CspB.
    @article{Waluyo13p58,
    title = {{Transformasi Genetik Tembakau dengan Gen Cold Shock Protein melalui Perantara Agrobacterium tumefaciens}},
    author = {S. Waluyo and Sustiprijatno and Suharsono},
    journal = {Jurnal AgroBiogen},
    pages = {58 - 65},
    volume = {9},
    number = {2},
    year = {2013},
    abstract = {Cold shock protein (Csp) merupakan komponen penting dalam organisme untuk ketahanan terhadap kondisi cekaman abiotik. Gen ini telah disisipkan ke dalam promotor ubiquitin di daerah T-DNA dari pCambia 1300int, dan diintroduksikan ke dalam Agrobacte-rium tumefaciens LBA 4404. Penelitian ini bertujuan untuk melakukan transformasi genetik Nicotiana tabacum L. cv. Samsun dengan gen CspB di bawah kendali promotor pUbiquitin dan terminator NOS yang diperantarai A. tumefaciens. Potongan daun dikokultivasikan dengan A. tumefaciens LBA 4404. Hasil ketahanan kalus terhadap higromisin menghasilkan efisiensi transformasi sebesar 57,5%. Pada media seleksi yang mengandung 50 mg/l higromisin, dihasilkan efisiensi regenerasi tunascalon transgenik sebesar 82,6%. Analisis PCR menggunakan primer yang menempel pada promotor ubiquitin dan gen Csp menunjukkan 18 tembakau putatif transgenik mengandung gen CspB.},
    keywords = {tembakau, nicotiana tabaccum, cold shock protein, csp, transformasi, agrobacterium tumefaciens},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Agrobiogen_9_2_2013_58-65.pdf}
    }
  8. Sukmadjaja, D., R. Purnamaningsih, and T. P. Priyatno. 2013. Seleksi In Vitro dan Pengujian Mutan Tanaman Pisang Ambon Kuning untuk Ketahanan terhadap Penyakit Layu Fusarium. Jurnal agrobiogen 9 (2):66-76.
    [BibTeX] [Abstract] [PDF: Seleksi In Vitro dan Pengujian Mutan Tanaman Pisang Ambon Kuning untuk Ketahanan terhadap Penyakit Layu Fusarium ]
    Serangan penyakit layu oleh Fusarium oxysporum f. sp. cubense (Foc) merupakan salah satu masalah yang dihadapi dalam usaha peningkatan produktivitas dan mutu hasil pada usaha tanaman pisang. Induksi mutasi merupakan salah satu cara yang dapat ditempuh dalam perbaikan tanaman yang tahan terhadap penyakit. Pembentukan tanaman mutan menggunakan mutagen kimia EMS diikuti seleksi in vitro serta dilanjutkan dengan pengujian ketahanan baik di rumah kaca maupun di lahan endemik merupakan salah satu metode pemuliaan mutasi untuk memperoleh kultivar baru yang tahan terhadap penyakit. Metode yang digunakan dalam penelitian ini berupa pembentukan multiple bud clumps (MBC) pada pisang Ambon Kuning menggunakan media dasar MS yang ditambah BA konsentrasi tinggi (5, 10, dan 20 mg/l) sebagai perlakuan. Regenerasi tanaman dari MBC digunakan media MS ditambah BA konsentrasi rendah (0, 0,2, dan 1 mg/l). Untuk induksi mutasi pada MBC digunakan mutagen kimia ethyl methane sulfonate (EMS) konsentrasi 0,1; 0,3; dan 0,5% yang dikombinasikan dengan waktu perendaman selama 1, 2, dan 3 jam. Untuk pengujian ketahanan terhadap toksin Fusarium digunakan asam fusarat konsentrasi 30, 45, dan 60 ppm sebagai agen seleksi. Pengujian ketahanan tanaman mutan putatif hasil seleksi in vitro dilakukan di rumah kaca menggunakan larutan spora Foc ras 4, sedangkan pengujian tanaman di lapangan dilakukan di lahan endemik penyakit layu Fusarium di Kebun Percobaan Pasirkuda, Bogor. Penelitian ini bertujuan untuk mendapatkan mutan-mutan tanaman pisang Ambon Kuning yang diinduksi dengan mutagen EMS dan menyeleksi ketahanannya terhadap penyakit layu Fusarium secara in vitro, di rumah kaca maupun di lahan endemik. Hasil penelitian menunjukkan bahwa pembentukan MBC sebagai target mutagenesis dari tanaman pisang Ambon Kuning secara in vitro dapat diperoleh menggunakan media MS dengan penambahan BA 10-20 mg/l + IAA 0,1 mg/l + asam askorbat 10 mg/l. Formulasi media terbaik untuk regenerasi MBC adalah media MS tanpa penambahan BAP. Pada percobaan induksi mutasi dengan EMS telah didapatkan 68 regeneran MBC mutan putatif yang toleran pada media seleksi yang mengandung asam fusarat 30, 45, dan 60 ppm. Pengujian ketahanan terhadap Fusarium pada 391 tanaman mutan putatif hasil seleksi in vitro dirumah kaca diperoleh 64 tanaman yang tahan penyakit layu Fusarium sampai dengan umur 6 bulan. Hasil pengujian selanjutnya di lahan endemik penyakit Fusarium diperoleh enam galur yang tahan sampai menghasilkan buah.
    @article{Sukmadjaja13p66,
    title = {{Seleksi In Vitro dan Pengujian Mutan Tanaman Pisang Ambon Kuning untuk Ketahanan terhadap Penyakit Layu Fusarium}},
    author = {D. Sukmadjaja and R. Purnamaningsih and T. P. Priyatno},
    journal = {Jurnal AgroBiogen},
    pages = {66 - 76},
    volume = {9},
    number = {2},
    year = {2013},
    abstract = {Serangan penyakit layu oleh Fusarium oxysporum f. sp. cubense (Foc) merupakan salah satu masalah yang dihadapi dalam usaha peningkatan produktivitas dan mutu hasil pada usaha tanaman pisang. Induksi mutasi merupakan salah satu cara yang dapat ditempuh dalam perbaikan tanaman yang tahan terhadap penyakit. Pembentukan tanaman mutan menggunakan mutagen kimia EMS diikuti seleksi in vitro serta dilanjutkan dengan pengujian ketahanan baik di rumah kaca maupun di lahan endemik merupakan salah satu metode pemuliaan mutasi untuk memperoleh kultivar baru yang tahan terhadap penyakit. Metode yang digunakan dalam penelitian ini berupa pembentukan multiple bud clumps (MBC) pada pisang Ambon Kuning menggunakan media dasar MS yang ditambah BA konsentrasi tinggi (5, 10, dan 20 mg/l) sebagai perlakuan. Regenerasi tanaman dari MBC digunakan media MS ditambah BA konsentrasi rendah (0, 0,2, dan 1 mg/l). Untuk induksi mutasi pada MBC digunakan mutagen kimia ethyl methane sulfonate (EMS) konsentrasi 0,1; 0,3; dan 0,5% yang dikombinasikan dengan waktu perendaman selama 1, 2, dan 3 jam. Untuk pengujian ketahanan terhadap toksin Fusarium digunakan asam fusarat konsentrasi 30, 45, dan 60 ppm sebagai agen seleksi. Pengujian ketahanan tanaman mutan putatif hasil seleksi in vitro dilakukan di rumah kaca menggunakan larutan spora Foc ras 4, sedangkan pengujian tanaman di lapangan dilakukan di lahan endemik penyakit layu Fusarium di Kebun Percobaan Pasirkuda, Bogor. Penelitian ini bertujuan untuk mendapatkan mutan-mutan tanaman pisang Ambon Kuning yang diinduksi dengan mutagen EMS dan menyeleksi ketahanannya terhadap penyakit layu Fusarium secara in vitro, di rumah kaca maupun di lahan endemik. Hasil penelitian menunjukkan bahwa pembentukan MBC sebagai target mutagenesis dari tanaman pisang Ambon Kuning secara in vitro dapat diperoleh menggunakan media MS dengan penambahan BA 10-20 mg/l + IAA 0,1 mg/l + asam askorbat 10 mg/l. Formulasi media terbaik untuk regenerasi MBC adalah media MS tanpa penambahan BAP. Pada percobaan induksi mutasi dengan EMS telah didapatkan 68 regeneran MBC mutan putatif yang toleran pada media seleksi yang mengandung asam fusarat 30, 45, dan 60 ppm. Pengujian ketahanan terhadap Fusarium pada 391 tanaman mutan putatif hasil seleksi in vitro dirumah kaca diperoleh 64 tanaman yang tahan penyakit layu
    Fusarium sampai dengan umur 6 bulan. Hasil pengujian
    selanjutnya di lahan endemik penyakit Fusarium diperoleh
    enam galur yang tahan sampai menghasilkan buah.},
    keywords = {Pisang Ambon Kuning, seleksi in vitro,
    Fusarium oxysporum, mutan putatif, EMS, asam
    fusarat},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Agrobiogen_9_2_2013_66-76.pdf}
    }
  9. Suryadi, Y., T. P. Priyatno, I. M. Samudra, D. N. Susilowati, N. Lawati, and E. Kustaman. 2013. Pemurnian Parsial dan Karakterisasi Kitinase Asal Jamur Entomopatogen Beauveria bassiana Isolat BB200109. Jurnal agrobiogen 9 (2):77-84.
    [BibTeX] [Abstract] [PDF: Pemurnian Parsial dan Karakterisasi Kitinase Asal Jamur Entomopatogen Beauveria bassiana Isolat BB200109 ]
    Beauveria bassiana merupakan salah satu jamur entomopatogen yang memproduksi kitinase saat menginfeksi inangnya. Penelitian ini bertujuan untuk melakukan pemurnian parsial, mengisolasi dan mengkarakterisasi kitinase B. bassiana isolat BB200109 secara kualitatif dan kuantitatif. Identitas patogen ditentukan secara morfologis maupun molekuler menggunakan primer ITS; sementara karakterisasi dilakukan pada berbagai kondisi suhu, pH, ion logam, dan waktu inkubasi. Hasil identifikasi menunjukkan isolat BB200109 tergolong ke dalam kelompok B. bassiana. Isolat B. bassiana BB200109 menghasilkan indeks kitinolitik sebesar 1,035. Hasil pemurnian parsial dengan pengendapan amonium sulfat 10, 30, dan 70% menghasilkan aktivitas enzim sebesar 1,2 kali, sementara hasil dialisis meningkatkan kemurnian sebesar 1,9 kali dibanding ekstrak kasar enzim. Hasil karakterisasi menunjukkan kitinase asal B. bassiana isolat BB200109 memiliki pH optimum 4, suhu optimum 50oC, dan waktu inkubasi optimum 90 menit. Pengaruh penambahan ion logam (60 mM) Mn2+ berfungsi sebagai aktivator, sementara ion EDTA, K+, Mg2+, Cu2+, Fe2+, Zn2+, dan Na+ bersifat sebagai inhibitor. Kitinase memiliki afinitas yang rendah terhadap substrat kitin ditunjukkan dengan nilai Km sebesar 0,266 mg/l dan Vmaks sebesar 0,067 mg/l detik. Hasil SDS-PAGE menunjukkan B. bassiana isolat BB200109 memiliki bobot molekul 60,25 kDa. Hasil penelitian ini mengindikasikan potensi B. bassiana isolat BB200109 sebagai penghasil kitinase ekstraseluler dengan karakteristik enzim yang diproduksinya dapat dikembangkan lebih lanjut sebagai agen biokontrol serangga hama.
    @article{Suryadi13p77,
    title = {{Pemurnian Parsial dan Karakterisasi Kitinase Asal Jamur Entomopatogen Beauveria bassiana Isolat BB200109}},
    author = {Y. Suryadi and T. P. Priyatno and I. M. Samudra and D. N. Susilowati and N. Lawati and E. Kustaman},
    journal = {Jurnal AgroBiogen},
    pages = {77 - 84},
    volume = {9},
    number = {2},
    year = {2013},
    abstract = {Beauveria bassiana merupakan salah satu jamur entomopatogen yang memproduksi kitinase saat menginfeksi inangnya. Penelitian ini bertujuan untuk melakukan pemurnian parsial, mengisolasi dan mengkarakterisasi kitinase B. bassiana isolat BB200109 secara kualitatif dan kuantitatif. Identitas patogen ditentukan secara morfologis maupun molekuler menggunakan primer ITS; sementara karakterisasi dilakukan pada berbagai kondisi suhu, pH, ion logam, dan waktu inkubasi. Hasil identifikasi menunjukkan isolat BB200109 tergolong ke dalam kelompok B. bassiana. Isolat B. bassiana BB200109 menghasilkan indeks kitinolitik sebesar 1,035. Hasil pemurnian parsial dengan pengendapan amonium sulfat 10, 30, dan 70% menghasilkan aktivitas enzim sebesar 1,2 kali, sementara hasil dialisis meningkatkan kemurnian sebesar 1,9 kali dibanding ekstrak kasar enzim. Hasil karakterisasi menunjukkan kitinase asal B. bassiana isolat BB200109 memiliki pH optimum 4, suhu optimum 50oC, dan waktu inkubasi optimum 90 menit. Pengaruh penambahan ion logam (60 mM) Mn2+ berfungsi sebagai aktivator, sementara ion EDTA, K+, Mg2+, Cu2+, Fe2+, Zn2+, dan Na+ bersifat sebagai inhibitor. Kitinase memiliki afinitas yang rendah terhadap substrat kitin ditunjukkan dengan nilai Km sebesar 0,266 mg/l dan Vmaks sebesar 0,067 mg/l detik. Hasil SDS-PAGE menunjukkan B. bassiana isolat BB200109 memiliki bobot molekul 60,25 kDa. Hasil penelitian ini mengindikasikan potensi B. bassiana isolat BB200109 sebagai penghasil kitinase ekstraseluler dengan karakteristik enzim yang diproduksinya dapat dikembangkan lebih lanjut sebagai agen biokontrol serangga hama.},
    keywords = {purifikasi parsial, kitinase, b, bassiana isolat bb200109, karakterisasi},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Agrobiogen_9_2_2013_77-84.pdf}
    }
  10. Tasma, I. M.. 2013. Gen dan QTL Pengendali Umur pada Kedelai. Jurnal agrobiogen 9 (2):85-96.
    [BibTeX] [Abstract] [PDF: Gen dan QTL Pengendali Umur pada Kedelai ]
    Karakter waktu berbunga dan kematangan polong pada kedelai menentukan umur panen. Di Indonesia kultivar berumur genjah diperlukan pada musim dengan masa pertumbuhan pendek karena terbatasnya ketersediaan air. Periode tumbuh pendek meningkatkan indeks panen. Keragaman genetik plasma nutfah kedelai nasional saat ini masih sangat rendah. Peningkatan keragaman melalui introduksi dari negara dengan empat musim menghadapi kendala lingkungan tumbuh. Teknologi pembentukan tanaman beradaptasi luas memudahkan pemindahan plasma nutfah dari beragam lingkungan. Tujuan dari ulasan ini untuk memaparkan gen dan quantitative trait loci (QTL) pengendali waktu berbunga dan umur panen pada kedelai. Ulasan didukung dengan mekanisme waktu berbunga pada tanaman model Arabidopsis thaliana karena studi genetik waktu berbunga dilakukan sangat intensif pada tanaman ini. Transisi dari fase vegetatif ke fase generatif hasil aktivasi gen bertanggung jawab pada pembentukan organ bunga. Inisiasi aktivasi merupakan hasil stimuli lingkungan yang memberikan sinyal waktu yang tepat untuk berbunga. Studi pada Arabidopsis menunjukkan bahwa transisi dari fase vegetatif ke fase generatif sangat kompleks melibatkan banyak gen dan lintasan genetik. Pada kedelai karakter waktu berbunga dan kematangan polong dikendalikan sedikitnya oleh sembilan gen, yaitu E1 sampai E8 dan Dt. Gen ini berinteraksi dengan panjang hari dan temperatur. QTL terkait karakter umur diidentifikasi menggunakan berbagai populasi pemetaan. QTL mayor dideteksi pada berbagai populasi dengan latar belakang genetik berbeda dan hasil uji pada lingkungan berbeda. Beberapa QTL berasosiasi dengan gen seri E dan beberapa lainnya tidak berasosiasi. Gen pengendali waktu berbunga pada Arabidopsis juga dipetakan pada kedelai. Marka gen E dan QTL efek besar menjadi target pemulia kedelai untuk pemuliaan dan pembentukan teknologi tanaman kedelai insensitif fotoperiodisitas. Gen pembungaan yang diisolasi dari Arabidopsis dapat digunakan untuk membentuk kedelai transgenik dengan daya adaptasi luas. Teknologi pembentukan kedelai beradaptasi luas memudahkan pemindahan materi genetik dari berbagai belahan dunia, untuk meningkatkan keragaman genetik materi pemuliaan dalam rangka mendukung program pemuliaan kedelai nasional yang sistematis dan berkelanjutan.
    @article{Tasma13p85,
    title = {{Gen dan QTL Pengendali Umur pada Kedelai}},
    author = {I. M. Tasma},
    journal = {Jurnal AgroBiogen},
    pages = {85 - 96},
    volume = {9},
    number = {2},
    year = {2013},
    abstract = {Karakter waktu berbunga dan kematangan polong pada kedelai menentukan umur panen. Di Indonesia kultivar berumur genjah diperlukan pada musim dengan masa pertumbuhan pendek karena terbatasnya ketersediaan air. Periode tumbuh pendek meningkatkan indeks panen. Keragaman genetik plasma nutfah kedelai nasional saat ini masih sangat rendah. Peningkatan keragaman melalui introduksi dari negara dengan empat musim menghadapi kendala lingkungan tumbuh. Teknologi pembentukan tanaman beradaptasi luas memudahkan pemindahan plasma nutfah dari beragam lingkungan. Tujuan dari ulasan ini untuk memaparkan gen dan quantitative trait loci (QTL) pengendali waktu berbunga dan umur panen pada kedelai. Ulasan didukung dengan mekanisme waktu berbunga pada tanaman model Arabidopsis thaliana karena studi genetik waktu berbunga dilakukan sangat intensif pada tanaman ini. Transisi dari fase vegetatif ke fase generatif hasil aktivasi gen bertanggung jawab pada pembentukan organ bunga. Inisiasi aktivasi merupakan hasil stimuli lingkungan yang memberikan sinyal waktu yang tepat untuk berbunga. Studi pada Arabidopsis menunjukkan bahwa transisi dari fase vegetatif ke fase generatif sangat kompleks melibatkan banyak gen dan lintasan genetik. Pada kedelai karakter waktu berbunga dan kematangan polong dikendalikan sedikitnya oleh sembilan gen, yaitu E1 sampai E8 dan Dt. Gen ini berinteraksi dengan panjang hari dan temperatur. QTL terkait karakter umur diidentifikasi menggunakan berbagai populasi pemetaan. QTL mayor dideteksi pada berbagai populasi dengan latar belakang genetik berbeda dan hasil uji pada lingkungan berbeda. Beberapa QTL berasosiasi dengan gen seri E dan beberapa lainnya tidak berasosiasi. Gen pengendali waktu berbunga pada Arabidopsis juga dipetakan pada kedelai. Marka gen E dan QTL efek besar menjadi target pemulia kedelai untuk pemuliaan dan pembentukan teknologi tanaman kedelai insensitif fotoperiodisitas. Gen pembungaan yang diisolasi dari Arabidopsis dapat digunakan untuk membentuk kedelai transgenik dengan daya adaptasi luas. Teknologi pembentukan kedelai beradaptasi luas memudahkan pemindahan materi genetik dari berbagai belahan dunia, untuk meningkatkan keragaman genetik materi pemuliaan dalam rangka mendukung program pemuliaan kedelai nasional yang sistematis dan berkelanjutan.},
    keywords = {kedelai, waktu berbunga, kematangan polong, fotoperiodisitas, qtl},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Agrobiogen_9_2_2013_85-96.pdf}
    }
  11. Santoso, T. J., A. Apriana, A. Sisharmini, and K. R. Trijatmiko. 2013. Identifikasi Galur dan Gen-gen Terkait Toleran Kekeringan pada Padi Transgenik cv. T309 yang Mengandung Vektor Penanda Aktivasi. Jurnal agrobiogen 9 (3):97-106.
    [BibTeX] [Abstract] [PDF: Identifikasi Galur dan Gen-gen Terkait Toleran Kekeringan pada Padi Transgenik cv. T309 yang Mengandung Vektor Penanda Aktivasi ]
    Penanda aktivasi merupakan cara yang efisien untuk menganalisis fungsi gen-gen tanaman. Sejumlah galur tanaman padi transgenik cv. T309 yang mengandung vektor penanda aktivasi telah dihasilkan dari penelitian terdahulu. Galur-galur tersebut belum dianalisis fenotipe dan genotipenya dalam kaitannya dengan toleransi cekaman kekeringan. Tujuan penelitian ini adalah untuk mengidentifikasi galur-Penanda aktivasi merupakan cara yang efisien untuk menganalisis fungsi gen-gen tanaman. Sejumlah galur tanaman padi transgenik cv. T309 yang mengandung vektor penanda aktivasi telah dihasilkan dari penelitian terdahulu. Galur-galur tersebut belum dianalisis fenotipe dan genotipenya dalam kaitannya dengan toleransi cekaman kekeringan. Tujuan penelitian ini adalah untuk mengidentifikasi galur-galur tanaman padi transgenik cv. T309 yang toleran terhadap kekeringan dan mengidentifikasi gen-gen yang mungkin berkaitan dengan sifat tersebut. Metode seleksi tanaman padi transgenik yang toleran kekeringan dilakukan dengan menguji ketahanannya terhadap Basta, menguji toleransinya terhadap kekeringan, dan mendeteksi keberadaan gen bar dan hptII. Gen-gen yang diduga terkait dalam mekanisme toleransi terhadap kekeringan diidentifikasi dengan analisis TAIL Thermal Asymetric Interlaced-PCR (TAIL-PCR). Dari 59 tanaman transgenik putatif penanda aktivasi cv. T309 yang diuji, 56 tanaman toleran Basta. Dari 56 tanaman tersebut, tiga tanaman toleran terhadap kekeringan, yaitu galur PA.T1.2, PA.T-4.1, dan PA.T-5.1. Hasil analisis PCR menunjukkan bahwa galur padi PA.T-1.2 dan PA.T-4.1 mengandung gen bar dan gen hptII, sedangkan PA.T-5.1 hanya mengandung gen bar. Hasil analisis TAIL-PCR pada PA.T-5.1, menunjukkan keberadaan dua gen yang mungkin terlibat dalam toleransi terhadap kekeringan, yaitu gen OSJNBa0004120.14 yang menghasilkan putative uridylate kinase dan gen OsPPCK2L yang menghasilkan phosphoenolpyruvate carboxylase kinase.
    @article{Santoso13p97,
    title = {{Identifikasi Galur dan Gen-gen Terkait Toleran Kekeringan pada Padi Transgenik cv. T309 yang Mengandung Vektor Penanda Aktivasi}},
    author = {T. J. Santoso and A. Apriana and A. Sisharmini and K. R. Trijatmiko},
    journal = {Jurnal AgroBiogen},
    pages = {97 - 106},
    volume = {9},
    number = {3},
    year = {2013},
    abstract = {Penanda aktivasi merupakan cara yang efisien untuk menganalisis fungsi gen-gen tanaman. Sejumlah galur tanaman padi transgenik cv. T309 yang mengandung vektor penanda aktivasi telah dihasilkan dari penelitian terdahulu. Galur-galur tersebut belum dianalisis fenotipe dan genotipenya dalam kaitannya dengan toleransi cekaman kekeringan. Tujuan penelitian ini adalah untuk mengidentifikasi galur-Penanda aktivasi merupakan cara yang efisien untuk menganalisis fungsi gen-gen tanaman. Sejumlah galur tanaman padi transgenik cv. T309 yang mengandung vektor penanda aktivasi telah dihasilkan dari penelitian terdahulu. Galur-galur tersebut belum dianalisis fenotipe dan genotipenya dalam kaitannya dengan toleransi cekaman kekeringan. Tujuan penelitian ini adalah untuk mengidentifikasi galur-galur tanaman padi transgenik cv. T309 yang toleran terhadap kekeringan dan mengidentifikasi gen-gen yang mungkin berkaitan dengan sifat tersebut. Metode seleksi tanaman padi transgenik yang toleran kekeringan dilakukan dengan menguji ketahanannya terhadap Basta, menguji toleransinya terhadap kekeringan, dan mendeteksi keberadaan gen bar dan hptII. Gen-gen yang diduga terkait dalam mekanisme toleransi terhadap kekeringan diidentifikasi dengan analisis TAIL Thermal Asymetric Interlaced-PCR (TAIL-PCR). Dari 59 tanaman transgenik putatif penanda aktivasi cv. T309 yang diuji, 56 tanaman toleran Basta. Dari 56 tanaman tersebut, tiga tanaman toleran terhadap kekeringan, yaitu galur PA.T1.2, PA.T-4.1, dan PA.T-5.1. Hasil analisis PCR menunjukkan bahwa galur padi PA.T-1.2 dan PA.T-4.1 mengandung gen bar dan gen hptII, sedangkan PA.T-5.1 hanya mengandung gen bar. Hasil analisis TAIL-PCR pada PA.T-5.1, menunjukkan keberadaan dua gen yang mungkin terlibat dalam toleransi terhadap kekeringan, yaitu gen OSJNBa0004120.14 yang menghasilkan putative uridylate kinase dan gen OsPPCK2L yang menghasilkan phosphoenolpyruvate carboxylase kinase. },
    keywords = {padi, oryza sativa l, penanda aktivasi, toleran kekeringan, tail-pcr},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_9_3_2013_97-106.pdf}
    }
  12. Tasliah, H. Rijzaani, T. Z. P. Hariyadi, S. Yuriyah, Rebin, Ma’sumah, and T. S. Silitonga. 2013. Analisis Keragaman Genetik 161 Aksesi Mangga Indonesia Menggunakan Marka Mikrosatelit. Jurnal agrobiogen 9 (3):125-134.
    [BibTeX] [Abstract] [PDF: Analisis Keragaman Genetik 161 Aksesi Mangga Indonesia Menggunakan Marka Mikrosatelit ]
    Mangga merupakan salah satu dari lima tanaman buah penting di dunia. Marka mikrosatelit bisa digunakan sebagai penanda molekuler untuk melihat keragaman genetik antar aksesi mangga. Tujuan dari penelitian ini adalah untuk mengetahui hubungan kekerabatan plasma nutfah mangga di Indonesia menggunakan marka mikrosatelit. Sebanyak 161 aksesi mangga yang berasal dari Balai Penelitian Tanaman Buah Tropika (KP Cukurgondang), Pasuruan, Jawa Timur, digunakan dalam penelitian ini. Dua puluh enam marka mikrosatelit digunakan untuk melihat pola fragmen DNA masing-masing aksesi. Pemisahan fragmen DNA hasil amplifikasi dilakukan menggunakan mesin Beckman Coulter® CEQ™ 8000. Hubungan kekerabatan dibuat menggunakan metode Unweighted Pair Group Method with Arithmetic Mean (UPGMA), dilanjutkan dengan analisis bootstrap. Hasil penelitian menunjukkan terjadi variasi alel yang cukup tinggi (15-75 alel) di antara aksesi mangga dengan rata-rata jumlah alel sekitar 38,69, sedangkan rata-rata nilai Polymophism Information Content (PIC) sebesar 0,548 (0,021-0,949). Lima belas marka mikrosatelit memiliki nilai PIC >0,5 yang menunjukkan marka tersebut memiliki informasi yang tinggi untuk penelitian keragaman genetik mangga. Analisis gerombol membagi koleksi mangga ke dalam dua kelompok. Kelompok I terdiri atas 95 aksesi dan kelompok II sebanyak 66 aksesi. Sebanyak 90 aksesi mangga asli Indonesia (84,11% dari total mangga Indonesia yang digunakan) bisa dipisahkan dari mangga introduksi.
    @article{Tasliah13p125,
    title = {{Analisis Keragaman Genetik 161 Aksesi Mangga Indonesia Menggunakan Marka Mikrosatelit}},
    author = {Tasliah and H. Rijzaani and T. Z. P. Hariyadi and S. Yuriyah and Rebin and Ma'sumah and T. S. Silitonga},
    journal = {Jurnal AgroBiogen},
    pages = {125 - 134},
    volume = {9},
    number = {3},
    year = {2013},
    abstract = { Mangga merupakan salah satu dari lima tanaman buah penting di dunia. Marka mikrosatelit bisa digunakan sebagai penanda molekuler untuk melihat keragaman genetik antar aksesi mangga. Tujuan dari penelitian ini adalah untuk mengetahui hubungan kekerabatan plasma nutfah mangga di Indonesia menggunakan marka mikrosatelit. Sebanyak 161 aksesi mangga yang berasal dari Balai Penelitian Tanaman Buah Tropika (KP Cukurgondang), Pasuruan, Jawa Timur, digunakan dalam penelitian ini. Dua puluh enam marka mikrosatelit digunakan untuk melihat pola fragmen DNA masing-masing aksesi. Pemisahan fragmen DNA hasil amplifikasi dilakukan menggunakan mesin Beckman Coulter® CEQ™ 8000. Hubungan kekerabatan dibuat menggunakan metode Unweighted Pair Group Method with Arithmetic Mean (UPGMA), dilanjutkan dengan analisis bootstrap. Hasil penelitian menunjukkan terjadi variasi alel yang cukup tinggi (15-75 alel) di antara aksesi mangga dengan rata-rata jumlah alel sekitar 38,69, sedangkan rata-rata nilai Polymophism Information Content (PIC) sebesar 0,548 (0,021-0,949). Lima belas marka mikrosatelit memiliki nilai PIC >0,5 yang menunjukkan marka tersebut memiliki informasi yang tinggi untuk penelitian keragaman genetik mangga. Analisis gerombol membagi koleksi mangga ke dalam dua kelompok. Kelompok I terdiri atas 95 aksesi dan kelompok II sebanyak 66 aksesi. Sebanyak 90 aksesi mangga asli Indonesia (84,11% dari total mangga Indonesia yang digunakan) bisa dipisahkan dari mangga introduksi.},
    keywords = {mangga, genetik, marka mikrosatelit, keragaman},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_9_3_2013_125-134.pdf}
    }
  13. Asadi. 2013. Pemuliaan Mutasi untuk Perbaikan terhadap Umur dan Produktivitas pada Kedelai. Jurnal agrobiogen 9 (3):135-142.
    [BibTeX] [Abstract] [PDF: Pemuliaan Mutasi untuk Perbaikan terhadap Umur dan Produktivitas pada Kedelai ]
    Untuk mendukung program pemerintah di dalam peningkatan produksi kedelai, sangat diperlukan penggunaan varietas unggul berumur genjah (<80 hari), toleran kekeringan dan berdaya hasil tinggi untuk dikembangkan pada pola tanam padi-padikedelai dan padi-padi-padi-kedelai, dan ke lahan kering pada pola tanam padi-kedelai atau padi-palawija lain. Pemuliaan mutasi merupakan salah satu metode untuk perbaikan terhadap umur dan produktivitas, metode ini baik oleh peneliti luar maupun dalam negeri telah dimanfaatkan untuk perbaikan terhadap umur dan produktivitas pada kedelai. Dalam prosedur pemuliaannya, seleksi menggunakan metode bulk pada populasi M1, dan dilanjutkan dengan metode pedigree pada generasi M2-M4. Evaluasi terhadap keseragaman (homozigot) galur dilakukan pada generasi M4. Pada generasi M5-M8 dilakukan uji daya hasil dan adaptasi. Hasil pemuliaan mutasi di luar negeri telah berhasil merakit varietas-varietas unggul kedelai yang berumur genjah. Di Indonesia, yaitu di Badan Tenaga Nuklir Nasional (Batan), kegiatan pemuliaan tanaman dengan teknik mutasi telah dimulai sejak tahun 1972, sementara di BB Biogen baru dimulai sejak tahun 2009. Hingga saat ini Batan telah menghasilkan 2 varietas unggul kedelai berumur genjah, yaitu Tengger (1991) dan Meratus (1998). Di Balai Besar Penelitian Bioteknologi dan Sumber Daya Genetik Pertanian (BB Biogen), melalui teknik mutasi kalus pada tahun 2011 telah dihasilkan 50 galur pilihan yang berumur genjah dan berdaya hasil tinggi, sedangkan melalui iradiasi benih pada tahun 2012 telah dihasilkan 15 galur harapan kedelai berumur genjah dan berdaya hasil lebih tinggi.
    @article{Asadi91p135,
    title = {{Pemuliaan Mutasi untuk Perbaikan terhadap Umur dan Produktivitas pada Kedelai}},
    author = {Asadi},
    journal = {Jurnal AgroBiogen},
    pages = {135 - 142},
    volume = {9},
    number = {3},
    year = {2013},
    abstract = {Untuk mendukung program pemerintah di dalam peningkatan produksi kedelai, sangat diperlukan penggunaan varietas unggul berumur genjah (<80 hari), toleran kekeringan dan berdaya hasil tinggi untuk dikembangkan pada pola tanam padi-padikedelai dan padi-padi-padi-kedelai, dan ke lahan kering pada pola tanam padi-kedelai atau padi-palawija lain. Pemuliaan mutasi merupakan salah satu metode untuk perbaikan terhadap umur dan produktivitas, metode ini baik oleh peneliti luar maupun dalam negeri telah dimanfaatkan untuk perbaikan terhadap umur dan produktivitas pada kedelai. Dalam prosedur pemuliaannya, seleksi menggunakan metode bulk pada populasi M1, dan dilanjutkan dengan metode pedigree pada generasi M2-M4. Evaluasi terhadap keseragaman (homozigot) galur dilakukan pada generasi M4. Pada generasi M5-M8 dilakukan uji daya hasil dan adaptasi. Hasil pemuliaan mutasi di luar negeri telah berhasil merakit varietas-varietas unggul kedelai yang berumur genjah. Di Indonesia, yaitu di Badan Tenaga Nuklir Nasional (Batan), kegiatan pemuliaan tanaman dengan teknik mutasi telah dimulai sejak tahun 1972, sementara di BB Biogen baru dimulai sejak tahun 2009. Hingga saat ini Batan telah menghasilkan 2 varietas unggul kedelai berumur genjah, yaitu Tengger (1991) dan Meratus (1998). Di Balai Besar Penelitian Bioteknologi dan Sumber Daya Genetik Pertanian (BB Biogen), melalui teknik mutasi kalus pada tahun 2011 telah dihasilkan 50 galur pilihan yang berumur genjah dan berdaya hasil tinggi, sedangkan melalui iradiasi benih pada tahun 2012 telah dihasilkan 15 galur harapan kedelai berumur genjah dan berdaya hasil lebih tinggi.},
    keywords = {kedelai, pemuliaan produktivitas tinggi, mutasi, umur genjah},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_9_3_2013_135-142.pdf}
    }
  14. Santosa, B., K. R. Trijatmiko, and T. J. Santoso. 2013. Deteksi Gen HptII dan Keragaan Agronomis pada Populasi BC1F1 Tanaman Padi Transgenik. Jurnal agrobiogen 9 (3):117-124.
    [BibTeX] [Abstract] [PDF: Deteksi Gen HptII dan Keragaan Agronomis pada Populasi BC1F1 Tanaman Padi Transgenik ]
    Varietas unggul padi toleran terhadap cekaman kekeringan dibutuhkan untuk mengurangi kehilangan hasil akibat cekaman tersebut. Padi Nipponbare transgenik yang mengandung gen hptII telah dihasilkan oleh BB Biogen. Padi transgenik tersebut diduga juga membawa gen OsDREB1A, karena gen hptII berada dalam satu konstruk dengan gen OsDREB1A. Padi kultivar Niponbare bukan merupakan padi yang dibudidayakan di Indonesia, sehingga gen OsDREB1A yang ada pada padi Nipponbare tersebut perlu dipindahkan ke dalam varietas budi daya untuk memperoleh varietas unggul baru yang toleran terhadap kekeringan. Tujuan dari penelitian ini adalah untuk mengetahui keberadaan gen hptII pada tanaman F1 dan BC1F1 transgenik dan keragaan agronomisnya. Populasi F1 dibentuk dengan menyilangkan Nipponbare transgenik, sebagai tetua donor, dengan genotipe padi Batutegi, Code, Ciherang, dan Konawe, sebagai tetua penerima. Populasi BC1F1 dibentuk dengan silang balik antara tanaman padi F1 transgenik dengan tetua penerimanya. Keberadaan gen hptII dianalisis dengan PCR menggunakan sepasang primer hptII. Pengamatan terhadap beberapa karakter agronomis dan fisiologis tanaman dilakukan di rumah kaca. Hasil penelitian menunjukkan bahwa padi BC1F1 Batutegi trans, BC1F1 Code trans, BC1F1 Konawe trans1, BC1F1 Konawe trans3, dan BC1F1 Konawe trans4 mengandung gen hptII setelah dianalisis dengan PCR. Berdasarkan pengamatan agronomis diketahui bahwa kelima tanaman padi BC1F1 transgenik menghasilkan jumlah malai, jumlah gabah isi maupun jumlah gabah total yang lebih banyak daripada tetua penerima. Jika dibandingkan dengan padi tetua penerima, padi BC1F1 Konawe trans1 dan BC1F1 Konawe trans3 memiliki jumlah stomata lebih sedikit pada permukaan daun bagian bawah dan jumlah stomata lebih banyak pada permukaan daun bagian atas.
    @article{Santosa13p117,
    title = {{Deteksi Gen HptII dan Keragaan Agronomis pada Populasi BC1F1 Tanaman Padi Transgenik}},
    author = {B. Santosa and K. R. Trijatmiko and T. J. Santoso},
    journal = {Jurnal AgroBiogen},
    pages = {117 - 124},
    volume = {9},
    number = {3},
    year = {2013},
    abstract = {Varietas unggul padi toleran terhadap cekaman kekeringan dibutuhkan untuk mengurangi kehilangan hasil akibat cekaman tersebut. Padi Nipponbare transgenik yang mengandung gen hptII telah dihasilkan oleh BB Biogen. Padi transgenik tersebut diduga juga membawa gen OsDREB1A, karena gen hptII berada dalam satu konstruk dengan gen OsDREB1A. Padi kultivar Niponbare bukan merupakan padi yang dibudidayakan di Indonesia, sehingga gen OsDREB1A yang ada pada padi Nipponbare tersebut perlu dipindahkan ke dalam varietas budi daya untuk memperoleh varietas unggul baru yang toleran terhadap kekeringan. Tujuan dari penelitian ini adalah untuk mengetahui keberadaan gen hptII pada tanaman F1 dan BC1F1 transgenik dan keragaan agronomisnya. Populasi F1 dibentuk dengan menyilangkan Nipponbare transgenik, sebagai tetua donor, dengan genotipe padi Batutegi, Code, Ciherang, dan Konawe, sebagai tetua penerima. Populasi BC1F1 dibentuk dengan silang balik antara tanaman padi F1 transgenik dengan tetua penerimanya. Keberadaan gen hptII dianalisis dengan PCR menggunakan sepasang primer hptII. Pengamatan terhadap beberapa karakter agronomis dan fisiologis tanaman dilakukan di rumah kaca. Hasil penelitian menunjukkan bahwa padi BC1F1 Batutegi trans, BC1F1 Code trans, BC1F1 Konawe trans1, BC1F1 Konawe trans3, dan BC1F1 Konawe trans4 mengandung gen hptII setelah dianalisis dengan PCR. Berdasarkan pengamatan agronomis diketahui bahwa kelima tanaman padi BC1F1 transgenik menghasilkan jumlah malai, jumlah gabah isi maupun jumlah gabah total yang lebih banyak daripada tetua penerima. Jika dibandingkan dengan padi tetua penerima, padi BC1F1 Konawe trans1 dan BC1F1 Konawe trans3 memiliki jumlah stomata lebih sedikit pada permukaan daun bagian bawah dan jumlah stomata lebih banyak pada permukaan daun bagian atas.},
    keywords = {gen hptii, padi transgenik, silang balik, keragaan agronomis},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_9_3_2013_117-124.pdf}
    }
  15. Sisharmini, A., A. Apriana, D. Nurmaliki, T. J. Santoso, and K. R. Trijatmiko. 2013. Identifikasi Perubahan Karakter Agronomis Padi Transgenik Penanda Aktivasi cv. Asemandi Generasi T1. Jurnal agrobiogen 9 (3):107-116.
    [BibTeX] [Abstract] [PDF: Identifikasi Perubahan Karakter Agronomis Padi Transgenik Penanda Aktivasi cv. Asemandi Generasi T1 ]
    Populasi T1 padi transgenik penanda aktivasi cv. Asemandi telah dibentuk dengan cara mengintroduksikan konstruk penanda aktivasi transposon Ac/Ds ke genom padi cv. Asemandi. Populasi tersebut telah mengandung konstruk penanda aktivasi, tetapi belum diketahui perubahan karakter fenotipenya. Penelitian ini bertujuan untuk mengidentifikasi galur yang tahan herbisida Basta, mengandung gen hpt dan bar, dan mengidentifikasi perubahan karakter agronomis populasi padi transgenik cv. Asemandi generasi T1. Tanaman tahan Basta diidentifikasi dengan perlakuan larutan Basta pada daun. Gen hpt and bar dideteksi dengan analisis PCR menggunakan primer spesifik. Karakter fenotipe tanaman diidentifikasi dengan mengamati dan mengukur beberapa parameter agronomisnya. Hasil penelitian menunjukkan bahwa dari 315 tanaman cv. Asemandi mutan transgenik generasi T1 yang diuji, 176 (55,87%) tanaman mempunyai ketahanan terhadap herbisida Basta. Secara umum, tanaman transgenik penanda aktivasi cv. Asemandi generasi T1 mengalami perubahan karakter agronomis jika dibandingkan dengan tanaman nontransgenik. Perubahan itu terjadi pada tinggi tanaman, umur berbunga, umur panen, waktu pengisian malai, dan bobot 100 butir. Pada tanaman transgenik tidak ada korelasi antara umur panen dengan bobot 100 butir, sedangkan pada tanaman nontransgenik ada korelasi antara umur panen dengan bobot 100 butir. Hasil analisis PCR menunjukkan bahwa delapan tanaman padi transgenik penanda aktivasi cv. Asemandi yang diuji mengandung gen hpt dan bar. Tanaman padi transgenik penanda aktivasi cv. Asemandi generasi T1 yang mempunyai karakter agronomis yang berbeda dengan tanaman nontransgenik akan bermanfaat untuk penelitian lebih lanjut, misalnya penelitian fungsi gen-gen.
    @article{Sisharmini13p107,
    title = {{Identifikasi Perubahan Karakter Agronomis Padi Transgenik Penanda Aktivasi cv. Asemandi Generasi T1}},
    author = {A. Sisharmini and A. Apriana and D. Nurmaliki and T. J. Santoso and K. R. Trijatmiko},
    journal = {Jurnal AgroBiogen},
    pages = {107 - 116},
    volume = {9},
    number = {3},
    year = {2013},
    abstract = {Populasi T1 padi transgenik penanda aktivasi cv. Asemandi telah dibentuk dengan cara mengintroduksikan konstruk penanda aktivasi transposon Ac/Ds ke genom padi cv. Asemandi. Populasi tersebut telah mengandung konstruk penanda aktivasi, tetapi belum diketahui perubahan karakter fenotipenya. Penelitian ini bertujuan untuk mengidentifikasi galur yang tahan herbisida Basta, mengandung gen hpt dan bar, dan mengidentifikasi perubahan karakter agronomis populasi padi transgenik cv. Asemandi generasi T1. Tanaman tahan Basta diidentifikasi dengan perlakuan larutan Basta pada daun. Gen hpt and bar dideteksi dengan analisis PCR menggunakan primer spesifik. Karakter fenotipe tanaman diidentifikasi dengan mengamati dan mengukur beberapa parameter agronomisnya. Hasil penelitian menunjukkan bahwa dari 315 tanaman cv. Asemandi mutan transgenik generasi T1 yang diuji, 176 (55,87%) tanaman mempunyai ketahanan terhadap herbisida Basta. Secara umum, tanaman transgenik penanda aktivasi cv. Asemandi generasi T1 mengalami perubahan karakter agronomis jika dibandingkan dengan tanaman nontransgenik. Perubahan itu terjadi pada tinggi tanaman, umur berbunga, umur panen, waktu pengisian malai, dan bobot 100 butir. Pada tanaman transgenik tidak ada korelasi antara umur panen dengan bobot 100 butir, sedangkan pada tanaman nontransgenik ada korelasi antara umur panen dengan bobot 100 butir. Hasil analisis PCR menunjukkan bahwa delapan tanaman padi transgenik penanda aktivasi cv. Asemandi yang diuji mengandung gen hpt dan bar. Tanaman padi transgenik penanda aktivasi cv. Asemandi generasi T1 yang mempunyai karakter agronomis yang berbeda dengan tanaman nontransgenik akan bermanfaat untuk penelitian lebih lanjut, misalnya penelitian fungsi gen-gen.},
    keywords = {padi, transgenik, penanda aktivasi, identifikasi gen},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_9_3_2013_107-116.pdf}
    }

2012

  1. Enggarini, Wening, Surjono H. Sutjahjo, Trikoesoemaningtyas, Sriani Sujiprihati, Utut Widyastuti, Kurniawan R. Trijatmiko, Sugiono Moeljopawiro, Masdiar Bustamam, and Casiana V. Cruz. 2012. Characterization of Donor Genome Segments of BC2 and BC4 Way Rarem x Oryzica Llanos-5 Progenies Detected by SNP Markers. Jurnal agrobiogen 8 (1):1-7.
    [BibTeX] [Abstract] [PDF: Characterization of Donor Genome Segments of BC2 and BC4 Way Rarem x Oryzica Llanos-5 Progenies Detected by SNP Markers ]
    Characterization of Donor Genome Segments of BC2 and BC4 Way Rarem x Oryzica Llanos-5 Progenies Detected by SNP Markers. Wening Enggarini, Surjono H. Sutjahjo, Trikoesoemaningtyas, Sriani Sujiprihati, Utut Widyastuti, Kurniawan R. Trijatmiko, Sugiono Moeljopawiro, Masdiar Bustamam, and Casiana V. Cruz. Plant breeders make a succession of backcrosses to introgress a character from a donor parent into genomic background of a recurrent parent. In several backcrossing, the proportion of a genome tends to return almost fully to recurrent parent, except the small donor genome segment harboring the character of interest. The estimation of the proportion donor segment through backcross generations has been analyzed theoretically using complex mathematical simulations. In this study, the proportion of donor introgression segments were directly analyzed in advanced backcross populations, BC2F7 and BC4F2. The analysis was done by using a set of single nucleotide polymorphism (SNP) markers covering the entire rice genome. Of the 384 SNP markers we found 124 markers which provide polymorphism between recurrent parent, Way Rarem and Oryzica Llanos-5 as donor parent. But only 55 SNP markers could detect Oryzica Llanos-5 alleles in BC2F7 and BC4F2 progenies. The result of this analysis demonstrated that the average of donor segment number was 14.5 in BC2F7 and 12.3 in BC4F2. It was reduced 15% from BC2F7 to BC4F2. The average of donor segment length was 31.2 cM (centiMorgan) in BC2F7 and 8.79 cM in BC4F2. It was decreased 72% during twice backcrossing. The average of donor genome size was 343.95 cM in BC2F7 and 71.35 cM in BC4F2, which means there was 79% decrease from BC2F7 to BC4F2. These results offered a simple method to describe the proportion of target genome segment from donor parent. It was required as one of the main selection criteria in backcross programs.
    @article{WeningEnggarini12p1,
    title = {{Characterization of Donor Genome Segments of BC2 and BC4 Way Rarem x Oryzica Llanos-5 Progenies Detected by SNP Markers}},
    author = {Wening Enggarini and Surjono H. Sutjahjo and Trikoesoemaningtyas and Sriani Sujiprihati and Utut Widyastuti and Kurniawan R. Trijatmiko and Sugiono Moeljopawiro and Masdiar Bustamam and Casiana V. Cruz},
    journal = {Jurnal AgroBiogen},
    pages = {1 - 7},
    volume = {8},
    number = {1},
    year = {2012},
    abstract = {Characterization of Donor Genome Segments of BC2 and BC4 Way Rarem x Oryzica Llanos-5 Progenies Detected by SNP Markers. Wening Enggarini, Surjono H. Sutjahjo, Trikoesoemaningtyas, Sriani Sujiprihati, Utut Widyastuti, Kurniawan R. Trijatmiko, Sugiono Moeljopawiro, Masdiar Bustamam, and Casiana V. Cruz. Plant breeders make a succession of backcrosses to introgress a character from a donor parent into genomic background of a recurrent parent. In several backcrossing, the proportion of a genome tends to return almost fully to recurrent parent, except the small donor genome segment harboring the character of interest. The estimation of the proportion donor segment through backcross generations has been analyzed theoretically using complex mathematical simulations. In this study, the proportion of donor introgression segments were directly analyzed in advanced backcross populations, BC2F7 and BC4F2. The analysis was done by using a set of single nucleotide polymorphism (SNP) markers covering the entire rice genome. Of the 384 SNP markers we found 124 markers which provide polymorphism between recurrent parent, Way Rarem and Oryzica Llanos-5 as donor parent. But only 55 SNP markers could detect Oryzica Llanos-5 alleles in BC2F7 and BC4F2 progenies. The result of this analysis demonstrated that the average of donor segment number was 14.5 in BC2F7 and 12.3 in BC4F2. It was reduced 15% from BC2F7 to BC4F2. The average of donor segment length was 31.2 cM (centiMorgan) in BC2F7 and 8.79 cM in BC4F2. It was decreased 72% during twice backcrossing. The average of donor genome size was 343.95 cM in BC2F7 and 71.35 cM in BC4F2, which means there was 79% decrease from BC2F7 to BC4F2. These results offered a simple method to describe the proportion of target genome segment from donor parent. It was required as one of the main selection criteria in backcross programs.},
    keywords = {Marker-assisted backcrossing, introgression, graphical genotype, donor},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen 8 (1) 1-7,2012.pdf}
    }
  2. Roostika, Ika, Ika Mariska, Nurul Khumaida, and Gustaaf A. Wattimena. 2012. Indirect Organogenesis and Somatic Embryogenesis of Pineapple Induced by Dichlorophenoxy Acetic Acid. Jurnal agrobiogen 8 (1):8-18.
    [BibTeX] [Abstract] [PDF: Indirect Organogenesis and Somatic Embryogenesis of Pineapple Induced by Dichlorophenoxy Acetic Acid ]
    Indirect Organogenesis and Somatic Embryogenesis of Pineapple Induced by Dichlorophenoxy Acetic Acid. Ika Roostika, Ika Mariska, Nurul Khumaida, and Gustaaf A. Wattimena. This research aimed to study the effect of 2,4-D, AdS, and basal media to the regeneration of pineapple through indirect organogenesis and somatic embryogenesis, and to study the complete event of somatic embryogenesis. Callus formation was induced by 21, 41, and 62 µM 2,4-D with addition of 9 µM TDZ. The non embryogenic calli were transferred onto 4.65 µM Kn containing medium. Embryogenic callus formation was induced on MS or Bac basal media consisted of N-organic compounds with addition of AdS (0, 0.05 and 0.1 µM). The embryogenic calli were regenerated on modified MS medium with addition of 0.9 µM IBA, 1.1 µM BA, 0.09 µM GA3 or MS medium supplemented with 0.018 mM BA. The result proved that the single auxin of 2,4-D was not enough to induce embryogenic cells. Therefore the non embryogenic calli were regenerated through organogenesis. The 21 µM 2,4-D yielded high level of callus formation (80%), higher fresh weight (0.2 g/explant) and higher number of shoot (25 shoots/explant in two months). Embryogenic calli were produced on N-organic compounds enriched media. The regeneration medium significantly affected the level of browning, where the MS medium with addition of 0.018 mM BA yielded lower level of browning. There was an interaction of embryogenic callus induction medium and regeneration medium to the number of mature somatic embryos. The embryogenic callus induction on MS medium enriched with N-organic compounds and 0.05 µM AdS followed by the regeneration of somatic embryos on MS medium with addition of 0.018 mM BA was the best treatment which yielded 17 mature somatic embryos/explant.
    @article{IkaRoostika12p8,
    title = {{Indirect Organogenesis and Somatic Embryogenesis of Pineapple Induced by Dichlorophenoxy Acetic Acid}},
    author = {Ika Roostika and Ika Mariska and Nurul Khumaida and Gustaaf A. Wattimena},
    journal = {Jurnal AgroBiogen},
    pages = {8 - 18},
    volume = {8},
    number = {1},
    year = {2012},
    abstract = {Indirect Organogenesis and Somatic Embryogenesis of Pineapple Induced by Dichlorophenoxy Acetic Acid. Ika Roostika, Ika Mariska, Nurul Khumaida, and Gustaaf A. Wattimena. This research aimed to study the effect of 2,4-D, AdS, and basal media to the regeneration of pineapple through indirect organogenesis and somatic embryogenesis, and to study the complete event of somatic embryogenesis. Callus formation was induced by 21, 41, and 62 µM 2,4-D with addition of 9 µM TDZ. The non embryogenic calli were transferred onto 4.65 µM Kn containing medium. Embryogenic callus formation was induced on MS or Bac basal media consisted of N-organic compounds with addition of AdS (0, 0.05 and 0.1 µM). The embryogenic calli were regenerated on modified MS medium with addition of 0.9 µM IBA, 1.1 µM BA, 0.09 µM GA3 or MS medium supplemented with 0.018 mM BA. The result proved that the single auxin of 2,4-D was not enough to induce embryogenic cells. Therefore the non embryogenic calli were regenerated through organogenesis. The 21 µM 2,4-D yielded high level of callus formation (80%), higher fresh weight (0.2 g/explant) and higher number of shoot (25 shoots/explant in two months). Embryogenic calli were produced on N-organic compounds enriched media. The regeneration medium significantly affected the level of browning, where the MS medium with addition of 0.018 mM BA yielded lower level of browning. There was an interaction of embryogenic callus induction medium and regeneration medium to the number of mature somatic embryos. The embryogenic callus induction on MS medium enriched with N-organic compounds and 0.05 µM AdS followed by the regeneration of somatic embryos on MS medium with addition of 0.018 mM BA was the best treatment which yielded 17 mature somatic embryos/explant.},
    keywords = {Organogenesis, somatic embryogenesis, pineapple, 2, 4-d, adenine sulphate},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen 8 (1) 8-18,2012.pdf}
    }
  3. Manzila, Ifa, Sri H. Hidayat, Ika Mariska, and Sriani Sujiprihati. 2012. Analisis Gen Selubung Protein Chilli Veinal Mottle Potyvirus dari Beberapa Daerah di Indonesia. Jurnal agrobiogen 8 (61):27-37.
    [BibTeX] [Abstract] [PDF: Analisis Gen Selubung Protein Chilli Veinal Mottle Potyvirus dari Beberapa Daerah di Indonesia ]
    Analysis of Coat Protein Gene of Chilli Veinal Mottle Potyvirus Collected from Several Means in Indonesia. Ifa Manzila, Sri H. Hidayat, Ika Mariska, and Sriani Sujiprihati. Variation on symptoms and virulence was observed on different isolates of ChiVMV collected from West Java, Central Java, East Java, South Kalimantan, West Sumatera and Central Aceh. Research was conducted to study genetic variation of six ChiVMV isolates based on sequence analysis of coat protein (CP) gene and amino acid. Sequence analysis of CP gene showed 87% to 99% homology among the six isolates with level of variation ranging from 0.02% to 1.48%. Sequence analysis of amino acid derived from CP gene showed 85% to 99% homology. Further analysis on amino acid motives of CP gene indicated mutation of octapeptide motif, i.e LSGQVQPQSRQSEMETEVPQVR on ChiVMV CKB and RMETFGLDGRVGTQEEDTERHT on other ChiVMV isolates. Other differences was observed on amino acid number 61 and 84 i.e. deletion of MET and mutation of GG to KV on ChiVMV BL and KR. Phyllogenetic analysis based on nucleotide and amino acid sequence showed that six isolates of ChiVMV can be differentiated into three groups. ChiVMV KR and BL were in the same group with ChiVMV Pataruman (GeneBank No. access DQ854961), ChiVMV CKB was in the same group with ChiVMV Cikabayan 2 (GeneBank No. access DQ854960), and ChiVMV TD, ChiVMV NI and GB ChiVMV were in the same group with ChiVMV Taiwan (GeneBank No. access DQ854948). Analysis of CP gene confirmed the occurrence of genetic variation among ChiVMV isolates although symptom variation is weak.
    @article{IfaManzila12p27,
    title = {{Analisis Gen Selubung Protein Chilli Veinal Mottle Potyvirus dari Beberapa Daerah di Indonesia}},
    author = {Ifa Manzila and Sri H. Hidayat and Ika Mariska and Sriani Sujiprihati},
    journal = {Jurnal AgroBiogen},
    pages = {27 - 37},
    volume = {8},
    number = {61},
    year = {2012},
    abstract = {Analysis of Coat Protein Gene of Chilli Veinal Mottle Potyvirus Collected from Several Means in Indonesia. Ifa Manzila, Sri H. Hidayat, Ika Mariska, and Sriani Sujiprihati. Variation on symptoms and virulence was observed on different isolates of ChiVMV collected from West Java, Central Java, East Java, South Kalimantan, West Sumatera and Central Aceh. Research was conducted to study genetic variation of six ChiVMV isolates based on sequence analysis of coat protein (CP) gene and amino acid. Sequence analysis of CP gene showed 87% to 99% homology among the six isolates with level of variation ranging from 0.02% to 1.48%. Sequence analysis of amino acid derived from CP gene showed 85% to 99% homology. Further analysis on amino acid motives of CP gene indicated mutation of octapeptide motif, i.e LSGQVQPQSRQSEMETEVPQVR on ChiVMV CKB and RMETFGLDGRVGTQEEDTERHT on other ChiVMV isolates. Other differences was observed on amino acid number 61 and 84 i.e. deletion of MET and mutation of GG to KV on ChiVMV BL and KR. Phyllogenetic analysis based on nucleotide and amino acid sequence showed that six isolates of ChiVMV can be differentiated into three groups. ChiVMV KR and BL were in the same group with ChiVMV Pataruman (GeneBank No. access DQ854961), ChiVMV CKB was in the same group with ChiVMV Cikabayan 2 (GeneBank No. access DQ854960), and ChiVMV TD, ChiVMV NI and GB ChiVMV were in the same group with ChiVMV Taiwan (GeneBank No. access DQ854948). Analysis of CP gene confirmed the occurrence of genetic variation among ChiVMV isolates although symptom variation is weak.},
    keywords = {Chilli veinal motlle potyvirus, coat protein gene, phyllogenetic analysis},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen 8 (1) 27-37,2012.pdf}
    }
  4. Lestari, Endang G.. 2012. Combination of Somaclonal Variation and Mutagenesis for Crop Improvement. Jurnal agrobiogen 8 (1):38-44.
    [BibTeX] [Abstract] [PDF: Combination of Somaclonal Variation and Mutagenesis for Crop Improvement ]
    Combination of Somaclonal Variation and Mutagenesis for Crop Improvement. Endang G. Lestari. Mutation-based plant improvement, which changes one or a few specific traits of a cultivar, can contribute to crop improvement. Tissue culture increases the efficiency of mutagenic treatment to induce variations. In vitro culture in combination with induced mutation can speed up the breeding program by generating variability, followed by selection and multiplication of the desired genotypes. In many vegetative propagated crops, mutation induction in combination with in vitro culture techniques can be the most effective method for plant improvement. In seed propagated species, the application of mutation coupled with doubled haploid systems seems to be highly promising in crop improvement. This approach speeds up the breeding program through generation of variability followed by selection of homozygousity and rapid multiplication of desired genotypes.
    @article{Lestari12p38,
    title = {{Combination of Somaclonal Variation and Mutagenesis for Crop Improvement}},
    author = {Endang G. Lestari},
    journal = {Jurnal AgroBiogen},
    pages = {38 - 44},
    volume = {8},
    number = {1},
    year = {2012},
    abstract = {Combination of Somaclonal Variation and Mutagenesis for Crop Improvement. Endang G. Lestari. Mutation-based plant improvement, which changes one or a few specific traits of a cultivar, can contribute to crop improvement. Tissue culture increases the efficiency of mutagenic treatment to induce variations. In vitro culture in combination with induced mutation can speed up the breeding program by generating variability, followed by selection and multiplication of the desired genotypes. In many vegetative propagated crops, mutation induction in combination with in vitro culture techniques can be the most effective method for plant improvement. In seed propagated species, the application of mutation coupled with doubled haploid systems seems to be highly promising in crop improvement. This approach speeds up the breeding program through generation of variability followed by selection of homozygousity and rapid multiplication of desired genotypes.},
    keywords = {Mutation, variation, plant improvement, somaclonal},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen 8 (1) 38-44,2012.pdf}
    }
  5. Chaerani, Ace M. Suhendar, and J. Harjosudarmo. 2012. Perbanyakan Nematoda Patogenik Serangga (Rhabditida: Steinernema dan Heterorhabditis) pada Media In Vitro Cair Statik. Jurnal agrobiogen 8 (1):19-26.
    [BibTeX] [Abstract] [PDF: Perbanyakan Nematoda Patogenik Serangga (Rhabditida: Steinernema dan Heterorhabditis) pada Media In Vitro Cair Statik ]
    Perbanyakan Nematoda Patogenik Serangga (Rhabditida: Steinernema dan Heterorhabditis) pada Media Cair In Vitro Statik. Chaerani, M. Ace Suhendar, dan J. Harjosudarmo. Nematoda patogenik serangga (NPS) dari genus Steinernema dan Heterorhabditis berpotensi menjadi pengendali hayati yang efektif dan aman untuk serangga-serangga hama, terutama yang hidup di dalam tanah dan di habitat tersembunyi. Aplikasi NPS di lapang masih terkendala oleh penyediaan nematoda juvenil infektif (JI) dalam jumlah besar. Lima media in vitro baku dan dua modifikasinya diuji untuk perbanyakan massal dua NPS lokal (H. indicus PLR2 dan Steinernema T96) dan satu strain komersial (S. carpocapsae #25). Hasil JI yang diperoleh bervariasi antar ulangan dan percobaan. Media F yang dimodifikasi dari berbagai formula media dan mengandung 1,0% ekstrak khamir (yeast extract), 2,5% kuning telur, dan 4,0% minyak kedelai, menghasilkan jumlah JI H. indicus PLR2 dan S. carpocapsae #25 tertinggi, berturut-turut 1,5×105 dan 2,9×105 JI ml-1 media, sedangkan media baku B, yang hanya mengandung 40% usus ayam, menghasilkan JI Steinernema T96 tertinggi (5,8×104 JI ml-1 media). Secara umum, kualitas JI yang diukur berdasarkan morfometrik dan patogenisitasnya kurang baik, karena mendapat pengaruh negatif dari perlakuan media in vitro. Hal ini menunjukkan media yang digunakan kekurangan nutrien esensial. Optimalisasi media buatan perlu dilakukan untuk meningkatkan kuantitas dan kualitas JI NPS yang diproduksi guna mencapai standar yang dibutuhkan untuk perbanyakan skala komersial.
    @article{Chaerani12p19,
    title = {{Perbanyakan Nematoda Patogenik Serangga (Rhabditida: Steinernema dan Heterorhabditis) pada Media In Vitro Cair Statik}},
    author = {Chaerani and M. Ace Suhendar and J. Harjosudarmo},
    journal = {Jurnal AgroBiogen},
    chapter = {},
    pages = {19 - 26},
    volume = {8},
    number = {1},
    year = {2012},
    abstract = {Perbanyakan Nematoda Patogenik Serangga (Rhabditida: Steinernema dan Heterorhabditis) pada Media Cair In Vitro Statik. Chaerani, M. Ace Suhendar, dan J. Harjosudarmo. Nematoda patogenik serangga (NPS) dari genus Steinernema dan Heterorhabditis berpotensi menjadi pengendali hayati yang efektif dan aman untuk serangga-serangga hama, terutama yang hidup di dalam tanah dan di habitat tersembunyi. Aplikasi NPS di lapang masih terkendala oleh penyediaan nematoda juvenil infektif (JI) dalam jumlah besar. Lima media in vitro baku dan dua modifikasinya diuji untuk perbanyakan massal dua NPS lokal (H. indicus PLR2 dan Steinernema T96) dan satu strain komersial (S. carpocapsae #25). Hasil JI yang diperoleh bervariasi antar ulangan dan percobaan. Media F yang dimodifikasi dari berbagai formula media dan mengandung 1,0% ekstrak khamir (yeast extract), 2,5% kuning telur, dan 4,0% minyak kedelai, menghasilkan jumlah JI H. indicus PLR2 dan S. carpocapsae #25 tertinggi, berturut-turut 1,5×105 dan 2,9×105 JI ml-1 media, sedangkan media baku B, yang hanya mengandung 40% usus ayam, menghasilkan JI Steinernema T96 tertinggi (5,8×104 JI ml-1 media). Secara umum, kualitas JI yang diukur berdasarkan morfometrik dan patogenisitasnya kurang baik, karena mendapat pengaruh negatif dari perlakuan media in vitro. Hal ini menunjukkan media yang digunakan kekurangan nutrien esensial. Optimalisasi media buatan perlu dilakukan untuk meningkatkan kuantitas dan kualitas JI NPS yang diproduksi guna mencapai standar yang dibutuhkan untuk perbanyakan skala komersial.},
    keywords = {Nematoda patogenik serangga, perbanyakan massal, media cair},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen 8 (1) 19-26,2012.pdf}
    }
  6. Santoso, T. J., M. Herman, S. H. Hidayat, H. Aswidinnoor, and Sudarsono. 2012. Molecular Analysis and Effectiveness Assay of AV1 Gene in Transgenic Tobacco for Resistance to Begomovirus. Jurnal agrobiogen 8 (2):45-53.
    [BibTeX] [Abstract] [PDF: Molecular Analysis and Effectiveness Assay of AV1 Gene in Transgenic Tobacco for Resistance to Begomovirus ]
    Genetic transformation of tobacco plant using AV1 gene was conducted at the previously experiment and generated transgenic tobacco plants positively carrying the selectable marker nptII gene. The objectives of this experiment were to (1) analyze the presence of Begomovirus AV1 gene in T0 generation putative transgenic tobacco plants using PCR technique with specific primers and its correlation with resistance phenotype, (2) analyze the integration and copy number of the transgene in T0 generation putative transgenic tobacco plants and its correlation with resistance response, (3) screen the T0 generation putative transgenic tobacco plants with the target virus infection and to detect the presence of the virus in the transgenic plant tissue using universal primers. PCR detection of AV1 gene in tobacco transgenic was conducted by using specific primer for Begomovirus AV1 gene. Meanwhile, Southern Blot analysis was conducted by using the AV1 gene probe. The effectiveness of AV1 gene in tobacco transgenic was tested by inoculation of target virus using whiteflies vector. Result of the experiments showed that there was a positive correlation between the presence of the AV1 transgene in T0 generation putative transgenic tobacco plants and the resistant phenotype. Transgenic plants with a single copy integration of the transgene exhibited more resistant than the multiple copy one. and non transgenic plant. The resistance as a result of AV1 gene expression was indicated with no symptom in T0 generation transgenic tobacco plants and the accumulation of the virus in the transgenic plants tissue. Northern and Western hybridization analysis need to be perfomed for investigating the presence of mRNA or protein accumulation so that the resistance mechanism of the AV1 gene could be explained more detail.
    @article{Santoso12p45,
    title = {{Molecular Analysis and Effectiveness Assay of AV1 Gene in Transgenic Tobacco for Resistance to Begomovirus}},
    author = {T. J. Santoso and M. Herman and S. H. Hidayat and H. Aswidinnoor and Sudarsono},
    journal = {Jurnal AgroBiogen},
    pages = {45 - 53},
    volume = {8},
    number = {2},
    year = {2012},
    abstract = {Genetic transformation of tobacco plant using AV1 gene was conducted at the previously experiment and generated transgenic tobacco plants positively carrying the selectable marker nptII gene. The objectives of this experiment were to (1) analyze the presence of Begomovirus AV1 gene in T0 generation putative transgenic tobacco plants using PCR technique with specific primers and its correlation with resistance phenotype, (2) analyze the integration and copy number of the transgene in T0 generation putative transgenic tobacco plants and its correlation with resistance response, (3) screen the T0 generation putative transgenic tobacco plants with the target virus infection and to detect the presence of the virus in the transgenic plant tissue using universal primers. PCR detection of AV1 gene in tobacco transgenic was conducted by using specific primer for Begomovirus AV1 gene. Meanwhile, Southern Blot analysis was conducted by using the AV1 gene probe. The effectiveness of AV1 gene in tobacco transgenic was tested by inoculation of target virus using whiteflies vector. Result of the experiments showed that there was a positive correlation between the presence of the AV1 transgene in T0 generation putative transgenic tobacco plants and the resistant phenotype. Transgenic plants with a single copy integration of the transgene exhibited more resistant than the multiple copy one. and non transgenic plant. The resistance as a result of AV1 gene expression was indicated with no symptom in T0 generation transgenic tobacco plants and the accumulation of the virus in the transgenic plants tissue. Northern and Western hybridization analysis need to be perfomed for investigating the presence of mRNA or protein accumulation so that the resistance mechanism of the AV1 gene could be explained more detail.},
    keywords = {tobacco, nicotiana tabaccum, molecular analysis, pcr technique, southern blot analysis, begomovirus av1 gene, transgenic},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Agrobiogen 8 (2) 45-53, 2012.pdf}
    }
  7. Koerniati, S. and H. Widhianata. 2012. Construction and Transformation of HVA1 Gene Expression Vector into Indonesian Elite Rice Varieties. Jurnal agrobiogen 8 (2):54-61.
    [BibTeX] [Abstract] [PDF: Construction and Transformation of HVA1 Gene Expression Vector into Indonesian Elite Rice Varieties ]
    Transfer of an osmoprotectant gene HVA1 is an effort to reduce the effect of drought in rice. HVA1 is one of the Late Embryogenesis Abundant (LEA) protein group that plays a role on cell protection during stresses. A study was done with an objective to construct a plasmid vector expressing HVA1 and to transform it into Indonesian elite rice varieties. Materials used in the study were plasmid pBY520 (source of HVA1; intermediate plasmid pRP9; plasmid pAY560326 (backbone); restriction enzymes BamHI, HindIII, XhoI, and SpeI; T4 DNA ligase, and gel DNA extraction kit. Methods used were standard procedure for plasmid vector construction and molecular biology. Step I: the pBY520 and pRP9 were cut with BamHI and HindIII, and electrophorated with 1% agarose gel. DNA fragments of HVA1 and pRP9 were purified, ligated with T4 DNA ligase, and transformed into Escherichia coli DH5-$\alpha$ by heat shock. E. coli were grown onto solid medium (+ kanamycin 100 mg/l). A new plasmid DNA was isolated from single colony culture of the bacteria, confirmed, and named pRP9_HVA1. Step II: DNA of pRP9_HVA1 and pAY560326 were cut with XhoI dan SpeI enzymes, purified, and ligated. The next procedure was similar to step I, and the resulted plasmid was confirmed by PCR and digestion with XhoI dan SpeI enzymes, and named pAY_HVA1. Step III: pAY_HVA1 was first transformed into Agrobacterium EHA-105 and then into rive varieties Ciherang and Inpari 6 using the early infection of scutellum transformation method. Nine transgenic rice lines that positively contain HVA1 were obtained.
    @article{Koerniati12p54,
    title = {{Construction and Transformation of HVA1 Gene Expression Vector into Indonesian Elite Rice Varieties}},
    author = {S. Koerniati and H. Widhianata},
    journal = {Jurnal AgroBiogen},
    pages = {54 - 61},
    volume = {8},
    number = {2},
    year = {2012},
    abstract = {Transfer of an osmoprotectant gene HVA1 is an effort to reduce the effect of drought in rice. HVA1 is one of the Late Embryogenesis Abundant (LEA) protein group that plays a role on cell protection during stresses. A study was done with an objective to construct a plasmid vector expressing HVA1 and to transform it into Indonesian elite rice varieties. Materials used in the study were plasmid pBY520 (source of HVA1; intermediate plasmid pRP9; plasmid pAY560326 (backbone); restriction enzymes BamHI, HindIII, XhoI, and SpeI; T4 DNA ligase, and gel DNA extraction kit. Methods used were standard procedure for plasmid vector construction and molecular biology. Step I: the pBY520 and pRP9 were cut with BamHI and HindIII, and electrophorated with 1% agarose gel. DNA fragments of HVA1 and pRP9 were purified, ligated with T4 DNA ligase, and transformed into Escherichia coli DH5-$\alpha$ by heat shock. E. coli were grown onto solid medium (+ kanamycin 100 mg/l). A new plasmid DNA was isolated from single colony culture of the bacteria, confirmed, and named pRP9_HVA1. Step II: DNA of pRP9_HVA1 and pAY560326 were cut with XhoI dan SpeI enzymes, purified, and ligated. The next procedure was similar to step I, and the resulted plasmid was confirmed by PCR and digestion with XhoI dan SpeI enzymes, and named pAY_HVA1. Step III: pAY_HVA1 was first transformed into Agrobacterium EHA-105 and then into rive varieties Ciherang and Inpari 6 using the early infection of scutellum transformation method. Nine transgenic rice lines that positively contain HVA1 were obtained.},
    keywords = {vector construction, over-expression, osmoprotectant gene hva1, drought tolerant rice},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Agrobiogen 8 (2) 54-61, 2012.pdf}
    }
  8. Hadiarto, T., Ma’sumah, and E. I. Riyanti. 2012. Pembentukan Populasi Mutan Azospirillum dengan Menggunakan Transposon untuk Sifat Superior terhadap Pelarutan P. Jurnal agrobiogen 8 (2):62-68.
    [BibTeX] [Abstract] [PDF: Pembentukan Populasi Mutan Azospirillum dengan Menggunakan Transposon untuk Sifat Superior terhadap Pelarutan P ]
    Azospirillum sp. which has the ability for nitrogen fixation and phosphate solubilization may support modern farming in Indonesia that is mostly dependent on the usage of chemical fertilizer N, P, and K. Genetic quality of Azospirillum was improved in this research to obtain superior characters toward phosphate solubilization so that it can become more effective in use for farmers. To achieve this goal, Azospirillum was mutated by means of electroporation using transposon EZ-Tn5<kan-2>Tnp. The electrotransformation resulted in 20 out of 22 transformants tested contained the marker gen (npt). 10, 6 and 4 mutants have increased, decreased and lost phosphate-solubilizing function, respectively. Mutant with elevated phosphatesolubilizing ability may be selected further to be utilized as biofertilizer while others may be useful for identification of genes responsible for phosphate solubilization
    @article{Hadiarto12p62,
    title = {{Pembentukan Populasi Mutan Azospirillum dengan Menggunakan Transposon untuk Sifat Superior terhadap Pelarutan P}},
    author = {T. Hadiarto and Ma'sumah and E. I. Riyanti},
    journal = {Jurnal AgroBiogen},
    pages = {62 - 68},
    volume = {8},
    number = {2},
    year = {2012},
    abstract = {Azospirillum sp. which has the ability for nitrogen fixation and phosphate solubilization may support modern farming in Indonesia that is mostly dependent on the usage of chemical fertilizer N, P, and K. Genetic quality of Azospirillum was improved in this research to obtain superior characters toward phosphate solubilization so that it can become more effective in use for farmers. To achieve this goal, Azospirillum was mutated by means of electroporation using transposon EZ-Tn5<kan-2>Tnp. The electrotransformation resulted in 20 out of 22 transformants tested contained the marker gen (npt). 10, 6 and 4 mutants have increased, decreased and lost phosphate-solubilizing function, respectively. Mutant with elevated phosphatesolubilizing ability may be selected further to be utilized as biofertilizer while others may be useful for identification of genes responsible for phosphate solubilization},
    keywords = {azospirillum, p solubilization, transposon},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Agrobiogen 8 (2) 62-68, 2012.pdf}
    }
  9. Lestari, P., A. Risliawati, and H. J. Koh. 2012. Identifikasi dan Aplikasi Marka Berbasis PCR untuk Identifikasi Varietas Padi dengan Palatabilitas Tinggi. Jurnal agrobiogen 8 (2):69-77.
    [BibTeX] [Abstract] [PDF: Identifikasi dan Aplikasi Marka Berbasis PCR untuk Identifikasi Varietas Padi dengan Palatabilitas Tinggi ]
    Sampai saat ini belum ada profil sidik jari DNA sebagai identitas unik varietas padi yang mempunyai palatabilitas (total mutu rasa) tinggi di Indonesia, sehingga identifikasi varietas premium menggunakan marka molekuler dipandang perlu. Tujuan penelitian ini adalah untuk membuat profil sidik jari DNA varietas padi indica dan japonica sekaligus identitas unik varietas padi yang mempunyai palatabilitas tinggi menggunakan marka terpaut palatabilitas. Total 22 varietas japonica dan 24 varietas indica dievaluasi mutu rasanya dan diuji secara molekuler menggunakan 20 marka STS (sequence-tagged site) yang berbasis genom padi japonica. Untuk mengidentifikasi fungsi gennya, semua amplikon marka tersebut dikloning, ditransformasi, disekuen, dan hasil sekuennya dianalisis homologinya dengan database genom. Varietas Ilpum (japonica) dan Rojolele (indica) teridentifikasi mempunyai palatabilitas tertinggi dibandingkan dengan varietas lainnya. Profil sidik jari DNA padi yang diidentifikasi dengan total marka STS tersebut belum dapat mendiferensiasi tiap varietas, namun varietas japonica dan indica premium teridentifikasi secara spesifik. Identitas unik varietas indica Indonesia yang memiliki palatabilitas tinggi, Rojolele berhasil dibuat menggunakan sebuah set marka. Profil sidik jari DNA dalam nilai digital memudahkan dalam sistem identifikasi varietas beras premium dari varietas lainnya. Fragmen dari primer STS tersebut diketahui bukan merupakan gen yang terpaut mutu rasa beras, sehingga marka tersebut lebih sesuai untuk identifikasi beras premium dengan palatabilitas tinggi daripada diferensiasi varietas berdasarkan palatabilitas. Dalam studi ini, identitas unik varietas padi dengan palatabilitas tinggi tersebut sangat berguna dalam membantu mengevaluasi kemurnian varietas untuk tujuan perlindungan plasma nutfah.
    @article{Lestari12p69,
    title = {{Identifikasi dan Aplikasi Marka Berbasis PCR untuk Identifikasi Varietas Padi dengan Palatabilitas Tinggi}},
    author = {P. Lestari and A. Risliawati and H. J. Koh},
    journal = {Jurnal AgroBiogen},
    pages = {69 - 77},
    volume = {8},
    number = {2},
    year = {2012},
    abstract = {Sampai saat ini belum ada profil sidik jari DNA sebagai identitas unik varietas padi yang mempunyai palatabilitas (total mutu rasa) tinggi di Indonesia, sehingga identifikasi varietas premium menggunakan marka molekuler dipandang perlu. Tujuan penelitian ini adalah untuk membuat profil sidik jari DNA varietas padi indica dan japonica sekaligus identitas unik varietas padi yang mempunyai palatabilitas tinggi menggunakan marka terpaut palatabilitas. Total 22 varietas japonica dan 24 varietas indica dievaluasi mutu rasanya dan diuji secara molekuler menggunakan 20 marka STS (sequence-tagged site) yang berbasis genom padi japonica. Untuk mengidentifikasi fungsi gennya, semua amplikon marka tersebut dikloning, ditransformasi, disekuen, dan hasil sekuennya dianalisis homologinya dengan database genom. Varietas Ilpum (japonica) dan Rojolele (indica) teridentifikasi mempunyai palatabilitas tertinggi dibandingkan dengan varietas lainnya. Profil sidik jari DNA padi yang diidentifikasi dengan total marka STS tersebut belum dapat mendiferensiasi tiap varietas, namun varietas japonica dan indica premium teridentifikasi secara spesifik. Identitas unik varietas indica Indonesia yang memiliki palatabilitas tinggi, Rojolele berhasil dibuat menggunakan sebuah set marka. Profil sidik jari DNA dalam nilai digital memudahkan dalam sistem identifikasi varietas beras premium dari varietas lainnya. Fragmen dari primer STS tersebut diketahui bukan merupakan gen yang terpaut mutu rasa beras, sehingga marka tersebut lebih sesuai untuk identifikasi beras premium dengan palatabilitas tinggi daripada diferensiasi varietas berdasarkan palatabilitas. Dalam studi ini, identitas unik varietas padi dengan palatabilitas tinggi tersebut sangat berguna dalam membantu mengevaluasi kemurnian varietas untuk tujuan perlindungan plasma nutfah.},
    keywords = {padi, palatabilitas, polymerase chain reaction, sequence-tagged site},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Agrobiogen 8 (2) 69-77, 2012.pdf}
    }
  10. Dewi, I. S. and B. S. Purwoko. 2012. Kultur Antera untuk Percepatan Perakitan Varietas Padi di Indonesia. Jurnal agrobiogen 8 (2):78-88.
    [BibTeX] [Abstract] [PDF: Kultur Antera untuk Percepatan Perakitan Varietas Padi di Indonesia ]
    Padi adalah komoditi pangan terpenting di Indonesia, sedangkan kebutuhan beras terus meningkat seiring dengan pertambahan jumlah penduduk dan adanya perubahan pola konsumsi penduduk fdari non beras ke beras. Hal tersebut harus diatasi dengan jalan meningkatkan produksi padi secara nasional melalui peningkatan produktivitas lahan sawah yang ada serta pengembangan lahan potensial lainnya termasuk lahan kering yang umumnya terdapat di luar pulau Jawa dan Bali. Saat ini varietas unggul baru yang bersifat semi dwarf (VUB), padi hibrida dan padi tipe baru (PTB) sedang dikembangkan pemulia padi di Indonesia. Untuk dapat mempercepat perakitan varietas padi harus diterapkan suatu kombinasi metode pemuliaan konvensional dengan metode bioteknologi. Kultur antera merupakan salah satu teknik kultur in vitro yang dapat mempercepat perolehan galur murni melalui tanaman dihaploid (DH) yang dihasilkan langsung pada generasi pertama dalam waktu kurang dari setahun. Diterapkannya teknik ini pada program pemuliaan konvensional akan meningkatkan efisiensi proses seleksi selain dapat lebih hemat dalam biaya untuk tenaga kerja, sewa lahan, dan waktu pemulia dibandingkan dengan program pemuliaan konvensional biasa. Regenerasi tanaman hijau melalui kultur antera padi subspesies indica telah ditingkatkan melalui penambahan 1 mM putresina ke media induksi dan regenerasi. Di Indonesia, saat ini dari berbagai penelitian perbaikan tanaman padi melalui kultur antera dalam waktu 2-3 tahun telah berhasil diperoleh galur-galur padi gogo toleran cekaman naungan, keracunan aluminium, tahan blas daun dan blas leher malai, galur-galur padi sawah tahan hawar daun bakteri dan blas, serta galur-galur mandul jantan beserta pelestarinya serta restorer untuk mendukung perakitan padi hibrida. Namun, potensi kultur antera dalam menyediakan material genetik untuk pemetaan yang dapat digunakan dalam functional genomics dan pemuliaan secara molekuler belum dieksplorasi. Hal tersebut menunjukkan bahwa teknologi kultur antera merupakan teknologi yang layak untuk digunakan dalam percepatan program pemuliaan padi di Indonesia.
    @article{Dewi12p78,
    title = {{Kultur Antera untuk Percepatan Perakitan Varietas Padi di Indonesia}},
    author = {I. S. Dewi and B. S. Purwoko},
    journal = {Jurnal AgroBiogen},
    pages = {78 - 88},
    volume = {8},
    number = {2},
    year = {2012},
    abstract = {Padi adalah komoditi pangan terpenting di Indonesia, sedangkan kebutuhan beras terus meningkat seiring dengan pertambahan jumlah penduduk dan adanya perubahan pola konsumsi penduduk fdari non beras ke beras. Hal tersebut harus diatasi dengan jalan meningkatkan produksi padi secara nasional melalui peningkatan produktivitas lahan sawah yang ada serta pengembangan lahan potensial lainnya termasuk lahan kering yang umumnya terdapat di luar pulau Jawa dan Bali. Saat ini varietas unggul baru yang bersifat semi dwarf (VUB), padi hibrida dan padi tipe baru (PTB) sedang dikembangkan pemulia padi di Indonesia. Untuk dapat mempercepat perakitan varietas padi harus diterapkan suatu kombinasi metode pemuliaan konvensional dengan metode bioteknologi. Kultur antera merupakan salah satu teknik kultur in vitro yang dapat mempercepat perolehan galur murni melalui tanaman dihaploid (DH) yang dihasilkan langsung pada generasi pertama dalam waktu kurang dari setahun. Diterapkannya teknik ini pada program pemuliaan konvensional akan meningkatkan efisiensi proses seleksi selain dapat lebih hemat dalam biaya untuk tenaga kerja, sewa lahan, dan waktu pemulia dibandingkan dengan program pemuliaan konvensional biasa. Regenerasi tanaman hijau melalui kultur antera padi subspesies indica telah ditingkatkan melalui penambahan 1 mM putresina ke media induksi dan regenerasi. Di Indonesia, saat ini dari berbagai penelitian perbaikan tanaman padi melalui kultur antera dalam waktu 2-3 tahun telah berhasil diperoleh galur-galur padi gogo toleran cekaman naungan, keracunan aluminium, tahan blas daun dan blas leher malai, galur-galur padi sawah tahan hawar daun bakteri dan blas, serta galur-galur mandul jantan beserta pelestarinya serta restorer untuk mendukung perakitan padi hibrida. Namun, potensi kultur antera dalam menyediakan material genetik untuk pemetaan yang dapat digunakan dalam functional genomics dan pemuliaan secara molekuler belum dieksplorasi. Hal tersebut menunjukkan bahwa teknologi kultur antera merupakan teknologi yang layak untuk digunakan dalam percepatan program pemuliaan padi di Indonesia.},
    keywords = {padi, kultur antera, dihaploid},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/Agrobiogen 8 (2) 78-88, 2012.pdf}
    }

2011

  1. Utami, D. W., T. S. Kadir, and S. d. Yuriyah. 2011. Faktor Virulensi AvrBs3/PthA pada Ras III, Ras IV, Ras VIII, dan IXO93-068 Patogen Hawar Daun Bakteri (Xanthomonas oryzae pv. Oryzae). Jurnal agrobiogen 7 (1):1-8.
    [BibTeX] [Abstract] [PDF: Faktor Virulensi AvrBs3/PthA pada Ras III, Ras IV, Ras VIII, dan IXO93-068 Patogen Hawar Daun Bakteri (Xanthomonas oryzae pv. Oryzae) ]
    AvrBs3/PthA Virulence Factor of Bacterial Leaf Blight Race III, Race IV, Race VIII, and IXO93-068. Dwinita W. Utami, Triny S. Kadir, and Siti Yuriyah. Bacterial leaf blight (BLB) is an important disease of rice and present throughout many of the rice-growing regions in the world, also in Indonesia. Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent and a member of the Protebacteria and like many other this phyllum have a type III secretion system for protein virulence effector (PVE) released on their pathogenicity system. Commonly, PVE in Xanthomonas sp., is coded by AvrBs3/PthA family gene. This research was coducted to identify the virulence factor of AvrBs3/PthA on dominant Indonesian BLB isolates (Race III, Race IV, Ras VIII, and IXO93-068). This objective was obtained by sequence analysis through designed markers for members of the virulence factor AvrBs3/PthA gene family (PthXo4, avrXa7#38, PthXoS and avrXa7sacB50). Results gave information that RaceIII is a dependent elicitor race due to no PVE transcript formed and intraceluler protein target with RLL type on NLS (nuclear localization signal). RaceIV and RaceVIII are the virulent race which PVE active formed with intraceluler protein target and have the RLL and RLLP type for the NLS signal. While isolate IXO93-068 is a virulen isolate that active formed a PVE but the extraceluler protein target is due to no type of NLS. Based on cluster analysis, Race VIII has a genetic distance closely to PthXoS and avrXa7sacB50.
    @article{Utami11p1,
    title = {{Faktor Virulensi AvrBs3/PthA pada Ras III, Ras IV, Ras VIII, dan IXO93-068 Patogen Hawar Daun Bakteri (Xanthomonas oryzae pv. Oryzae)}},
    author = {D. W. Utami and T. S. Kadir and d. S. Yuriyah },
    journal = {Jurnal AgroBiogen},
    pages = {1 - 8},
    volume = {7},
    number = {1},
    year = {2011},
    abstract = {AvrBs3/PthA Virulence Factor of Bacterial Leaf Blight Race III, Race IV, Race VIII, and IXO93-068. Dwinita W. Utami, Triny S. Kadir, and Siti Yuriyah. Bacterial leaf blight (BLB) is an important disease of rice and present throughout many of the rice-growing regions in the world, also in Indonesia. Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent and a member of the Protebacteria and like many other this phyllum have a type III secretion system for protein virulence effector (PVE) released on their pathogenicity system. Commonly, PVE in Xanthomonas sp., is coded by AvrBs3/PthA family gene. This research was coducted to identify the virulence factor of AvrBs3/PthA on dominant Indonesian BLB isolates (Race III, Race IV, Ras VIII, and IXO93-068). This objective was obtained by sequence analysis through designed markers for members of the virulence factor AvrBs3/PthA gene family (PthXo4, avrXa7#38, PthXoS and avrXa7sacB50). Results gave information that RaceIII is a dependent elicitor race due to no PVE transcript formed and intraceluler protein target with RLL type on NLS (nuclear localization signal). RaceIV and RaceVIII are the virulent race which PVE active formed with intraceluler protein target and have the RLL and RLLP type for the NLS signal. While isolate IXO93-068 is a virulen isolate that active formed a PVE but the extraceluler protein target is due to no type of NLS. Based on cluster analysis, Race VIII has a genetic distance closely to PthXoS and avrXa7sacB50.},
    keywords = {bacterial leaf blight, xanthomonas oryzae pv, oryzae, avrbs3, ptha virulence factor.},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_7_1_2011_01.pdf}
    }
  2. Santoso, T. J., M. Herman, S. H. Hidayat, H. Aswidinnoor, and d. Sudarsono. 2011. Konstruksi Kandidat Gen AV1 Begomovirus pada pBI121 dan Introduksinya ke dalam Tembakau Menggunakan Vektor Agrobacterium tumefaciens. Jurnal agrobiogen 7 (1):9-18.
    [BibTeX] [Abstract] [PDF: Konstruksi Kandidat Gen AV1 Begomovirus pada pBI121 dan Introduksinya ke dalam Tembakau Menggunakan Vektor Agrobacterium tumefaciens ]
    Infection of Begomovirus has caused leaf curl disease in tomato. This infection has significantly impact on yield losses of tomato production. Recently, in Indonesia there was no effectively way to control this disease. The use of resistant tomato variety is one of strategies to control this virus. Genetic engineering technology gives an opportunity to develop the transgenic tomato resistant to Begomovirus through pathogen derived resistance (PDR) approach. The objectives of this study were to construct the Begomovirus AV1 candidate gene in the pBI121 and to introduce the construct into tobacco plant genome through Agrobacterium tumefaciens vector. A series activites in gene construct have been conducted include PCR amplification of AV1 gene using a pair of specific primer, cloning the gene into pGEM-T easy, transformation of the clone into Escherichia coli DH5$\alpha$ competent cell, construct the gene into pBI121, and transform the construct into A. tumefaciens. Leaf segments of in vitro tobacco plant were transformed by co-cultivation with A. tumefaciens containing ToLCV-AV1 construct. In the research activitiy, Indonesian Begomovirus AV1 gene was successfully amplified and inserted in expression vector plasmid pBI121. Tobacco transformants carrying kanamycin-resistant gene (nptII gene) were regenerated and established in the glasshouse. Those transformant plants are expected containing the AV1 gene.
    @article{Santoso11p9,
    title = {{Konstruksi Kandidat Gen AV1 Begomovirus pada pBI121 dan Introduksinya ke dalam Tembakau Menggunakan Vektor Agrobacterium tumefaciens}},
    author = {T. J. Santoso and M. Herman and S. H. Hidayat and H. Aswidinnoor and d. Sudarsono},
    journal = {Jurnal AgroBiogen},
    pages = {9 - 18},
    volume = {7},
    number = {1},
    year = {2011},
    abstract = {Infection of Begomovirus has caused leaf curl disease in tomato. This infection has significantly impact on yield losses of tomato production. Recently, in Indonesia there was no effectively way to control this disease. The use of resistant tomato variety is one of strategies to control this virus. Genetic engineering technology gives an opportunity to develop the transgenic tomato resistant to Begomovirus through pathogen derived resistance (PDR) approach. The objectives of this study were to construct the Begomovirus AV1 candidate gene in the pBI121 and to introduce the construct into tobacco plant genome through Agrobacterium tumefaciens vector. A series activites in gene construct have been conducted include PCR amplification of AV1 gene using a pair of specific primer, cloning the gene into pGEM-T easy, transformation of the clone into Escherichia coli DH5$\alpha$ competent cell, construct the gene into pBI121, and transform the construct into A. tumefaciens. Leaf segments of in vitro tobacco plant were transformed by co-cultivation with A. tumefaciens containing ToLCV-AV1 construct. In the research activitiy, Indonesian Begomovirus AV1 gene was successfully amplified and inserted in expression vector plasmid pBI121. Tobacco transformants carrying kanamycin-resistant gene (nptII gene) were regenerated and established in the glasshouse. Those transformant plants are expected containing the AV1 gene.},
    keywords = {av1 gene, begomovirus, nicotiana tabaccum, agrobacterium tumefaciens, coat protein},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_7_1_2011_02.pdf}
    }
  3. Apriana, A., A. Sisharmini, W. Enggarini, Sudarsono, N. Khumaida, and K. R. d. Trijatmiko. 2011. Introduksi Konstruk Over-Ekspresi Kandidat Gen OsWRKY76 melalui Agrobacterium tumefaciens pada Tanaman Padi Nipponbare. Jurnal agrobiogen 7 (1):19-27.
    [BibTeX] [Abstract] [PDF: Introduksi Konstruk Over-Ekspresi Kandidat Gen OsWRKY76 melalui Agrobacterium tumefaciens pada Tanaman Padi Nipponbare ]
    Plant genetic improvement can be done through classical breeding or genetic engineering. WRKY is a transcription factor involved in regulating plant defense responses. OsWRKY76 gene is located in a narrow segment of chromosome 9 which is identified previously to be related to wide spectrum resistance in rice. A sequence of OsWRKY76 (+1.200 bp) has available in the gene bank and it makes possible to isolate, clone, and construct the gene into over-expression vector. The aim of this research was to assemble an overexpression construct of OsWRKY76 candidate gene and introduce it into rice through Agrobacterium-mediated transformation. A construct of pCAMBIA1301::35S::OsWRKY76 has been successfully assembled and transformed into embryogenic calli of rice cv. Nipponbare using A. tumefaciens strain Agl-1 and EHA 105. A number of 126 independent lines has been produced, in which Agl-1 showed 3.8 times more efficient than EHA 105. PCR analysis of randomly selected 25 independent lines showed that all of them positively contained hptII gene, a selectable marker used in the over-expression construct of the OsWRKY76 candidate gene. Based on the result, it could be concluded that the over-expression construct of OsWRKY76 candidate gene have been successfully introduced into the tissue of Nipponbare.
    @article{Apriana11p19,
    title = {{Introduksi Konstruk Over-Ekspresi Kandidat Gen OsWRKY76 melalui Agrobacterium tumefaciens pada Tanaman Padi Nipponbare}},
    author = {A. Apriana and A. Sisharmini and W. Enggarini and Sudarsono and N. Khumaida and d. K. R. Trijatmiko},
    journal = {Jurnal AgroBiogen},
    pages = {19 - 27},
    volume = {7},
    number = {1},
    year = {2011},
    abstract = {Plant genetic improvement can be done through classical breeding or genetic engineering. WRKY is a transcription factor involved in regulating plant defense responses. OsWRKY76 gene is located in a narrow segment of chromosome 9 which is identified previously to be related to wide spectrum resistance in rice. A sequence of OsWRKY76 (+1.200 bp) has available in the gene bank and it makes possible to isolate, clone, and construct the gene into over-expression vector. The aim of this research was to assemble an overexpression construct of OsWRKY76 candidate gene and introduce it into rice through Agrobacterium-mediated transformation. A construct of pCAMBIA1301::35S::OsWRKY76 has been successfully assembled and transformed into embryogenic calli of rice cv. Nipponbare using A. tumefaciens strain Agl-1 and EHA 105. A number of 126 independent lines has been produced, in which Agl-1 showed 3.8 times more efficient than EHA 105. PCR analysis of randomly selected 25 independent lines showed that all of them positively contained hptII gene, a selectable marker used in the over-expression construct of the OsWRKY76 candidate gene. Based on the result, it could be concluded that the over-expression construct of OsWRKY76 candidate gene have been successfully introduced into the tissue of Nipponbare.},
    keywords = {transcription factor, oswrky resistance, rice, nipponbare, gene, blast},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_7_1_2011_03.pdf}
    }
  4. Ambarwati, A. D., S. M. Sumaraw, A. Purwito, M. Herman, E. Suryaningsih, and H. d. Aswidinnoor. 2011. Efikasi Gen RB pada Tanaman Kentang Transgenik Katahdin SP904 dan SP951 terhadap Empat Isolat Phytophthora infestans dari Jawa Barat. Jurnal agrobiogen 7 (1):28-36.
    [BibTeX] [Abstract] [PDF: Efikasi Gen RB pada Tanaman Kentang Transgenik Katahdin SP904 dan SP951 terhadap Empat Isolat Phytophthora infestans dari Jawa Barat ]
    Potato late blight, caused by Phytophthora infestans is one of the most devastating plant disease. Potato yield losses due to this disease ranged from 47-100%. A major late blight resistance gene, called RB, previously was identified in the wild potato species Solanum bulbocastanum. RB gene has been integrated into cultivated potato Katahdin using Agrobacterium-mediated transformation, and showed durable and broad spectrum resistance either in laboratory assay or in confined field trial. Evaluation of transgenic Katahdin SP904 and SP951 was conducted to verify whether the RB gene with broad spectrum to all known races of P. infestans in the United States and in Toluca, Mexico was also effective against P. infestans isolates in Indonesia. Efficacy of RB gene was evaluated for foliar and tuber resistance to West Java isolates. Transgenic Katahdin were more resistant in foliar than non transgenic plants, at 14 days after inoculation. Diseases intensity of transgenic Katahdin SP904 and SP951 were 19.8-43.8%, whereas non transgenic Katahdin, Granola, and Atlantic were 46.9-100%. In contrast to the foliar resistance phenotype, RB-containing tubers in transgenic Katahdin did not exhibit increased resistance to Lembang, Pangalengan and Galunggung isolates. Tubers of transgenic Katahdin SP904, SP951, and non transgenic Katahdin showed lesion volume of 0.93, 0.91, and 0.91 cm3, respectively. RB gene in transgenic Katahdin showed efficacy against late blight P. infestans in foliar, but did not showed efficacy in tuber. Transgenic Katahdin RB thus providing a potential source of resistance for breeding programs.
    @article{Ambarwati11p28,
    title = {{Efikasi Gen RB pada Tanaman Kentang Transgenik Katahdin SP904 dan SP951 terhadap Empat Isolat Phytophthora infestans dari Jawa Barat}},
    author = {A. D. Ambarwati and S. M. Sumaraw and A. Purwito and M. Herman and E. Suryaningsih and d. H. Aswidinnoor},
    journal = {Jurnal AgroBiogen},
    pages = {28 - 36},
    volume = {7},
    number = {1},
    year = {2011},
    abstract = {Potato late blight, caused by Phytophthora infestans is one of the most devastating plant disease. Potato yield losses due to this disease ranged from 47-100%. A major late blight resistance gene, called RB, previously was identified in the wild potato species Solanum bulbocastanum. RB gene has been integrated into cultivated potato Katahdin using Agrobacterium-mediated transformation, and showed durable and broad spectrum resistance either in laboratory assay or in confined field trial. Evaluation of transgenic Katahdin SP904 and SP951 was conducted to verify whether the RB gene with broad spectrum to all known races of P. infestans in the United States and in Toluca, Mexico was also effective against P. infestans isolates in Indonesia. Efficacy of RB gene was evaluated for foliar and tuber resistance to West Java isolates. Transgenic Katahdin were more resistant in foliar than non transgenic plants, at 14 days after inoculation. Diseases intensity of transgenic Katahdin SP904 and SP951 were 19.8-43.8%, whereas non transgenic Katahdin, Granola, and Atlantic were 46.9-100%. In contrast to the foliar resistance phenotype, RB-containing tubers in transgenic Katahdin did not exhibit increased resistance to Lembang, Pangalengan and Galunggung isolates. Tubers of transgenic Katahdin SP904, SP951, and non transgenic Katahdin showed lesion volume of 0.93, 0.91, and 0.91 cm3, respectively. RB gene in transgenic Katahdin showed efficacy against late blight P. infestans in foliar, but did not showed efficacy in tuber. Transgenic Katahdin RB thus providing a potential source of resistance for breeding programs.},
    keywords = {rb gene, transgenic infestans, west java, potato, phytophthora},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_7_1_2011_04.pdf}
    }
  5. Tasma, I. M., D. Satyawan, A. Warsun, M. Yunus, and B. Santosa. 2011. Phylogenetic and Maturity Analyses of Sixty Soybean Genotypes Used for DNA Marker Development of Early Maturity Quantitative Trait Loci in Soybean. Jurnal agrobiogen 7 (1):37-46.
    [BibTeX] [Abstract] [PDF: Phylogenetic and Maturity Analyses of Sixty Soybean Genotypes Used for DNA Marker Development of Early Maturity Quantitative Trait Loci in Soybean ]
    Produktivitas kedelai Indonesia saat ini masih rendah dengan rataan nasional 1,3 t/ha. Salah satu cara meningkatkan produksi kedelai nasional dengan memanipulasi indeks panen menggunakan varietas super genjah. Pemuliaan kedelai super genjah dipercepat dengan menggunakan bantuan marka molekuler. Tujuan dari penelitian ini untuk memilih tetua-tetua dengan perbedaan kontras karakter umur genjah dan menunjukkan jarak genetik jauh. Tetua terpilih digunakan untuk membentuk populasi untuk pengembangan marka molekuler terkait umur genjah. Uji kegenjahan 60 genotipe kedelai dilakukan di dua lokasi, KP Cikeumeuh (Bogor) dan KP Pacet (Cianjur) menggunakan rancangan acak kelompok, tiga ulangan. DNA genomik 60 genotipe kedelai dianalisis menggunakan 18 marka SSR dan dendrogram kekerabatan antar aksesi dikonstruksi menggunakan Unweighted Pair-Group Method Arithmatic melalui program Numerical Taxonomy and Multivariate System versi 2.1-pc. Hasil penelitian menunjukkan bahwa distribusi normal 60 genotipe kedelai di kedua lokasi pada karakter waktu berbunga (32-48 hari), waktu berpolong (35-55 hari), waktu matang fisiologis (75-92 hari), dan waktu panen (78-99 hari). Diperoleh empat genotipe berumur genjah (umur masak tergenjah 75,3 hari dan warna pubescent coklat), tiga genotipe umur dalam (umur masak terdalam 89,7 hari dan warna pubescent abu-abu). Jumlah alel SSR total 237, rataan alel per lokus 12,6 (3-29), rataan nilai PIC 0,78 (0,55-0,89). Tingkat kesamaan genetik berkisar 74,8-95%. Pada kemiripan 77% membagi genotipe menjadi enam klaster (empat genotipe umur genjah ada pada klaster III dan IV dan tiga genotipe umur dalam ada pada klaster II). Berdasarkan analisis data umur, warna pubescent, dan analisis filogenetik terpilih tujuh tetua yang digunakan untuk pengembangan marka terkait umur genjah, yaitu empat tetua berumur genjah B1430, B2973, B3611, B4433 dan tiga tetua berumur dalam B1635, B1658, dan B3570. Dua belas populasi F2 dibentuk menggunakan bantuan marka Satt300 dan Satt516. Dua di antara populasi tersebut dapat digunakan untuk pengembangan marka molekuler umur genjah.
    @article{Tasma11p37,
    title = {{Phylogenetic and Maturity Analyses of Sixty Soybean Genotypes Used for DNA Marker Development of Early Maturity Quantitative Trait Loci in Soybean}},
    author = {I. M. Tasma and D. Satyawan and A. Warsun and M. Yunus and B. Santosa},
    journal = {Jurnal AgroBiogen},
    pages = {37 - 46},
    volume = {7},
    number = {1},
    year = {2011},
    abstract = {Produktivitas kedelai Indonesia saat ini masih rendah dengan rataan nasional 1,3 t/ha. Salah satu cara meningkatkan produksi kedelai nasional dengan memanipulasi indeks panen menggunakan varietas super genjah. Pemuliaan kedelai super genjah dipercepat dengan menggunakan bantuan marka molekuler. Tujuan dari penelitian ini untuk memilih tetua-tetua dengan perbedaan kontras karakter umur genjah dan menunjukkan jarak genetik jauh. Tetua terpilih digunakan untuk membentuk populasi untuk pengembangan marka molekuler terkait umur genjah. Uji kegenjahan 60 genotipe kedelai dilakukan di dua lokasi, KP Cikeumeuh (Bogor) dan KP Pacet (Cianjur) menggunakan rancangan acak kelompok, tiga ulangan. DNA genomik 60 genotipe kedelai dianalisis menggunakan 18 marka SSR dan dendrogram kekerabatan antar aksesi dikonstruksi menggunakan Unweighted Pair-Group Method Arithmatic melalui program Numerical Taxonomy and Multivariate System versi 2.1-pc. Hasil penelitian menunjukkan bahwa distribusi normal 60 genotipe kedelai di kedua lokasi pada karakter waktu berbunga (32-48 hari), waktu berpolong (35-55 hari), waktu matang fisiologis (75-92 hari), dan waktu panen (78-99 hari). Diperoleh empat genotipe berumur genjah (umur masak tergenjah 75,3 hari dan warna pubescent coklat), tiga genotipe umur dalam (umur masak terdalam 89,7 hari dan warna pubescent abu-abu). Jumlah alel SSR total 237, rataan alel per lokus 12,6 (3-29), rataan nilai PIC 0,78 (0,55-0,89). Tingkat kesamaan genetik berkisar 74,8-95%. Pada kemiripan 77% membagi genotipe menjadi enam klaster (empat genotipe umur genjah ada pada klaster III dan IV dan tiga genotipe umur dalam ada pada klaster II). Berdasarkan analisis data umur, warna pubescent, dan analisis filogenetik terpilih tujuh tetua yang digunakan untuk pengembangan marka terkait umur genjah, yaitu empat tetua berumur genjah B1430, B2973, B3611, B4433 dan tiga tetua berumur dalam B1635, B1658, dan B3570. Dua belas populasi F2 dibentuk menggunakan bantuan marka Satt300 dan Satt516. Dua di antara populasi tersebut dapat digunakan untuk pengembangan marka molekuler umur genjah.},
    keywords = {marka molekuler, umur genjah, kekerabatan genetik, kedelai, qtl},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_7_1_2011_05.pdf}
    }
  6. Satyawan, D. and I. M. Tasma. 2011. Genetic Diversity Analysis of Jatropha Curcas Provenances Using Randomly Amplified Polymorphic DNA Markers. Jurnal agrobiogen 7 (1):47-55.
    [BibTeX] [Abstract] [PDF: Genetic Diversity Analysis of Jatropha Curcas Provenances Using Randomly Amplified Polymorphic DNA Markers ]
    Jarak pagar (Jatropha curcas L.) adalah tanaman non pangan yang bijinya dapat menghasilkan minyak untuk digunakan dalam produksi biodiesel atau langsung dipakai sebagai bahan bakar bagi mesin diesel yang telah dimodifikasi. Tujuan penelitian ini adalah untuk mengetahui keragaman genetik koleksi tanaman jarak pagar Badan Penelitian dan Pengembangan Pertanian yang ditanam di Kebun Percobaan Pakuwon (Sukabumi, Jawa Barat) dengan menggunakan marka RAPD. Sebanyak 50 aksesi jarak pagar dan satu aksesi Jatopha integerrima dianalisis keragaman genetiknya menggunakan 14 primer RAPD dengan kandungan G+C antara 60-80%. Dari 14 primer tersebut diperoleh 64 pita DNA dengan tingkat polimorfisme sebanyak 95,7%. Beberapa pita DNA yang dihasilkan tidak konsisten dan reproducible sehingga dilakukan reaksi ulangan untuk setiap primer yang digunakan demi meminimalisir kesalahan skor marka. Data pita DNA yang dihasilkan selanjutnya digunakan untuk analisis keragaman genetik dengan menggunakan Unweighted Pair Group Method Arithmetic (UPGMA) dan koefisien Dice, dan hasil yang didapat menunjukkan bahwa aksesi yang dianalisis memiliki koefisien kesamaan antara 0,2 dan 0,98, dengan rerata sebesar 0,75. Analisis dendrogram membagi aksesiaksesi ke dalam dua kelompok besar, dengan satu outlier dari Lampung Selatan. Pembagian kelompok tidak berkorelasi dengan daerah asal masing-masing aksesi, sehingga konsisten dengan hipotesis bahwa tanaman jarak pagar baru masuk ke Indonesia sekitar 4 abad lalu dan penyebarannya lebih banyak difasilitasi oleh manusia. Tingginya rerata koefisien kesamaan menunjukkan bahwa keragaman genetik koleksi ini cukup rendah, sehingga di masa depan diperlukan penambahan aksesi dengan latar belakang genetik yang bervariasi untuk semakin meningkatkan produktivitas tanaman hasil pemuliaan jarak pagar.
    @article{Satyawan11p47,
    title = {{Genetic Diversity Analysis of Jatropha Curcas Provenances Using Randomly Amplified Polymorphic DNA Markers}},
    author = {D. Satyawan and I. M. Tasma},
    journal = {Jurnal AgroBiogen},
    pages = {47 - 55},
    volume = {7},
    number = {1},
    year = {2011},
    abstract = {Jarak pagar (Jatropha curcas L.) adalah tanaman non pangan yang bijinya dapat menghasilkan minyak untuk digunakan dalam produksi biodiesel atau langsung dipakai sebagai bahan bakar bagi mesin diesel yang telah dimodifikasi. Tujuan penelitian ini adalah untuk mengetahui keragaman genetik koleksi tanaman jarak pagar Badan Penelitian dan Pengembangan Pertanian yang ditanam di Kebun Percobaan Pakuwon (Sukabumi, Jawa Barat) dengan menggunakan marka RAPD. Sebanyak 50 aksesi jarak pagar dan satu aksesi Jatopha integerrima dianalisis keragaman genetiknya menggunakan 14 primer RAPD dengan kandungan G+C antara 60-80%. Dari 14 primer tersebut diperoleh 64 pita DNA dengan tingkat polimorfisme sebanyak 95,7%. Beberapa pita DNA yang dihasilkan tidak konsisten dan reproducible sehingga dilakukan reaksi ulangan untuk setiap primer yang digunakan demi meminimalisir kesalahan skor marka. Data pita DNA yang dihasilkan selanjutnya digunakan untuk analisis keragaman genetik dengan menggunakan Unweighted Pair Group Method Arithmetic (UPGMA) dan koefisien Dice, dan hasil yang didapat menunjukkan bahwa aksesi yang dianalisis memiliki koefisien kesamaan antara 0,2 dan 0,98, dengan rerata sebesar 0,75. Analisis dendrogram membagi aksesiaksesi ke dalam dua kelompok besar, dengan satu outlier dari Lampung Selatan. Pembagian kelompok tidak berkorelasi dengan daerah asal masing-masing aksesi, sehingga konsisten dengan hipotesis bahwa tanaman jarak pagar baru masuk ke Indonesia sekitar 4 abad lalu dan penyebarannya lebih banyak difasilitasi oleh manusia. Tingginya rerata koefisien kesamaan menunjukkan bahwa keragaman genetik koleksi ini cukup rendah, sehingga di masa depan diperlukan penambahan aksesi dengan latar belakang genetik yang bervariasi untuk semakin meningkatkan produktivitas tanaman hasil pemuliaan jarak pagar.},
    keywords = {jatropha curcas, marka rapd, keragaman genetik},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_7_1_2011_06.pdf}
    }
  7. Lestari, E. G.. 2011. Peranan Zat Pengatur Tumbuh dalam Perbanyakan Tanaman melalui Kultur Jaringan. Jurnal agrobiogen 7 (1):63-68.
    [BibTeX] [Abstract] [PDF: Peranan Zat Pengatur Tumbuh dalam Perbanyakan Tanaman melalui Kultur Jaringan ]
    In plant tissue culture, growth regulator has significant roles such as to control root and shoot development in the plant formation and callus induction. Cytokinin and auxin are two prominent growth regulator. Cytokinin consists of BA (benzil adenin), kinetin (furfuril amino purin), 2-Ip (dimethyl allyl amino purin), and zeatin. While auksin covers IAA (indone acetic acid), NAA (napthalene acetic acid), IBA (indole butiric acid) 2.4-D (2.4dicholophenoxy acetic acid), dicamba (3,6 dicloro-O-anisic acid), and picloram (4-amino 3,5,6-tricloropicolinic acid). The emphasis of plant growth purposes decide the use of growth regulator. Cytokinin is applied mainly for the purpose of shoot, while auxin is mainly used for the purpose of root and callus. The application of growth regulator application is varied, depending on the genotype and physiological condition of the plant. The existence of a certain growth regulating substances can enhance growth regulator activity of other substances. The type and concentration of the appropriate growth regulators for each plant is not the same because it depends on the genotype and physiological condition of plant tissue. However so often both are frequently required depend on the ratio/ratio of auxin cytokines or vice versa. The existence of a certain growth regulating substances can enhance growth regulator activity of other substances. The type and concentration of the appropriate growth regulators for each plant is not the same because it depends on the genotype and physiological condition of plant tissue. For the propagation, multiple and adventive shoots along with embriosomatic formation could be applied. The seedling is obtained from one somatic cell. Here, strong auxin, such as dicamba and picloram 2.4-D, is utilized for callus production. For this reason, seedling per unit could be produced more than that of organogenesis.
    @article{Lestari11p63,
    title = {{Peranan Zat Pengatur Tumbuh dalam Perbanyakan Tanaman melalui Kultur Jaringan}},
    author = {E. G. Lestari},
    journal = {Jurnal AgroBiogen},
    pages = {63 - 68},
    volume = {7},
    number = {1},
    year = {2011},
    abstract = {In plant tissue culture, growth regulator has significant roles such as to control root and shoot development in the plant formation and callus induction. Cytokinin and auxin are two prominent growth regulator. Cytokinin consists of BA (benzil adenin), kinetin (furfuril amino purin), 2-Ip (dimethyl allyl amino purin), and zeatin. While auksin covers IAA (indone acetic acid), NAA (napthalene acetic acid), IBA (indole butiric acid) 2.4-D (2.4dicholophenoxy acetic acid), dicamba (3,6 dicloro-O-anisic acid), and picloram (4-amino 3,5,6-tricloropicolinic acid). The emphasis of plant growth purposes decide the use of growth regulator. Cytokinin is applied mainly for the purpose of shoot, while auxin is mainly used for the purpose of root and callus. The application of growth regulator application is varied, depending on the genotype and physiological condition of the plant. The existence of a certain growth regulating substances can enhance growth regulator activity of other substances. The type and concentration of the appropriate growth regulators for each plant is not the same because it depends on the genotype and physiological condition of plant tissue. However so often both are frequently required depend on the ratio/ratio of auxin cytokines or vice versa. The existence of a certain growth regulating substances can enhance growth regulator activity of other substances. The type and concentration of the appropriate growth regulators for each plant is not the same because it depends on the genotype and physiological condition of plant tissue. For the propagation, multiple and adventive shoots along with embriosomatic formation could be applied. The seedling is obtained from one somatic cell. Here, strong auxin, such as dicamba and picloram 2.4-D, is utilized for callus production. For this reason, seedling per unit could be produced more than that of organogenesis.},
    keywords = {growth culture, regulator, auxin, cytokinin, tissue},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_7_1_2011_08.pdf}
    }
  8. Tasma, I. M., A. Warsun, D. Satyawan, S. J. Pardal, and Slamet. 2011. Genetic Mapping of SSR Markers in Eight Soybean Chromosomes Based on F2 Population B3462 x B3293. Jurnal agrobiogen 7 (2):69-75.
    [BibTeX] [Abstract] [PDF: Genetic Mapping of SSR Markers in Eight Soybean Chromosomes Based on F2 Population B3462 x B3293 ]
    Peta Genetik Marka SSR pada Delapan Kromosom Kedelai Berdasarkan Populasi F2 B3462 x B3293. I Made Tasma, Ahmad Warsun, Dani Satyawan, Saptowo J. Pardal, dan Slamet. Keracunan aluminium merupakan salah satu kendala utama dalam budi daya kedelai pada lahan masam. Pemetaan genetik marka SSR merupakan langkah awal untuk mendeteksi quantitative trait loci (QTL) karakter toleran keracunan Al pada kedelai. Langkah lainnya, yaitu uji fenotipe populasi yang sama pada berbagai lingkungan keracunan Al. Tujuan dari penelitian ini adalah untuk menganalisis segregasi marka SSR pada populasi F2 dan memetakan marka SSR pada delapan kromosom kedelai. Populasi F2 sebelumnya dikembangkan dengan menyilangkan tetua toleran keracunan Al B3462 dan tetua sensitif keracunan Al B3293. Primer SSR ditapis untuk mendapatkan pasangan primer yang polimorfis pada kedua tetua. Pasangan primer yang polimorfis diamplikasikan dengan PCR pada DNA progeni populasi F2. Pita DNA dipisahkan menggunakan gel poliakrilamid atau gel agarose. Pola segregasi marka SSR pada progeni F2 diuji menggunakan uji Chi Kuadrat dengan hipotesis awal bahwa marka bersegregasi 1 : 2 : 1. Peta genetik dikonstruksi menggunakan program Mapmaker. Hasil penelitian menunjukkan bahwa 125 marka SSR polimorfis pada kedua tetua. Dari 125 marka SSR yang polimorfis, 122 bersegregasi 1 : 2 : 1. Hanya 8 marka SSR (5,6%) yang tidak bersegregasi 1 : 2 : 1. Seratus sembilan belas marka SSR telah dipetakan pada 8 kromosom kedelai. Delapan belas marka dipetakan pada kromosom A2, 10 pada kromosom B1, 16 (C1), 16 (F), 10 (G), 23 (J), 16 (L), dan 10 (N). Panjang peta genetik total yang telah diperoleh, 1.194,8 cM dengan rataan jarak genetik antar dua marka yang berdampingan, 10,7 cM. Diperlukan pengkayaan marka pada beberapa kromosom untuk mengurangi jurang pemisah (gap) antara dua marka. Peta genetik hasil studi ini tentunya akan bermanfaat untuk mendeteksi QTL toleransi keracunan Al pada kedelai.
    @article{Tasma11p69,
    title = {{Genetic Mapping of SSR Markers in Eight Soybean Chromosomes Based on F2 Population B3462 x B3293}},
    author = {I. M. Tasma and A. Warsun and D. Satyawan and S. J. Pardal and Slamet},
    journal = {Jurnal AgroBiogen},
    pages = {69 - 75},
    volume = {7},
    number = {2},
    year = {2011},
    abstract = {Peta Genetik Marka SSR pada Delapan Kromosom Kedelai Berdasarkan Populasi F2 B3462 x B3293. I Made Tasma, Ahmad Warsun, Dani Satyawan, Saptowo J. Pardal, dan Slamet. Keracunan aluminium merupakan salah satu kendala utama dalam budi daya kedelai pada lahan masam. Pemetaan genetik marka SSR merupakan langkah awal untuk mendeteksi quantitative trait loci (QTL) karakter toleran keracunan Al pada kedelai. Langkah lainnya, yaitu uji fenotipe populasi yang sama pada berbagai lingkungan keracunan Al. Tujuan dari penelitian ini adalah untuk menganalisis segregasi marka SSR pada populasi F2 dan memetakan marka SSR pada delapan kromosom kedelai. Populasi F2 sebelumnya dikembangkan dengan menyilangkan tetua toleran keracunan Al B3462 dan tetua sensitif keracunan Al B3293. Primer SSR ditapis untuk mendapatkan pasangan primer yang polimorfis pada kedua tetua. Pasangan primer yang polimorfis diamplikasikan dengan PCR pada DNA progeni populasi F2. Pita DNA dipisahkan menggunakan gel poliakrilamid atau gel agarose. Pola segregasi marka SSR pada progeni F2 diuji menggunakan uji Chi Kuadrat dengan hipotesis awal bahwa marka bersegregasi 1 : 2 : 1. Peta genetik dikonstruksi menggunakan program Mapmaker. Hasil penelitian menunjukkan bahwa 125 marka SSR polimorfis pada kedua tetua. Dari 125 marka SSR yang polimorfis, 122 bersegregasi 1 : 2 : 1. Hanya 8 marka SSR (5,6%) yang tidak bersegregasi 1 : 2 : 1. Seratus sembilan belas marka SSR telah dipetakan pada 8 kromosom kedelai. Delapan belas marka dipetakan pada kromosom A2, 10 pada kromosom B1, 16 (C1), 16 (F), 10 (G), 23 (J), 16 (L), dan 10 (N). Panjang peta genetik total yang telah diperoleh, 1.194,8 cM dengan rataan jarak genetik antar dua marka yang berdampingan, 10,7 cM. Diperlukan pengkayaan marka pada beberapa kromosom untuk mengurangi jurang pemisah (gap) antara dua marka. Peta genetik hasil studi ini tentunya akan bermanfaat untuk mendeteksi QTL toleransi keracunan Al pada kedelai.},
    keywords = {marka ssr, kedelai, keracunan aluminium, peta genetik, populasi f2},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_7_2_2011_69-75.pdf}
    }
  9. Utami, D. W., Sutoro, N. Hidayatun, A. Risliawati, and I. d. Hanarida. 2011. Keragaman Genetik 96 Aksesi Plasma Nutfah Padi Berdasarkan 30 Marka SSR Terpaut Gen Pengatur Waktu Pembungaan (HD Genes). Jurnal agrobiogen 7 (2):76-84.
    [BibTeX] [Abstract] [PDF: Keragaman Genetik 96 Aksesi Plasma Nutfah Padi Berdasarkan 30 Marka SSR Terpaut Gen Pengatur Waktu Pembungaan (HD Genes) ]
    Genetic Diversity of 96 Accession of Rice Germplasm Using 30 SSR Markers Linked to Heading Date Genes (HD Genes). Dwinita W. Utami, Sutoro, Nurul Hidayatun, Andari Risliawati, and Ida Hanarida. Rice with early maturity is one of an important genetic resources in rice germplasm collection. Characterization and identification of genetic diversity is an important issue for plant variety protection. Molecular identification by microsatellite markers using Genetic Analyzer enables resolve of this issue. The objective of this research is to identify the genetic diversity of 96 rice accessions based on their specific DNA fingerprint using microsatellite markers. A total of 96 accessions consisting of a diverse variety of maturity classification were genotyped with 30 SSR markers linked to HD genes which spread out in 12 chromosomes of rice geneome. The total 297 alleles were detected indicated the level of marker informativeness. RM5607 generated 7 allele with the size range from 103 to 197 and the highest PIC at 0.90. RM3571 (linked to HD12 gene) has a significant value associated with varieties which have early maturity trait. Clustering analysis showed the cluster based on Sub Species genome background and on early maturity trait
    @article{Utami11p76,
    title = {{Keragaman Genetik 96 Aksesi Plasma Nutfah Padi Berdasarkan 30 Marka SSR Terpaut Gen Pengatur Waktu Pembungaan (HD Genes)}},
    author = {D. W. Utami and Sutoro and N. Hidayatun and A. Risliawati and d. I. Hanarida},
    journal = {Jurnal AgroBiogen},
    pages = {76 - 84},
    volume = {7},
    number = {2},
    year = {2011},
    abstract = {Genetic Diversity of 96 Accession of Rice Germplasm Using 30 SSR Markers Linked to Heading Date Genes (HD Genes). Dwinita W. Utami, Sutoro, Nurul Hidayatun, Andari Risliawati, and Ida Hanarida. Rice with early maturity is one of an important genetic resources in rice germplasm collection. Characterization and identification of genetic diversity is an important issue for plant variety protection. Molecular identification by microsatellite markers using Genetic Analyzer enables resolve of this issue. The objective of this research is to identify the genetic diversity of 96 rice accessions based on their specific DNA fingerprint using microsatellite markers. A total of 96 accessions consisting of a diverse variety of maturity classification were genotyped with 30 SSR markers linked to HD genes which spread out in 12 chromosomes of rice geneome. The total 297 alleles were detected indicated the level of marker informativeness. RM5607 generated 7 allele with the size range from 103 to 197 and the highest PIC at 0.90. RM3571 (linked to HD12 gene) has a significant value associated with varieties which have early maturity trait. Clustering analysis showed the cluster based on Sub Species genome background and on early maturity trait},
    keywords = {dna fingerprinting, ssr marker, hd genes, early maturity trait},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_7_2_2011_76-84.pdf}
    }
  10. Priyatno, T. P., Y. A. Dahliani, Y. Suryadi, I. M. Samudra, D. N. Susilowati, I. Rusmana, B. S. Wibowo, and C. d. Irwan. 2011. Identifikasi Entomopatogen Bakteri Merah pada Wereng Batang Coklat (Nilaparvata lugens Stål.). Jurnal agrobiogen 2 (1):85-95.
    [BibTeX] [Abstract] [PDF: Identifikasi Entomopatogen Bakteri Merah pada Wereng Batang Coklat (Nilaparvata lugens Stål.) ]
    Red bacteria isolated from brown planthopper (BPH) has been proven pathogenic against BPH and others insects. Application of 106 to 107 cells/ml of red bacteria caused 65.6-78.2% mortality of BPH. The 50% effective concentration (EC50) and lethal time of red bacteria against BPH is 2.8 x 105 cells/ml and 6.8 days, respectively. Based on phenotypic characters tested on GN MicroPlateTM Biolog kit and 16S rRNA sequneces analysis, red bacteria was identified as Serratia marcescens with 99% similarity. Red pigmen produced by S. marcescens strain BPH is secondary metabolite determined as prodigiosin showing bactericidal activities against Xanthomonas oryzae pv. oryzae. We concluded that S. marcescens did not only potent as biocontrol agent to BPH, but also it can be used to control plant pathogenic bacteria.
    @article{Priyatno11p85,
    title = {{Identifikasi Entomopatogen Bakteri Merah pada Wereng Batang Coklat (Nilaparvata lugens St{\aa{}}l.)}},
    author = {T. P. Priyatno and Y. A. Dahliani and Y. Suryadi and I. M. Samudra and D. N. Susilowati and I. Rusmana and B. S. Wibowo and d. C. Irwan},
    journal = {Jurnal AgroBiogen},
    pages = {85 - 95},
    volume = {2},
    number = {1},
    year = {2011},
    abstract = {Red bacteria isolated from brown planthopper (BPH) has been proven pathogenic against BPH and others insects. Application of 106 to 107 cells/ml of red bacteria caused 65.6-78.2% mortality of BPH. The 50% effective concentration (EC50) and lethal time of red bacteria against BPH is 2.8 x 105 cells/ml and 6.8 days, respectively. Based on phenotypic characters tested on GN MicroPlateTM Biolog kit and 16S rRNA sequneces analysis, red bacteria was identified as Serratia marcescens with 99% similarity. Red pigmen produced by S. marcescens strain BPH is secondary metabolite determined as prodigiosin showing bactericidal activities against Xanthomonas oryzae pv. oryzae. We concluded that S. marcescens did not only potent as biocontrol agent to BPH, but also it can be used to control plant pathogenic bacteria.},
    keywords = {entomopathogenic bacteria, nilaparvata lugens, serratia marcescens, prodigiosin},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_7_2_2011_85-95.pdf}
    }
  11. Chaerani, N. Hidayatun, and D. W. d. Utami. 2011. Keragaman Genetik 50 Aksesi Plasma Nutfah Kedelai Berdasarkan Sepuluh Penanda Mikrosatelit. Jurnal agrobiogen 7 (2):96-105.
    [BibTeX] [Abstract] [PDF: Keragaman Genetik 50 Aksesi Plasma Nutfah Kedelai Berdasarkan Sepuluh Penanda Mikrosatelit ]
    Soybean accessions in germplasm collection have increased in number as a result of exploration, introduction as well as development or release of new commercial varieties. This complicates accurate and reliable evaluation of an accession for purposes of utilization in breeding program and discrimination of a new commercial variety for purposes of plant variety protection. The aims of this study were to identify the genetic diversity of soybean germplasm to complement the existing phenotypic database as the basis for efficient management and accurate discrimination of commercial varieties, and to identify potential parents for hybridizations. Fifty soybean accessions consisting of 12 released varieties, 32 local varieties, and 6 introductions were analyzed using microsatellite DNA markers based on semi-automatic sizing system. A total of 86 alleles were detected with the number of alleles per locus ranged from 4 to 16. Rare alleles were detected at a rate of 53% which was shown by 68% of the genotypes. Informativeness of the microsatellite markers as measured by the average gene diversity (D) or polymorphism information content (PIC) was 0.60 and 0.58, respectively. A heterozygosity level of 0.09 as detected by seven loci was observed among 64% of the genotypes. The average genetic distance among the genotypes was 0.56, which indicated the relatively low polymorphism among the analyzed soybean germplasm. Four microsatellites that showed a high D or PIC value (over 0.75) were able to discriminate between accession reliably. Each soybean accession had different DNA microsatellite fingerprint which can be used for accurate discrimination to complement the previous conventional characterizations. UPGMA clustering separated the 50 accessions into 10 major clusters, which showed no clear pattern of clustering according to varietal group or geographical origin. Genetic similarity data identified five clusters and 15 genotypes with highest intercluster or inter-genotype genetic distances which are potential candidates to be exploited as parents in hybridizations for development of new commercial varieties.
    @article{Chaerani11p96,
    title = {{Keragaman Genetik 50 Aksesi Plasma Nutfah Kedelai Berdasarkan Sepuluh Penanda Mikrosatelit}},
    author = {Chaerani and N. Hidayatun and d. D. W. Utami},
    journal = {Jurnal AgroBiogen},
    pages = {96 - 105},
    volume = {7},
    number = {2},
    year = {2011},
    abstract = {Soybean accessions in germplasm collection have increased in number as a result of exploration, introduction as well as development or release of new commercial varieties. This complicates accurate and reliable evaluation of an accession for purposes of utilization in breeding program and discrimination of a new commercial variety for purposes of plant variety protection. The aims of this study were to identify the genetic diversity of soybean germplasm to complement the existing phenotypic database as the basis for efficient management and accurate discrimination of commercial varieties, and to identify potential parents for hybridizations. Fifty soybean accessions consisting of 12 released varieties, 32 local varieties, and 6 introductions were analyzed using microsatellite DNA markers based on semi-automatic sizing system. A total of 86 alleles were detected with the number of alleles per locus ranged from 4 to 16. Rare alleles were detected at a rate of 53% which was shown by 68% of the genotypes. Informativeness of the microsatellite markers as measured by the average gene diversity (D) or polymorphism information content (PIC) was 0.60 and 0.58, respectively. A heterozygosity level of 0.09 as detected by seven loci was observed among 64% of the genotypes. The average genetic distance among the genotypes was 0.56, which indicated the relatively low polymorphism among the analyzed soybean germplasm. Four microsatellites that showed a high D or PIC value (over 0.75) were able to discriminate between accession reliably. Each soybean accession had different DNA microsatellite fingerprint which can be used for accurate discrimination to complement the previous conventional characterizations. UPGMA clustering separated the 50 accessions into 10 major clusters, which showed no clear pattern of clustering according to varietal group or geographical origin. Genetic similarity data identified five clusters and 15 genotypes with highest intercluster or inter-genotype genetic distances which are potential candidates to be exploited as parents in hybridizations for development of new commercial varieties.},
    keywords = {dna fingerprinting, microsatellite, automatic sizing, soybean genetic diversity, variety identification, genetic improvement},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_7_2_2011_96-105.pdf}
    }
  12. dan. Mulyana, Sukmadjaja. D. A.. 2011. Regenerasi dan Pertumbuhan Beberapa Varietas Tebu (Saccharum officinarum L.) Secara In Vitro. Jurnal agrobiogen 7 (2):106-118.
    [BibTeX] [Abstract] [PDF: Regenerasi dan Pertumbuhan Beberapa Varietas Tebu (Saccharum officinarum L.) Secara In Vitro ]
    The research was conducted at the Laboratory of Tissue Culture The Biology of Cell and Tissue Researcher Group ICABIOGRAD, Bogor from June to November 2009 to studied growth and regenerations response some varieties of sugarcane through in vitro culture. The research activities have been carried out in three steps, i.e., callus formation, regeneration of shoots and roots regeneration. The type of explants used in the study was in vitro planlet explants of both sugarcane varieties. Seven media formulations were used for the callus induction and regeneration of shoots, while five media formulations were used for the roots regeneration. The results showed that the highest respond for calluses induction was Bulu Lawang varieties at media formulation MS + 2.4-D 2 mg.l-1 + BAP 0.4 mg.l-1 + CH 2000 mg.l-1 and PS 951 varieties at media formulation MS + 2.4-D 1 mg.l-1 + BAP 0.4 mg.l-1. While the highest respond for regeneration of shoots was Bulu Lawang varieties at media formulation MS0 (control MS) dan PS 951 varieties at media formulation MS + BAP 1 mg.l-1 + kinetin 1 mg.l-1 + NAA 0.5 mg.l-1 + GA3 0.5 mg.l-1. The highest respond of roots regeneration was Bulu Lawang and PS 951 varieties at media formulation MS + IBA 1 mg.l-1. Acclimatization of plantlets produced were grew successfully about 90-100% in greenhouse.
    @article{Mulyana11p106,
    title = {{Regenerasi dan Pertumbuhan Beberapa Varietas Tebu (Saccharum officinarum L.) Secara In Vitro}},
    author = {D. Sukmadjaja. dan. A. Mulyana},
    journal = {Jurnal AgroBiogen},
    pages = {106 - 118},
    volume = {7},
    number = {2},
    year = {2011},
    abstract = {The research was conducted at the Laboratory of Tissue Culture The Biology of Cell and Tissue Researcher Group ICABIOGRAD, Bogor from June to November 2009 to studied growth and regenerations response some varieties of sugarcane through in vitro culture. The research activities have been carried out in three steps, i.e., callus formation, regeneration of shoots and roots regeneration. The type of explants used in the study was in vitro planlet explants of both sugarcane varieties. Seven media formulations were used for the callus induction and regeneration of shoots, while five media formulations were used for the roots regeneration. The results showed that the highest respond for calluses induction was Bulu Lawang varieties at media formulation MS + 2.4-D 2 mg.l-1 + BAP 0.4 mg.l-1 + CH 2000 mg.l-1 and PS 951 varieties at media formulation MS + 2.4-D 1 mg.l-1 + BAP 0.4 mg.l-1. While the highest respond for regeneration of shoots was Bulu Lawang varieties at media formulation MS0 (control MS) dan PS 951 varieties at media formulation MS + BAP 1 mg.l-1 + kinetin 1 mg.l-1 + NAA 0.5 mg.l-1 + GA3 0.5 mg.l-1. The highest respond of roots regeneration was Bulu Lawang and PS 951 varieties at media formulation MS + IBA 1 mg.l-1. Acclimatization of plantlets produced were grew successfully about 90-100% in greenhouse.},
    keywords = {sugarcane, varieties, media formulation, growth, regeneration},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_7_2_2011_106-118.pdf}
    }
  13. Hidayatun, N., Chaerani, and D. W. d. Utami. 2011. Sidik Jari DNA 88 Plasma Nutfah Ubi Jalar di Indonesia Berdasarkan Delapan Penanda SSR. Jurnal agrobiogen 7 (2):119-127.
    [BibTeX] [Abstract] [PDF: Sidik Jari DNA 88 Plasma Nutfah Ubi Jalar di Indonesia Berdasarkan Delapan Penanda SSR ]
    Indonesia possesses a great number of sweet potato varieties. Understanding the diversity and distribution of this genetic resource is essential for its management and future use. The objective of this study was to elaborate the molecular character as DNA finger print of Indonesian sweet potato germplasm. Eight fluorescent labeled SSR primers were used to amplify DNA of 88 sweet potato accessions consisting of improved varieties and landraces collected from 7 islands in Indonesia. The amplified products were detected using capillary electrophoresis method in CEQ Genetic Analysis System machine. A total of 135 alleles ranging from 8 to 36 alleles per locus with an average of 17 alleles were generated. Each accession had a unique microsatellite finger print marked by specific combination of 11 to 22 alleles in 8 SSR loci. Dendrogram generated by UPGMA based on simple matching coefficients produced 4 nonspecific groups at 80% similarity. The groups revealed the possibilities that the accessions were distributed from similar genetic resources.
    @article{Hidayatun11p119,
    title = {{Sidik Jari DNA 88 Plasma Nutfah Ubi Jalar di Indonesia Berdasarkan Delapan Penanda SSR}},
    author = {N. Hidayatun and Chaerani and d. D. W. Utami},
    journal = {Jurnal AgroBiogen},
    pages = {119 - 127},
    volume = {7},
    number = {2},
    year = {2011},
    abstract = {Indonesia possesses a great number of sweet potato varieties. Understanding the diversity and distribution of this genetic resource is essential for its management and future use. The objective of this study was to elaborate the molecular character as DNA finger print of Indonesian sweet potato germplasm. Eight fluorescent labeled SSR primers were used to amplify DNA of 88 sweet potato accessions consisting of improved varieties and landraces collected from 7 islands in Indonesia. The amplified products were detected using capillary electrophoresis method in CEQ Genetic Analysis System machine. A total of 135 alleles ranging from 8 to 36 alleles per locus with an average of 17 alleles were generated. Each accession had a unique microsatellite finger print marked by specific combination of 11 to 22 alleles in 8 SSR loci. Dendrogram generated by UPGMA based on simple matching coefficients produced 4 nonspecific groups at 80% similarity. The groups revealed the possibilities that the accessions were distributed from similar genetic resources.},
    keywords = {sweet potato, dna fingerprinting, ssr marker},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_7_2_2011_119-127.pdf}
    }
  14. Bahagiawati. 2011. Plot Refugi untuk Pengelolaan Resistensi Hama terhadap Tanaman Transgenik Bt. Jurnal agrobiogen 7 (2):128-137.
    [BibTeX] [Abstract] [PDF: Plot Refugi untuk Pengelolaan Resistensi Hama terhadap Tanaman Transgenik Bt ]
    The objective of this review is to share information on several cases of target insects became resistance to transgenic-Bt crops in the field and the refuge strategy used to manage this problem. Bt corn and Bt cotton have been planted widely for several years globally. One of the risks of planting transgenic Bt crop is the ability of the target insects adapted to the Bt protein and caused the resistance breakdown the transgenic Bt plants. This phenomenon was hypothesized in early 1990s based on the cases of several insects resistance to microbial Bt sprayed in laboratories and in the field. The mode of action of the pest resistance to Bt-toxin have been studied in several laboratories. In USA, to avoid the target insect resistance to transgenic Bt crops, a program called Insect Resistance Management (IRM) has been applied since 2001 for farmers growing Bt crops. Lately, there have been some reports of target insects became resistance to cry1F, cry1Ab, and cry1Ac in transgenic Bt crops. A report informed about the resistance of target insect in Puerto Rico was published in 2006, and so in South Africa in 2006/2007, and the last one in India in 2009. To avoid target’s insect become resistance to Bt crops, a program called structural IRM and unstructural IRM were introduced and applied in several countries. One of the components of IRM is planting refuge plot, a plot that planting with isogenic line of Bt crops in/near by the area of Bt crops. This review will discuss about the cases of target insect became resistance to Bt crops in the field, mode of action of insect resistance to Bt, the model of IRM program in USA and the Philippines and finally the recommendation for Indonesia to prepare its IRM program for implementing Bt crops.
    @article{Bahagiawati11p128,
    title = {{Plot Refugi untuk Pengelolaan Resistensi Hama terhadap Tanaman Transgenik Bt}},
    author = {Bahagiawati},
    journal = {Jurnal AgroBiogen},
    pages = {128 - 137},
    volume = {7},
    number = {2},
    year = {2011},
    abstract = {The objective of this review is to share information on several cases of target insects became resistance to transgenic-Bt crops in the field and the refuge strategy used to manage this problem. Bt corn and Bt cotton have been planted widely for several years globally. One of the risks of planting transgenic Bt crop is the ability of the target insects adapted to the Bt protein and caused the resistance breakdown the transgenic Bt plants. This phenomenon was hypothesized in early 1990s based on the cases of several insects resistance to microbial Bt sprayed in laboratories and in the field. The mode of action of the pest resistance to Bt-toxin have been studied in several laboratories. In USA, to avoid the target insect resistance to transgenic Bt crops, a program called Insect Resistance Management (IRM) has been applied since 2001 for farmers growing Bt crops. Lately, there have been some reports of target insects became resistance to cry1F, cry1Ab, and cry1Ac in transgenic Bt crops. A report informed about the resistance of target insect in Puerto Rico was published in 2006, and so in South Africa in 2006/2007, and the last one in India in 2009. To avoid target's insect become resistance to Bt crops, a program called structural IRM and unstructural IRM were introduced and applied in several countries. One of the components of IRM is planting refuge plot, a plot that planting with isogenic line of Bt crops in/near by the area of Bt crops. This review will discuss about the cases of target insect became resistance to Bt crops in the field, mode of action of insect resistance to Bt, the model of IRM program in USA and the Philippines and finally the recommendation for Indonesia to prepare its IRM program for implementing Bt crops.},
    keywords = {refuge, insect resistance, bacillus thuringiensis, irm},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_7_2_2011_128-137.pdf}
    }

2010

  1. Utami, Dwinita W., Endang M. Septiningsih, Triny S. Kadir, Fatimah, and Siti Yuriyah. 2010. Allele Mining of Bacterial Blight Resistance Gene, Xa7 on Indonesian Local Rice Germplasm. Jurnal agrobiogen 6 (1):1-9.
    [BibTeX] [Abstract] [PDF: Allele Mining of Bacterial Blight Resistance Gene, Xa7 on Indonesian Local Rice Germplasm ]
    The abundance of novel genetic variation existing in germplasm collections is the foundation for variety improvement in plant breeding program. Nevertheless, studies on Indonesian genetic diversity rice germplasm using molecular markers are still poorly. Recent advances in utilizing of simple sequence repeat (SSR) in QTL mapping and whole rice genome sequences were positive support on genetic diversity of rice germplasm research. Based on these advance technology, we developed the research to discover new alleles at important gene loci that can be used for rice improvement. This approach is recognized as allele mining technology. On this study the target genes for allele mining research is the resistance gene for bacterial leaf blight pathogen, Xa7. This point was introduced by identify the genetic diversity of 96 accessions Indonesian local rice germplasm. The Xa7 allele mining was done by SNP (single nucleotide polymorphism) designing primers based on DNA sequence around the gene target. The significant LD map was detected by association mapping between phenotype and SNP genotyping data of the selected germplasm which having superior performance on BLB resistance and representing on genetic diversity clustering. The results shown that Xa7 allele variation were found in Parekaligolara (Indica, 15141), and Gajah Mada (Indica, 5856), which resistant to BLB races IV and VIII on generative stage and field condition. The significant Xa7-SNP8 and Xa7-SNP11 markers were associating with the LD map position of Xa7 gene on 28, 05-28,1Mb of chromosome 6 in rice genome.
    @article{Utami10p1,
    title = {{Allele Mining of Bacterial Blight Resistance Gene, Xa7 on Indonesian Local Rice Germplasm}},
    author = {Dwinita W. Utami and Endang M. Septiningsih and Triny S. Kadir and Fatimah and Siti Yuriyah},
    journal = {Jurnal AgroBiogen},
    pages = {1 - 9},
    volume = {6},
    number = {1},
    year = {2010},
    abstract = {The abundance of novel genetic variation existing in germplasm collections is the foundation for variety improvement in plant breeding program. Nevertheless, studies on Indonesian genetic diversity rice germplasm using molecular markers are still poorly. Recent advances in utilizing of simple sequence repeat (SSR) in QTL mapping and whole rice genome sequences were positive support on genetic diversity of rice germplasm research. Based on these advance technology, we developed the research to discover new alleles at important gene loci that can be used for rice improvement. This approach is recognized as allele mining technology. On this study the target genes for allele mining research is the resistance gene for bacterial leaf blight pathogen, Xa7. This point was introduced by identify the genetic diversity of 96 accessions Indonesian local rice germplasm. The Xa7 allele mining was done by SNP (single nucleotide polymorphism) designing primers based on DNA sequence around the gene target. The significant LD map was detected by association mapping between phenotype and SNP genotyping data of the selected germplasm which having superior performance on BLB resistance and representing on genetic diversity clustering. The results shown that Xa7 allele variation were found in Parekaligolara (Indica, 15141), and Gajah Mada (Indica, 5856), which resistant to BLB races IV and VIII on generative stage and field condition. The significant Xa7-SNP8 and Xa7-SNP11 markers were associating with the LD map position of Xa7 gene on 28, 05-28,1Mb of chromosome 6 in rice genome.},
    keywords = {xa7, allele mining, indonesian rice local},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_6_1_2010_1-9.pdf},
    note = {Pencarian Alel untuk Identifikasi Gen Ketahanan Penyakit Hawar Daun Bakteri, Xa7 pada Plasma Nutfah Padi Lokal Indonesia}
    }
  2. Roberdi, Hajrial Aswidinnoor, Asep Setiawan, Sutrisno, Marcia B. Pabendon, and M. Azrai. 2010. Linkage of 23 Microsatellite Marker on Chromosome 6 and 7 to Downy Mildew Resistance on Maize. Jurnal agrobiogen 6 (1):10-17.
    [BibTeX] [Abstract] [PDF: Linkage of 23 Microsatellite Marker on Chromosome 6 and 7 to Downy Mildew Resistance on Maize ]
    Downy mildew caused by Peronosclerospora is one of most important maize disease in several countries, including Indonesia. Parental and progenies selection based on conventional breeding is time consuming and laborious. Development of molecular biology produces many DNA markers used for selection, one of them is microsatellite. The aim of this research to identify microsatellite markers associated with downy mildew resistance on maize progeny MR-4 X AMATLCOHS-9-1-1-1-11-2-B, on chromosome 6 and 7. This research was consisted of two activities, phenotypic and genotypic analysis. Phenotypic analysis used 175 progenies BC1F2 and both of parents. This analysis included planting of spreading row, inoculums preparation, inoculation of spreader rows, test material planting, inoculation of test material and observation. Genotypic analysis used 175 progenies BC1F1 and both of parents. This analysis included DNA genome isolation, PCR analysis, electrophoresis, gel staining and data scoring. Percentage of downy mildew infections on MR-4 was 76%, while these on AMATLCOHS-9-1-1-1-1-1-2-B was 16%, and on 175 progenies had range from 10.1-100%. Out of 23 SSR, 12 markers could be mapped in chromosome 6 and 11 markers in chromosome 7. QTL analyses showed that chromosome 7 contain one QTL in position between phi082 and phi116I marker as far as 18.6 cM with 2.6 LOD value.
    @article{Roberdi10p10,
    title = {{Linkage of 23 Microsatellite Marker on Chromosome 6 and 7 to Downy Mildew Resistance on Maize}},
    author = {Roberdi and Hajrial Aswidinnoor and Asep Setiawan and Sutrisno and Marcia B.
    Pabendon and M. Azrai},
    journal = {Jurnal AgroBiogen},
    pages = {10 - 17},
    volume = {6},
    number = {1},
    year = {2010},
    abstract = {Downy mildew caused by Peronosclerospora is one of most important maize disease in several countries, including Indonesia. Parental and progenies selection based on conventional breeding is time consuming and laborious. Development of molecular biology produces many DNA markers used for selection, one of them is microsatellite. The aim of this research to identify microsatellite markers associated with downy mildew resistance on maize progeny MR-4 X AMATLCOHS-9-1-1-1-11-2-B, on chromosome 6 and 7. This research was consisted of two activities, phenotypic and genotypic analysis. Phenotypic analysis used 175 progenies BC1F2 and both of parents. This analysis included planting of spreading row, inoculums preparation, inoculation of spreader rows, test material planting, inoculation of test material and observation. Genotypic analysis used 175 progenies BC1F1 and both of parents. This analysis included DNA genome isolation, PCR analysis, electrophoresis, gel staining and data scoring. Percentage of downy mildew infections on MR-4 was 76%, while these on AMATLCOHS-9-1-1-1-1-1-2-B was 16%, and on 175 progenies had range from 10.1-100%. Out of 23 SSR, 12 markers could be mapped in chromosome 6 and 11 markers in chromosome 7. QTL analyses showed that chromosome 7 contain one QTL in position between phi082 and phi116I marker as far as 18.6 cM with 2.6 LOD value.},
    keywords = {quantitative trait loci, microsatellite marker, downy mildew-disease, peronosclerospora maydis, zea mays},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_6_1_2010_10-19.pdf},
    note = {Keterpautan 23 Marka Mikrosatelit pada Kromosom 6 dan 7 dengan Karakter Ketahanan Populasi Jagung terhadap Penyakit Bulai (Peronosclerospora maydis)}
    }
  3. Purnamaningsih, Ragapadmi. 2010. Introduction of DefH9-iaaM and DefH9-RI-iaaM Gene Into Tomato Genome Using Agrobacterium tumefaciens. Jurnal agrobiogen 6 (1):18-25.
    [BibTeX] [Abstract] [PDF: Introduction of DefH9-iaaM and DefH9-RI-iaaM Gene Into Tomato Genome Using Agrobacterium tumefaciens ]
    Plant genetic improvement can be conducted through genetic engineering. Parthenocarpic fruit production could increase fruit production and its qulities. IAA genes were introduced into three tomato cultivars Ratna, Opal and LV 6117 using two constract genes DefH9-iaaM and DefH9-RI-iaaM. The iaaM gene is able to increase auxin biosynthesis in transgenic plant cells and organs because indol-eacetamide, synthesized by the product of the iaaM gene, is converted either chemically or enzimatically to indole-3-acetic acid (IAA), while the promotor DefH9 enable IAA gene expressed specifically in the ovules. The objectives of this experiment was to identify gene introduction into plant genom of three tomato cultivars. The factors tested were two constract of IAA genes (DefH9-iaaM or DefH9-RI-iaaM), tomato cultivars (Ratna, Opal, and LV 6117) and time of explant inoculation (5, 15, 30 minute). The result showed that the best time inoculation was 5 minute. Otherwise three tomato cultivars response better to DefH9-RI-iaaM than DefH9-iaaM. The total efficiency of regeneration and total efficiency of transformation of both genes were 25.38% and 20.32%. PCR analysis showed that 10 plant have positive PCR, were 1 plant carried (Opal) DefH9-iaaM gene and 9 plant (Ratna, Opal, LV 6117) carried DefH9-RI-iaaM gene.
    @article{RagapadmiPurnamaningsih10p18,
    title = {{Introduction of DefH9-iaaM and DefH9-RI-iaaM Gene Into Tomato Genome Using Agrobacterium tumefaciens}},
    author = {Ragapadmi Purnamaningsih},
    journal = {Jurnal AgroBiogen},
    pages = {18 - 25},
    volume = {6},
    number = {1},
    year = {2010},
    abstract = {Plant genetic improvement can be conducted through genetic engineering. Parthenocarpic fruit production could increase fruit production and its qulities. IAA genes were introduced into three tomato cultivars Ratna, Opal and LV 6117 using two constract genes DefH9-iaaM and DefH9-RI-iaaM. The iaaM gene is able to increase auxin biosynthesis in transgenic plant cells and organs because indol-eacetamide, synthesized by the product of the iaaM gene, is converted either chemically or enzimatically to indole-3-acetic acid (IAA), while the promotor DefH9 enable IAA gene expressed specifically in the ovules. The objectives of this experiment was to identify gene introduction into plant genom of three tomato cultivars. The factors tested were two constract of IAA genes (DefH9-iaaM or DefH9-RI-iaaM), tomato cultivars (Ratna, Opal, and LV 6117) and time of explant inoculation (5, 15, 30 minute). The result showed that the best time inoculation was 5 minute. Otherwise three tomato cultivars response better to DefH9-RI-iaaM than DefH9-iaaM. The total efficiency of regeneration and total efficiency of transformation of both genes were 25.38% and 20.32%. PCR analysis showed that 10 plant have positive PCR, were 1 plant carried (Opal) DefH9-iaaM gene and 9 plant (Ratna, Opal, LV 6117) carried DefH9-RI-iaaM gene.},
    keywords = {transformation, tomato, genetic engineering},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_6_1_2010_18-25.pdf},
    note = {Introduksi Gen DefH9-iaaM dan DefH9-RI-iaaM ke dalam Genom Tanaman Tomat Menggunakan Vektor Agrobacterium tumefaciens}
    }
  4. Lestari, Endang G., Ragapadmi Purnamaningsih, M. Syukur, and Rosa Yunita. 2010. Somaclonal Variability for the Improvement of Plants Artemisia (Artemisia annua L.) By In Vitro Culture. Jurnal agrobiogen 6 (1):26-32.
    [BibTeX] [Abstract] [PDF: Somaclonal Variability for the Improvement of Plants Artemisia (Artemisia annua L.) By In Vitro Culture ]
    Artemisia annua L., a family member of Asteraceae, is medicinal plants originated from China. The plant has been widely used by the local people for malaria remedy. Its active substance, artemisine, has been proved to hamper the malaria bacteria incubation, Plasmodium sp. In accordance with the WHO recomendation, the Department of Health of Indonesia is now in the attempt of developing this plant as the subtitute of chloroquin because of the malaria bacteria resistance to this antidote. In Indonesia, the artemisine content of the plant less than 0,5% is the crucial problem leading no investors are interested in its economic value. Therefore, Indonesian Medicinal and Spice Crops Research Institute; BPTO Tawangmangu, Indonesian Institute of Sciences; and PT Kimia Farma cooperate for obtaining the prime clone by breeding, selection, as well as environmental adaptation. In coping with the problem, ICABIOGRAD in the collaboration with Bogor Agricultural University have conducted the research for genetic improvement through mutative induction and field selection. This research on somaclonal variation. was conducted from Januari 2006 to Juni 2008. Eksplan used for experiment were shoots radiated with 10-100 Gy gamma ray. The result showed that the shoot radiated with the dosage of 70-100 Gy was unable to grow. On the other hand, the high level of multiplication was acquired in the one radiated with 10-30 Gy. The optimum radiation for somaclonal radiation was eventually gained with 40-60 Gy. The somaclone lines with 10-60 Gy radiation have been aclimatized and planted in Gunung Putri plot in the elevation of 1545 asl. Artemisinin content at the high biomases genotype is 0,49-0,52%.
    @article{Lestari10p26,
    title = {{Somaclonal Variability for the Improvement of Plants Artemisia (Artemisia annua L.) By In Vitro Culture}},
    author = {Endang G. Lestari and Ragapadmi Purnamaningsih and M. Syukur and Rosa Yunita},
    journal = {Jurnal AgroBiogen},
    pages = {26 - 32},
    volume = {6},
    number = {1},
    year = {2010},
    abstract = {Artemisia annua L., a family member of Asteraceae, is medicinal plants originated from China. The plant has been widely used by the local people for malaria remedy. Its active substance, artemisine, has been proved to hamper the malaria bacteria incubation, Plasmodium sp. In accordance with the WHO recomendation, the Department of Health of Indonesia is now in the attempt of developing this plant as the subtitute of chloroquin because of the malaria bacteria resistance to this antidote. In Indonesia, the artemisine content of the plant less than 0,5% is the crucial problem leading no investors are interested in its economic value. Therefore, Indonesian Medicinal and Spice Crops Research Institute; BPTO Tawangmangu, Indonesian Institute of Sciences; and PT Kimia Farma cooperate for obtaining the prime clone by breeding, selection, as well as environmental adaptation. In coping with the problem, ICABIOGRAD in the collaboration with Bogor Agricultural University have conducted the research for genetic improvement through mutative induction and field selection. This research on somaclonal variation. was conducted from Januari 2006 to Juni 2008. Eksplan used for experiment were shoots radiated with 10-100 Gy gamma ray. The result showed that the shoot radiated with the dosage of 70-100 Gy was unable to grow. On the other hand, the high level of multiplication was acquired in the one radiated with 10-30 Gy. The optimum radiation for somaclonal radiation was eventually gained with 40-60 Gy. The somaclone lines with 10-60 Gy radiation have been aclimatized and planted in Gunung Putri plot in the elevation of 1545 asl. Artemisinin content at the high biomases genotype is 0,49-0,52%.},
    keywords = {artemisia annua l, artemisinine, somaclone, varieties, gamma ray},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_6_1_2010_26-32.pdf},
    note = {Keragaman Somaklonal untuk Perbaikan Tanaman Artemisia (Artemisia annua L.) Melalui Kultur In Vitro}
    }
  5. Kosmiatin, Mia, Rosa Yunita, and Ali Husni. 2010. Aluminum Tolerance Improvement of Rootstock Citrus through Repeated In Vitro Selection. Jurnal agrobiogen 6 (1):33-39.
    [BibTeX] [Abstract] [PDF: Aluminum Tolerance Improvement of Rootstock Citrus through Repeated In Vitro Selection ]
    National orange productivity was trend to decrease because of pathogen attack and reducing of planting area. One of alternative ways to preserve and increase orange productivity was using marginal soil mainly acid soil. This matter pushed the breeder to prepare tolerant rootstock and stable in the acid soil. In vitro culture technique was effective and efficient methods to produce tolerant and stable rootstock in acid soil through simulation of acid soil with addition of high aluminum and low pH in the medium. By the simulation the selection could be done in cell level, so cell was selected after induction of variation. A rootstock which high compatibility with scion, useful rooting, and aluminum tolerance could be increased orange productivity through acid soil development. The research was conducted in 3 phase: (1) induction of embryogenic calli, (2) improvement of genetic variation through mutation, and (3) In vitro selection with AlCl3.6H2O for aluminum and low pH tolerant. Immature embryos of rootstock were use as explant. The result showed that the best embryogenic calli were induced on MS basal medium with MW vitamin + NAA 7,5 mg/l + kinetin 0,5 mg/l. Before selection, 1.000 rad dosage was the most tolerant dosage to growth embryogenic calli. After selection, 2.000 rad dosage was the best dosage to produce shoots which stable tolerant to aluminum. Selected 88 mutant shoots were produced after three times selection on the same medium which AlCl3.6H2O added at low pH.
    @article{MiaKosmiatin10p33,
    title = {{Aluminum Tolerance Improvement of Rootstock Citrus through Repeated In Vitro Selection}},
    author = {Mia Kosmiatin and Rosa Yunita and Ali Husni},
    journal = {Jurnal AgroBiogen},
    pages = {33 - 39},
    volume = {6},
    number = {1},
    year = {2010},
    abstract = {National orange productivity was trend to decrease because of pathogen attack and reducing of planting area. One of alternative ways to preserve and increase orange productivity was using marginal soil mainly acid soil. This matter pushed the breeder to prepare tolerant rootstock and stable in the acid soil. In vitro culture technique was effective and efficient methods to produce tolerant and stable rootstock in acid soil through simulation of acid soil with addition of high aluminum and low pH in the medium. By the simulation the selection could be done in cell level, so cell was selected after induction of variation. A rootstock which high compatibility with scion, useful rooting, and aluminum tolerance could be increased orange productivity through acid soil development. The research was conducted in 3 phase: (1) induction of embryogenic calli, (2) improvement of genetic variation through mutation, and (3) In vitro selection with AlCl3.6H2O for aluminum and low pH tolerant. Immature embryos of rootstock were use as explant. The result showed that the best embryogenic calli were induced on MS basal medium with MW vitamin + NAA 7,5 mg/l + kinetin 0,5 mg/l. Before selection, 1.000 rad dosage was the most tolerant dosage to growth embryogenic calli. After selection, 2.000 rad dosage was the best dosage to produce shoots which stable tolerant to aluminum. Selected 88 mutant shoots were produced after three times selection on the same medium which AlCl3.6H2O added at low pH.},
    keywords = {citrus rootstock, japansche citroen, aluminum tolerance, in vitro selection},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_6_1_2010_33-39.pdf},
    note = {Peningkatan Toleransi Alumunium pada Jeruk Batang Bawah dengan Teknik Seleksi In Vitro Berulang}
    }
  6. Saragih, Edwin S., Santun R. P. Sitorus, Harianto, and Sugiono Moeljopawiro. 2010. Analysis of Regulation and Policy on Biosafety and Likelihood of Transgenic Seeds Adoption in Indonesia. Jurnal agrobiogen 6 (1):40-48.
    [BibTeX] [Abstract] [PDF: Analysis of Regulation and Policy on Biosafety and Likelihood of Transgenic Seeds Adoption in Indonesia ]
    Since more than 10 years, a number of works in field of modern biotechnology have been programmed in public research institutes and universities in Indonesia and few foreign companies have put efforts in introducing transgenic varieties. This significant development raises intriguing question as to why there has not been any transgenic food crop seed planted by farmers in the country. A status quo was observed in which regulatory regime on biosafety has been in a situation of prolonged transitional phase and necessary institutional framework has not been firmly in place. There were distinguished lines among stakeholders on benefit awareness, risks perception and worry on multinational companies’ control over seed supply. There is a fair expectation that similar benefits experienced by adopting countries could also help increase food production in Indonesia. However, potential contribution of transgenic seeds for the country is still largely unexplored. There are numbers of potential transgenic seeds namely transgenic rice, soybean, potato, tomato and corn, with the latter would show slightly better likelihood of success once adoption happens. Decision making instrument as determinant factor in ensuring safe application and release of transgenic seeds has not yet existed despite the fact that capacity for biosafety assessment conduct is undoubtedly sufficient. It is important to note that the new regulation on biosafety (PP No. 21/2005) open opportunities for assessing transgenic product under a transitional clause. Nonetheless, the new regulation has not been able securing food safety statement of imported transgenic products (especially corn and soybean) which have been used for domestic consumption.
    @article{Saragih10p40,
    title = {{Analysis of Regulation and Policy on Biosafety and Likelihood of Transgenic Seeds Adoption in Indonesia}},
    author = {Edwin S. Saragih and Santun R. P. Sitorus and Harianto and Sugiono Moeljopawiro},
    journal = {Jurnal AgroBiogen},
    pages = {40 - 48},
    volume = {6},
    number = {1},
    year = {2010},
    abstract = {Since more than 10 years, a number of works in field of modern biotechnology have been programmed in public research institutes and universities in Indonesia and few foreign companies have put efforts in introducing transgenic varieties. This significant development raises intriguing question as to why there has not been any transgenic food crop seed planted by farmers in the country. A status quo was observed in which regulatory regime on biosafety has been in a situation of prolonged transitional phase and necessary institutional framework has not been firmly in place. There were distinguished lines among stakeholders on benefit awareness, risks perception and worry on multinational companies' control over seed supply. There is a fair expectation that similar benefits experienced by adopting countries could also help increase food production in Indonesia. However, potential contribution of transgenic seeds for the country is still largely unexplored. There are numbers of potential transgenic seeds namely transgenic rice, soybean, potato, tomato and corn, with the latter would show slightly better likelihood of success once adoption happens. Decision making instrument as determinant factor in ensuring safe application and release of transgenic seeds has not yet existed despite the fact that capacity for biosafety assessment conduct is undoubtedly sufficient. It is important to note that the new regulation on biosafety (PP No. 21/2005) open opportunities for assessing transgenic product under a transitional clause. Nonetheless, the new regulation has not been able securing food safety statement of imported transgenic products (especially corn and soybean) which have been used for domestic consumption.},
    keywords = {institutional framework, biosafety evaluation, transgenic crops adoption},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_6_1_2010_40-48.pdf},
    note = {Analisis Regulasi dan Kebijakan Keamanan Hayati dan Peluang Keberhasilan Adopsi Benih Transgenik di Indonesia}
    }
  7. Silitonga, Tiur S.. 2010. Jurnal agrobiogen 6 (1):49-56.
    [BibTeX] [Abstract] [PDF: ]
    Penggunaan Bioteknologi dalam Karakterisasi, Evaluasi, dan Pemanfaatan Plasma Nutfah Padi Indonesia. Tiur S. Silitonga. Beras merupakan makanan pokok penduduk Indonesia yang terus meningkat kebutuhannya. Untuk memenuhi kebutuhan beras nasional, peningkatan produktivitas varietas padi terus diupayakan melalui peningkatan potensi hasil dengan cara merakit varietas tipe baru dan padi hibrida yang berdaya hasil tinggi dan genjah, tahan terhadap cekaman biotik dan abiotik. Sejak tahun 2006 sampai saat ini jumlah varietas yang dihasilkan sebanyak 31 varietas. Perakitan varietas itu semua dilakukan dengan menggunakan plasma nutfah. Sampai saat ini plasma nutfah yang dilestarikan di Bank Gen Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumberdaya Genetik Pertanian (BB-Biogen) berjumlah sekitar 4.000 aksesi yang terdiri atas varietas padi lokal, varietas padi unggul lama, varietas unggul tipe baru, galur-galur elit, and kerabat spesies padi liar. Untuk menjaga keselamatan koleksi, sebanyak 2.500 aksesi dilestarikan di Balai Besar Penelitian Padi sebagai koleksi duplikat. Di samping itu, sebagai mitra kerja sama internasional, koleksi ini juga disimpan di pusat pelestarian plasma nutfah padi International Rice Research Institute (IRRI) sebanyak lebih dari 8.900 aksesi. Plasma nutfah ini memiliki peranan yang sangat besar sebagai sumber gen dalam program pemuliaan padi. Untuk mempermudah pemanfaatannya, koleksi ini telah di karakterisasi, dievaluasi, and didokumentasikan di dalam database. Karena plasma nutfah memiliki nilai potensial dan nilai aktual bagi kehidupan manusia, maka sangat penting untuk melestarikannya baik secara in situ, ex situ, and lekat lahan (on farm). Pada tulisan ini diuraikan status koleksi plasma nutfah, bagaimana dikoleksi, karakterisasi, evaluasi, and didokumentasikan dalam database dan dimanfaatkan dalam program pemuliaan padi serta dalam pertukaran plasma nutfah padi. Dalam pemanfaatan dan pertukaran plasma nutfah, Indonesia telah meratifikasi perjanjian pertukaran sumber daya genetik dan mengimplementasikannya dengan menggunakan Standard Material Transfer Agreement (sMTA) melalui UU No. 4 Tahun 2006.
    @article{Silitonga10p49,
    author = {Tiur S. Silitonga},
    journal = {Jurnal AgroBiogen},
    pages = {49 - 56},
    volume = {6},
    number = {1},
    year = {2010},
    abstract = {Penggunaan Bioteknologi dalam Karakterisasi, Evaluasi, dan Pemanfaatan Plasma Nutfah Padi Indonesia. Tiur S. Silitonga. Beras merupakan makanan pokok penduduk Indonesia yang terus meningkat kebutuhannya. Untuk memenuhi kebutuhan beras nasional, peningkatan produktivitas varietas padi terus diupayakan melalui peningkatan potensi hasil dengan cara merakit varietas tipe baru dan padi hibrida yang berdaya hasil tinggi dan genjah, tahan terhadap cekaman biotik dan abiotik. Sejak tahun 2006 sampai saat ini jumlah varietas yang dihasilkan sebanyak 31 varietas. Perakitan varietas itu semua dilakukan dengan menggunakan plasma nutfah. Sampai saat ini plasma nutfah yang dilestarikan di Bank Gen Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumberdaya Genetik Pertanian (BB-Biogen) berjumlah sekitar 4.000 aksesi yang terdiri atas varietas padi lokal, varietas padi unggul lama, varietas unggul tipe baru, galur-galur elit, and kerabat spesies padi liar. Untuk menjaga keselamatan koleksi, sebanyak 2.500 aksesi dilestarikan di Balai Besar Penelitian Padi sebagai koleksi duplikat. Di samping itu, sebagai mitra kerja sama internasional, koleksi ini juga disimpan di pusat pelestarian plasma nutfah padi International Rice Research Institute (IRRI) sebanyak lebih dari 8.900 aksesi. Plasma nutfah ini memiliki peranan yang sangat besar sebagai sumber gen dalam program pemuliaan padi. Untuk mempermudah pemanfaatannya, koleksi ini telah di karakterisasi, dievaluasi, and didokumentasikan di dalam database. Karena plasma nutfah memiliki nilai potensial dan nilai aktual bagi kehidupan manusia, maka sangat penting untuk melestarikannya baik secara in situ, ex situ, and lekat lahan (on farm). Pada tulisan ini diuraikan status koleksi plasma nutfah, bagaimana dikoleksi, karakterisasi, evaluasi, and didokumentasikan dalam database dan dimanfaatkan dalam program pemuliaan padi serta dalam pertukaran plasma nutfah padi. Dalam pemanfaatan dan pertukaran plasma nutfah, Indonesia telah meratifikasi perjanjian pertukaran sumber daya genetik dan mengimplementasikannya dengan menggunakan Standard Material Transfer Agreement (sMTA) melalui UU No. 4 Tahun 2006.},
    keywords = {plasma nutfah, padi, bioteknologi},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_6_1_2010_49.pdf},
    note = {The use of Biotechnology in the Characterization, Evaluation, and Utilization of Indonesian Rice Germplasm}
    }
  8. Lestari, P., N. Richana, A. A. Darwis, K. Syamsu, and U. d. Murdiyatmo. 2010. Purifikasi dan Karakterisasi $\alpha$-amilase Termostabil dari Bacillus stearothermophilus TII-12. Jurnal agrobiogen 7 (1):56-62.
    [BibTeX] [Abstract] [PDF: Purifikasi dan Karakterisasi $\alpha$-amilase Termostabil dari Bacillus stearothermophilus TII-12 ]
    Thermostable $\alpha$-amylase is a potential enzyme employed in the starch processing and widely used in food industries, but this enzyme is still imported. The local enzyme production would be more economist and useful for its broad applications. Here we report $\alpha$-amylase from indigenous bacteria TII-12 which was purified and characterized, as well as analyzed its hydrolysis product on cassava starch. The enzyme of Bacillus stearothermophilus TII-12 partially purified by ultrafiltration, acetone precipitation and gel filtration (Sephadex G-100) showed the reduced total activity, total protein and yield, but increased the specific activity. The enzyme had a Km of 1,06 mg/ml and Vmax of 1,21 mol/min, with optimal activity at pH 7 and 90oC. An apparent molecular mass was of 192.932,8 Dalton, as estimated by Native-Polyacrylamide Agarose Gel electrophoresis. Its activity was inhibited by the divalent cation chelator such as EDTA and CuSO4 but activated by calcium ion. Hydrolysis products of this enzyme on cassava starch were glucose, dextrin, maltose and oligosaccharides. After 24 hours of hydrolysis, the concentration of glucose and maltose reached 51.970 and 10.090 ppm, respectively. The thermostable $\alpha$-amylase of TII-12 is an endo-$\alpha$-amylase and prospective to be applied on starch liquefaction with high temperature process.
    @article{Lestari10p56,
    title = {{Purifikasi dan Karakterisasi $\alpha$-amilase Termostabil dari Bacillus stearothermophilus TII-12}},
    author = {P. Lestari and N. Richana and A. A. Darwis and K. Syamsu and d. U. Murdiyatmo},
    journal = {Jurnal AgroBiogen},
    pages = {56 - 62},
    volume = {7},
    number = {1},
    year = {2010},
    abstract = {Thermostable $\alpha$-amylase is a potential enzyme employed in the starch processing and widely used in food industries, but this enzyme is still imported. The local enzyme production would be more economist and useful for its broad applications. Here we report $\alpha$-amylase from indigenous bacteria TII-12 which was purified and characterized, as well as analyzed its hydrolysis product on cassava starch. The enzyme of Bacillus stearothermophilus TII-12 partially purified by ultrafiltration, acetone precipitation and gel filtration (Sephadex G-100) showed the reduced total activity, total protein and yield, but increased the specific activity. The enzyme had a Km of 1,06 mg/ml and Vmax of 1,21 mol/min, with optimal activity at pH 7 and 90oC. An apparent molecular mass was of 192.932,8 Dalton, as estimated by Native-Polyacrylamide Agarose Gel electrophoresis. Its activity was inhibited by the divalent cation chelator such as EDTA and CuSO4 but activated by calcium ion. Hydrolysis products of this enzyme on cassava starch were glucose, dextrin, maltose and oligosaccharides. After 24 hours of hydrolysis, the concentration of glucose and maltose reached 51.970 and 10.090 ppm, respectively. The thermostable $\alpha$-amylase of TII-12 is an endo-$\alpha$-amylase and prospective to be applied on starch liquefaction with high temperature process.},
    keywords = {bacillus stearothermophilus, characterization, purification, thermostable $\alpha$-amylase},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_7_1_2011_07.pdf}
    }

2009

  1. Tasma, Made I. and Ahmad Warsun. 2009. Analisis Diversitas Genetik Genotipe Kedelai Toleran dan Peka Keracunan Aluminium Menggunakan Marka Mikrosatelit. Jurnal agrobiogen 5 (1):1-6.
    [BibTeX] [Abstract] [PDF: Analisis Diversitas Genetik Genotipe Kedelai Toleran dan Peka Keracunan Aluminium Menggunakan Marka Mikrosatelit ]
    Persilangan dua genotipe kedelai dengan jarak genetik jauh menghasilkan progeni dengan polimorfisme tinggi pada banyak lokus yang memfasilitasi keberhasilan program pemuliaan dan pemetaan karakter agronomi penting kedelai. Tujuan penelitian ini untuk mengetahui diversitas genetik genotipe kedelai toleran dan peka keracunan aluminium (Al), informasi diversitas alel dan tingkat polimorfisme marka SSR dari genotipe kedelai yang diuji, menentukan genotipe dengan jarak genetik jauh sebagai tetua dalam pembentukan populasi pemetaan karakter toleran Al, and informasi diversitas genetik dalam pemilihan tetua untuk program pemuliaan kedelai toleran keracunan Al. Dua puluh empat genotipe kedelai toleran dan peka keracunan Al dianalisis menggunakan 15 marka SSR. Marka SSR lokasinya menyebar pada 14 kromosom kedelai. Dendrogram dikonstruksi menggunakan Unweighted Pair-Group Method Arithmatic (UPGMA) melalui program Numerical Taxonomy and Multivariate System (NTSYS) versi 2.1-pc. Diversitas genetik antara dua genotipe kedelai berkisar antara 2-33,2%. Pada diversitas 33,2% uji klaster UPGMA membagi genotipe menjadi 2 kelompok masing-masing terdiri dari 19 dan 5 genotipe untuk kelompok 1 dan 2. Jumlah alel SSR total 81dengan rata-rata jumlah alel per lokus SSR 4,4 dan rata-rata tingkat polimorfisme 0,55. Menggunakan diversitas tertinggi 33,2% dua genotipe paling peka Al (B3293 dan B3442) dari kelompok 1 dan dua genotipe paling toleran Al (B3462 dan B3851) dari kelompok 2 dipilih untuk membentuk populasi pemetaan karakter toleran Al. Berdasarkan nilai diversitas genetik tertinggi 33,2% banyak kemungkinan kombinasi persilangan dapat dilakukan antara genotipe toleran Al untuk pemuliaan kedelai toleran Al.
    @article{MadeTasma09p1,
    title = {{Analisis Diversitas Genetik Genotipe Kedelai Toleran dan Peka Keracunan Aluminium Menggunakan Marka Mikrosatelit}},
    author = {I. Made Tasma and Ahmad Warsun},
    journal = {Jurnal AgroBiogen},
    pages = {1 - 6},
    volume = {5},
    number = {1},
    year = {2009},
    abstract = {Persilangan dua genotipe kedelai dengan jarak genetik jauh menghasilkan progeni dengan polimorfisme tinggi pada banyak lokus yang memfasilitasi keberhasilan program pemuliaan dan pemetaan karakter agronomi penting kedelai. Tujuan penelitian ini untuk mengetahui diversitas genetik genotipe kedelai toleran dan peka keracunan aluminium (Al), informasi diversitas alel dan tingkat polimorfisme marka SSR dari genotipe kedelai yang diuji, menentukan genotipe dengan jarak genetik jauh sebagai tetua dalam pembentukan populasi pemetaan karakter toleran Al, and informasi diversitas genetik dalam pemilihan tetua untuk program pemuliaan kedelai toleran keracunan Al. Dua puluh empat genotipe kedelai toleran dan peka keracunan Al dianalisis menggunakan 15 marka SSR. Marka SSR lokasinya menyebar pada 14 kromosom kedelai. Dendrogram dikonstruksi menggunakan Unweighted Pair-Group Method Arithmatic (UPGMA) melalui program Numerical Taxonomy and Multivariate System (NTSYS) versi 2.1-pc. Diversitas genetik antara dua genotipe kedelai berkisar antara 2-33,2%. Pada diversitas 33,2% uji klaster UPGMA membagi genotipe menjadi 2 kelompok masing-masing terdiri dari 19 dan 5 genotipe untuk kelompok 1 dan 2. Jumlah alel SSR total 81dengan rata-rata jumlah alel per lokus SSR 4,4 dan rata-rata tingkat polimorfisme 0,55. Menggunakan diversitas tertinggi 33,2% dua genotipe paling peka Al (B3293 dan B3442) dari kelompok 1 dan dua genotipe paling toleran Al (B3462 dan B3851) dari kelompok 2 dipilih untuk membentuk populasi pemetaan karakter toleran Al. Berdasarkan nilai diversitas genetik tertinggi 33,2% banyak kemungkinan kombinasi persilangan dapat dilakukan antara genotipe toleran Al untuk pemuliaan kedelai toleran Al.},
    keywords = {diversitas genetik, marka ssr, keracunan aluminium, kedelai},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_5_1_2009_1-6.pdf},
    note = {Genetic Diversity Analysis of Aluminum-toxicity Tolerant and Sensitive Soybean Genotypes Assessed with Microsattelite Markers}
    }
  2. Riyanti, Eny I. and Peter L. Rogers. 2009. Konstruksi dan Ekspresi Pet Operon Menggunakan Shuttle Vector untuk Bakteri Mesofilik dan Termofilik. Jurnal agrobiogen 5 (1):7-15.
    [BibTeX] [Abstract] [PDF: Konstruksi dan Ekspresi Pet Operon Menggunakan Shuttle Vector untuk Bakteri Mesofilik dan Termofilik ]
    Keuntungan fermentasi etanol pada suhu tinggi mendorong penelitian perakitan bakteri termofilik etalogenik. Selain itu, kemampuan bakteri termofilik dalam penggunaan gula pentosa hasil degradasi biomasa memberi peluang untuk menekan biaya produksi bioetanol. Tujuan dari penelitian ini adalah untuk mengkonstruksi pet (production of ethanol) operon dengan menggunakan shuttle vector pMK18 dan melihat ekspresinya dalam bakteri mesofilik dan termofilik. Konstruksi dan ekspresi pet operon dengan menggunakan adhT dari bakteri termofilik dan pdc dari bakteri mesofilik, and penggunaan mesofilik-termofilik shuttle vector sebagai backbone-nya baru pertama kali dilaporkan. Pet operon adalah suatu susunan gen penyandi produksi etanol yang terdiri dari gen pdc (pyruvate decarboxylase) dan adh (alcohol dehydrogenase). Konstruksi pet operon menggunakan gen adhT dari bakteri termofilik Geobacillus thermoglucosidasius M10EXG dan pdc (pyruvate dehydrogenase) dari bakteri mesofilik Zymomonas mobilis ZM4 telah dilakukan dengan menggunakan mesofilik-termofilik shuttle vector pMK18. Ekspresi pet operon pada bakteri mesofilik Eschericia coli dapat memproduksi 0,3 g/l etanol dengan aktivitas adhT sekitar 0,02 U/mg protein dan aktivitas pdc sekitar 0,004 U/mg protein. Perlu dilakukan penelitian lanjutan untuk perbaikan konstruksi pet operon untuk sistem termofik pada Thermus thermophilus HB27, karena konstruksi yang didapat belum optimum untuk sistem termofilik ini. Hasil ini diharapkan akan mengawali pengembangan teknik manipulasi genetik pada bakteri termofilik yang masih sangat terbatas, khususnya pengembangan teknik manipulasi termofilik etanologenik.
    @article{Riyanti09p7,
    title = {{Konstruksi dan Ekspresi Pet Operon Menggunakan Shuttle Vector untuk Bakteri Mesofilik dan Termofilik}},
    author = {Eny I. Riyanti and Peter L. Rogers},
    journal = {Jurnal AgroBiogen},
    pages = {7 - 15},
    volume = {5},
    number = {1},
    year = {2009},
    abstract = {Keuntungan fermentasi etanol pada suhu tinggi mendorong penelitian perakitan bakteri termofilik etalogenik. Selain itu, kemampuan bakteri termofilik dalam penggunaan gula pentosa hasil degradasi biomasa memberi peluang untuk menekan biaya produksi bioetanol. Tujuan dari penelitian ini adalah untuk mengkonstruksi pet (production of ethanol) operon dengan menggunakan shuttle vector pMK18 dan melihat ekspresinya dalam bakteri mesofilik dan termofilik. Konstruksi dan ekspresi pet operon dengan menggunakan adhT dari bakteri termofilik dan pdc dari bakteri mesofilik, and penggunaan mesofilik-termofilik shuttle vector sebagai backbone-nya baru pertama kali dilaporkan. Pet operon adalah suatu susunan gen penyandi produksi etanol yang terdiri dari gen pdc (pyruvate decarboxylase) dan adh (alcohol dehydrogenase). Konstruksi pet operon menggunakan gen adhT dari bakteri termofilik Geobacillus thermoglucosidasius M10EXG dan pdc (pyruvate dehydrogenase) dari bakteri mesofilik Zymomonas mobilis ZM4 telah dilakukan dengan menggunakan mesofilik-termofilik shuttle vector pMK18. Ekspresi pet operon pada bakteri mesofilik Eschericia coli dapat memproduksi 0,3 g/l etanol dengan aktivitas adhT sekitar 0,02 U/mg protein dan aktivitas pdc sekitar 0,004 U/mg protein. Perlu dilakukan penelitian lanjutan untuk perbaikan konstruksi pet operon untuk sistem termofik pada Thermus thermophilus HB27, karena konstruksi yang didapat belum optimum untuk sistem termofilik ini. Hasil ini diharapkan akan mengawali pengembangan teknik manipulasi genetik pada bakteri termofilik yang masih sangat terbatas, khususnya pengembangan teknik manipulasi termofilik etanologenik.},
    keywords = {etanol, bakteri termofilik, bakteri mesofilik, pet operon, ekspresi gen},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_5_1_2009_7-15.pdf},
    note = {Construction and Expression of Pet Operon using Shuttle Vector for Mesophilic and Thermophilic Bacteria}
    }
  3. Koerniati, Sri and Andrzej Kilian. 2009. Pengembangan Sistem Perangkap Enhancer yang Difasilitasi oleh Aktivator Transkripsi GAL4/VP16 untuk Perbaikan Tanaman Padi. Jurnal agrobiogen 5 (1):16-24.
    [BibTeX] [Abstract] [PDF: Pengembangan Sistem Perangkap Enhancer yang Difasilitasi oleh Aktivator Transkripsi GAL4/VP16 untuk Perbaikan Tanaman Padi ]
    Peningkatan produksi padi untuk memenuhi kebutuhan nasional dilakukan melalui perbaikan tanaman, termasuk pencarian dan isolasi gen-gen baru melalui mutasi. Aplikasi berbagai sekuen mutagen, elemen loncat atau T-DNA, didukung dengan teknik PCR merupakan perdekatan yang lebih baik dibandingkan dengan metode klasik. Perangkap enhancer adalah sistem yang dikembangkan untuk mengatasi masalah rendahnya tingkat perolehan mutan, akibat banyak gen berfungsi sama atau satu gen berfungsi pada beberapa tingkat perkembangan tanaman. Sistem ini mampu menampilkan ekspresi pada jaringan tertentu (spatial) dan atau pada waktu tertentu (temporal) pada tanaman hemizigot (hemizygous plants). Penelitian ini bertujuan untuk (1) mengembangkan vector cassette perangkap enhancer dengan komponen utama aktivator transkripsi GAL4/VP16 dan dua gen reporter (gus dan gusPlus), and (2) memperoleh informasi tentang ekspresinya pada padi. Sepuluh vector diperoleh dan ditransformasikan ke kalus padi Nipponbare dan Millin dengan Agrobacterium tumefaciens. Kajian vektor melalui ekspresi gen reporter diamati pada kalus 3 hari setelah co-cultivation dan jaringan vegetatif dari 745 lini penangkap enhancer. Sembilan puluh lima persen nomor memiliki ekspresi dan persentase lebih tinggi daripada yang telah dilaporkan sebelumnya. Lini dengan vektor GAL4/VP16 delesi tidak memiliki ekspresi pada kalus dan jaringan vegetatif, walaupun hasil Southern Blot menunjukkan tanaman ini memiliki dua T-DNA. Tiga puluh dua persen lini gusPlus memiliki ekspresi yang kuat, sedangkan 30% berekspresi lemah dibandingkan dengan masing-masing 12% dan 47% untuk lini gus. Lini gusPlus juga tersebar pada lebih banyak pola ekspresi. Jumlah insersi pada lini perangkap enhancer berkisar antara 1-7 T-DNA dan 49% di antaranya memiliki satu T-DNA. gusPlus merupakan gen reporter yang lebih sensitif daripada gus dan GAL4/VP16 terbukti berfungsi.
    @article{SriKoerniati09p16,
    title = {{Pengembangan Sistem Perangkap Enhancer yang Difasilitasi oleh Aktivator Transkripsi GAL4/VP16 untuk Perbaikan Tanaman Padi}},
    author = {Sri Koerniati and Andrzej Kilian},
    journal = {Jurnal AgroBiogen},
    pages = {16 - 24},
    volume = {5},
    number = {1},
    year = {2009},
    abstract = {Peningkatan produksi padi untuk memenuhi kebutuhan nasional dilakukan melalui perbaikan tanaman, termasuk pencarian dan isolasi gen-gen baru melalui mutasi. Aplikasi berbagai sekuen mutagen, elemen loncat atau T-DNA, didukung dengan teknik PCR merupakan perdekatan yang lebih baik dibandingkan dengan metode klasik. Perangkap enhancer adalah sistem yang dikembangkan untuk mengatasi masalah rendahnya tingkat perolehan mutan, akibat banyak gen berfungsi sama atau satu gen berfungsi pada beberapa tingkat perkembangan tanaman. Sistem ini mampu menampilkan ekspresi pada jaringan tertentu (spatial) dan atau pada waktu tertentu (temporal) pada tanaman hemizigot (hemizygous plants). Penelitian ini bertujuan untuk (1) mengembangkan vector cassette perangkap enhancer dengan komponen utama aktivator transkripsi GAL4/VP16 dan dua gen reporter (gus dan gusPlus), and (2) memperoleh informasi tentang ekspresinya pada padi. Sepuluh vector diperoleh dan ditransformasikan ke kalus padi Nipponbare dan Millin dengan Agrobacterium tumefaciens. Kajian vektor melalui ekspresi gen reporter diamati pada kalus 3 hari setelah co-cultivation dan jaringan vegetatif dari 745 lini penangkap enhancer. Sembilan puluh lima persen nomor memiliki ekspresi dan persentase lebih tinggi daripada yang telah dilaporkan sebelumnya. Lini dengan vektor GAL4/VP16 delesi tidak memiliki ekspresi pada kalus dan jaringan vegetatif, walaupun hasil Southern Blot menunjukkan tanaman ini memiliki dua T-DNA. Tiga puluh dua persen lini gusPlus memiliki ekspresi yang kuat, sedangkan 30% berekspresi lemah dibandingkan dengan masing-masing 12% dan 47% untuk lini gus. Lini gusPlus juga tersebar pada lebih banyak pola ekspresi. Jumlah insersi pada lini perangkap enhancer berkisar antara 1-7 T-DNA dan 49% di antaranya memiliki satu T-DNA. gusPlus merupakan gen reporter yang lebih sensitif daripada gus dan GAL4/VP16 terbukti berfungsi.},
    keywords = {sistem perangkap enhancer, gen reporter gus dan gusplus, padi},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_5_1_2009_16-24.pdf},
    note = {Development of GAL4/VP16 Facilitated-enhancer Trap System for Rice Crop Improvement}
    }
  4. Ambarwati, Dinar A., Agus Purwito, M. Herman, S. M. Sumaraow, and Hajrial Aswidinnoor. 2009. Integration and Segregation Analysis of Late Blight Resistance Gene in F1 Progenies of Transgenic and Non Transgenic Potato Crosses. Jurnal agrobiogen 5 (1):25-31.
    [BibTeX] [Abstract] [PDF: Integration and Segregation Analysis of Late Blight Resistance Gene in F1 Progenies of Transgenic and Non Transgenic Potato Crosses ]
    Potato late blight, caused by Phytophthora infestans is one of the most devastating plant diseases. Potato yield losses due to this disease ranged from 47-100%. Frequent intervals and high rates of fungicide spray, currently practiced by potato growers to control the disease are expensive. Host resistance is an alternative control measure that is more economically and environmentally sustainable. Development of late blight resistant plants was conducted by crossing RB transgenic Katahdin SP904 and SP951 as male and two susceptible (Atlantic, Granola) varieties as female parents. F1 progenies were molecularly characterized for the integration of the RB transgene and evaluated for their segregations. Crossing data of Atlantic x transgenic Katahdin SP904 and SP951 produced 71 (57.72%) berries with average number of seeds per berry 139.58 and 83 (41.29%) berries with average number of seeds/berry 85.23, respectively. Granola x transgenic Katahdin SP904 and SP951 crosses gave higher results in terms of berry set (79.55 and 84.44%, respectively) than Atlantic x transgenic Katahdin crosses. A total of 554 F1 progenies were analyzed for the presence of the RB PCR marker. An expected 619-bp and 840-bp band were amplified in the progenies that contain the RB gene. The RB gene was integrated in 65 (45.45%), 77 (47.83%), 47 (45.63%), and 71 (48.30%) F1 progenies of Atlantic x transgenic Katahdin SP904, Atlantic x transgenic Katahdin SP951, Granola x transgenic Katahdin SP904, and Granola x transgenic Katahdin SP951, respectively. Chisquare tests showed that all the four cross combinations followed a 1 : 1 segregation ratio.
    @article{DinarAmbarwati09p25,
    title = {{Integration and Segregation Analysis of Late Blight Resistance Gene in F1 Progenies of Transgenic and Non Transgenic Potato Crosses}},
    author = {A. Dinar Ambarwati and Agus Purwito and M. Herman and S. M. Sumaraow and Hajrial Aswidinnoor},
    journal = {Jurnal AgroBiogen},
    pages = {25 - 31},
    volume = {5},
    number = {1},
    year = {2009},
    abstract = {Potato late blight, caused by Phytophthora infestans is one of the most devastating plant diseases. Potato yield losses due to this disease ranged from 47-100%. Frequent intervals and high rates of fungicide spray, currently practiced by potato growers to control the disease are expensive. Host resistance is an alternative control measure that is more economically and environmentally sustainable. Development of late blight resistant plants was conducted by crossing RB transgenic Katahdin SP904 and SP951 as male and two susceptible (Atlantic, Granola) varieties as female parents. F1 progenies were molecularly characterized for the integration of the RB transgene and evaluated for their segregations. Crossing data of Atlantic x transgenic Katahdin SP904 and SP951 produced 71 (57.72%) berries with average number of seeds per berry 139.58 and 83 (41.29%) berries with average number of seeds/berry 85.23, respectively. Granola x transgenic Katahdin SP904 and SP951 crosses gave higher results in terms of berry set (79.55 and 84.44%, respectively) than Atlantic x transgenic Katahdin crosses. A total of 554 F1 progenies were analyzed for the presence of the RB PCR marker. An expected 619-bp and 840-bp band were amplified in the progenies that contain the RB gene. The RB gene was integrated in 65 (45.45%), 77 (47.83%), 47 (45.63%), and 71 (48.30%) F1 progenies of Atlantic x transgenic Katahdin SP904, Atlantic x transgenic Katahdin SP951, Granola x transgenic Katahdin SP904, and Granola x transgenic Katahdin SP951, respectively. Chisquare tests showed that all the four cross combinations followed a 1 : 1 segregation ratio.},
    keywords = {rb gene, simplex, nulliplex, potato, sexual hybridization},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_5_1_2009_25-31.pdf},
    note = {Analisis Integrasi dan Segregasi Gen Ketahanan terhadap Hawar Daun pada Progeni F1 Hasil Persilangan Tanaman Kentang Transgenik dengan Non Transgenik}
    }
  5. Damayanti, Diani, Sudarsono, Ika Mariska, and M. Herman. 2009. Transformation of ACC Oxidase Antisense Gene in Papaya using the Particle Bombardment Technique. Jurnal agrobiogen 5 (1):32-38.
    [BibTeX] [Abstract] [PDF: Transformation of ACC Oxidase Antisense Gene in Papaya using the Particle Bombardment Technique ]
    Papaya (Carica papaya L.) is a climacteric fruit that exhibit a very fast ripening rate. Ethylene controls the ripening event in the papaya fruit. 1-aminocyclopropane-1-carbocxylic acid (ACC) oxidase gene encodes a specific enzyme for ethylene biosynthesis. The gene had become a target for manipulation to make a gene construct of an antisense ACC oxidase to regenerate transgenic papaya that has a characteristic of delayed ripening. The objective of the experiment is to engineer transgenic papaya that has a delayed ripening characteristic by transforming papaya with the antisense ACC oxidase gene through particle bombardment technique. The immature embryos of papaya variety Burung were used for the explants. Antisense ACC oxidase and reporter (gus) genes were co-transformed to papaya calli. Four hundreds eighteen calli were bombarded by the antisense ACC oxidase gene. The transformation experiment resulted 25 putatives transgenic plants out of fifty plants acclimatized in a greenhouse. Gus gene expression assay observed at 9 days after bombardment showed that the papaya explants bombarded twice at 9 cm shoot distance had 53.3% transformation rate of gus positive and 5.25 blue spots number in average. The results of PCR analysis showed that four out of 25 transgenic putative papaya plants (TR6, TR9, TR20, and TR24), indicated a positive PCR of the antisense ACC oxidase gene with the amplified fragment DNA size of 800 base pair.
    @article{DianiDamayanti09p32,
    title = {{Transformation of ACC Oxidase Antisense Gene in Papaya using the Particle Bombardment Technique}},
    author = {Diani Damayanti and Sudarsono and Ika Mariska and M. Herman},
    journal = {Jurnal AgroBiogen},
    pages = {32 - 38},
    volume = {5},
    number = {1},
    year = {2009},
    abstract = {Papaya (Carica papaya L.) is a climacteric fruit that exhibit a very fast ripening rate. Ethylene controls the ripening event in the papaya fruit. 1-aminocyclopropane-1-carbocxylic acid (ACC) oxidase gene encodes a specific enzyme for ethylene biosynthesis. The gene had become a target for manipulation to make a gene construct of an antisense ACC oxidase to regenerate transgenic papaya that has a characteristic of delayed ripening. The objective of the experiment is to engineer transgenic papaya that has a delayed ripening characteristic by transforming papaya with the antisense ACC oxidase gene through particle bombardment technique. The immature embryos of papaya variety Burung were used for the explants. Antisense ACC oxidase and reporter (gus) genes were co-transformed to papaya calli. Four hundreds eighteen calli were bombarded by the antisense ACC oxidase gene. The transformation experiment resulted 25 putatives transgenic plants out of fifty plants acclimatized in a greenhouse. Gus gene expression assay observed at 9 days after bombardment showed that the papaya explants bombarded twice at 9 cm shoot distance had 53.3% transformation rate of gus positive and 5.25 blue spots number in average. The results of PCR analysis showed that four out of 25 transgenic putative papaya plants (TR6, TR9, TR20, and TR24), indicated a positive PCR of the antisense ACC oxidase gene with the amplified fragment DNA size of 800 base pair.},
    keywords = {papaya, delayed fruit ripening, acc oxidase antisense gene, transformation},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_5_1_2009_32-38.pdf},
    note = {Transformasi Gen Antisens ACC Oksidase pada Pepaya dengan Teknik Penembakan Partikel}
    }
  6. Suryadi, Yadi, Ifa Manzila, and M. Machmud. 2009. Prospect of the Use of Serological Diagnostic Kits ELISA and Its Variants for Detection of Plant Pathogens. Jurnal agrobiogen 5 (1):39-48.
    [BibTeX] [Abstract] [PDF: Prospect of the Use of Serological Diagnostic Kits ELISA and Its Variants for Detection of Plant Pathogens ]
    Diseases are major constrains to agricultural crop productions in Indonesia. In the current free world trade system, the chances of introduction of plant quarantine agents are higher, and are difficult to control, due to importation of seeds and other planting materials. Principles of the plant disease control include exclusion and eradication. Early and accurate disease diagnosis is an early and important step for a successful disease control. Enzyme-linked Immunosorbent Assay (ELISA) is a promising technique for an aneffective and efficient disease diagnosis. Some advantages of technique over the conventional and molecular diagnostic techniques are economical use of reagents, high sensitivity, relatively simple and quick, suitable for large numbers of samples, and adaptable for automation. In the past decade, several variants and kits of ELISA had been introduced, such as Indirect ELISA, F(ab’)2 ELISA, Dot Blot ELISA, and Immuno Fluorescence Assay (ELFA). Based on the solid membrane used, the Dot Blot ELISA some variants were developed, such as the NCM-ELISA, Tissue Blotting ELISA, and Paper ELISA. The ELISA variants had different limit of detection levels. The limit detection of the variants for bacteria is ranging from 102-105 cells/ml, while those for viruses were from 1-10 ng/ml. The times required for the ELISA tests ranging from 5-48 hours. Models and components of ELISA kits for some viral and bacterial plant pathogens had been developed, but more are still needed since generally for each pathogen needs a different kit. The commercially available ELISA kits are limited in numbers, some of them are for pathogens that are not present in Indonesia. Production of ELISA kits for domestic uses will be more effective and efficent, particularly for pathogens that are present in the country. The ELISA kits are applicable not only fo detection and identification of pathogens, but also for ecological study of the pathogens in conjuction with epidemiological study of the disease. This paper is a brief review on the ELISA technique and its variants and potential uses for detection of plant pathogens.
    @article{YadiSuryadi09p39,
    title = {{Prospect of the Use of Serological Diagnostic Kits ELISA and Its Variants for Detection of Plant Pathogens}},
    author = {Yadi Suryadi and Ifa Manzila and M. Machmud},
    journal = {Jurnal AgroBiogen},
    pages = {39 - 48},
    volume = {5},
    number = {1},
    year = {2009},
    abstract = {Diseases are major constrains to agricultural crop productions in Indonesia. In the current free world trade system, the chances of introduction of plant quarantine agents are higher, and are difficult to control, due to importation of seeds and other planting materials. Principles of the plant disease control include exclusion and eradication. Early and accurate disease diagnosis is an early and important step for a successful disease control. Enzyme-linked Immunosorbent Assay (ELISA) is a promising technique for an aneffective and efficient disease diagnosis. Some advantages of technique over the conventional and molecular diagnostic techniques are economical use of reagents, high sensitivity, relatively simple and quick, suitable for large numbers of samples, and adaptable for automation. In the past decade, several variants and kits of ELISA had been introduced, such as Indirect ELISA, F(ab')2 ELISA, Dot Blot ELISA, and Immuno Fluorescence Assay (ELFA). Based on the solid membrane used, the Dot Blot ELISA some variants were developed, such as the NCM-ELISA, Tissue Blotting ELISA, and Paper ELISA. The ELISA variants had different limit of detection levels. The limit detection of the variants for bacteria is ranging from 102-105 cells/ml, while those for viruses were from 1-10 ng/ml. The times required for the ELISA tests ranging from 5-48 hours. Models and components of ELISA kits for some viral and bacterial plant pathogens had been developed, but more are still needed since generally for each pathogen needs a different kit. The commercially available ELISA kits are limited in numbers, some of them are for pathogens that are not present in Indonesia. Production of ELISA kits for domestic uses will be more effective and efficent, particularly for pathogens that are present in the country. The ELISA kits are applicable not only fo detection and identification of pathogens, but also for ecological study of the pathogens in conjuction with epidemiological study of the disease. This paper is a brief review on the ELISA technique and its variants and potential uses for detection of plant pathogens.},
    keywords = {elisa variants, diagnostic kit, plant disease diagnosis},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_5_1_2009_39-48.pdf},
    note = {Potensi Pemanfaatan Perangkat Diagnostik ELISA serta Variannya untuk Deteksi Patogen Tanaman}
    }
  7. Sisharmini, Atmitri, Aniversari Apriana, Wening Enggarini, and Kurniawan R. Trijatmiko. 2009. Development of Activation Tagging Mutants Population: I. Agrobacterium-mediated Transform-ation of Tropical Japonica Rice of Local Sulawesi cv. Asemandi. Jurnal agrobiogen 5 (2):49-56.
    [BibTeX] [Abstract] [PDF: Development of Activation Tagging Mutants Population: I. Agrobacterium-mediated Transform-ation of Tropical Japonica Rice of Local Sulawesi cv. Asemandi ]
    The rice transformation technology is not only provides valuable methods for the introduction of useful genes into rice plant to improve important agronomic traits, but also helps in studying gene function and regulation based on rice genome sequence information. Knockout of genes by insertional mutagenesis is a straightforward method to identify gene functions. One of the methods to develop rice mutants is through genetic transformation mediated by Agrobacterium using activation tagging by Ac-Ds system. A study was done with an objective to obtain mutant rice of local tropical japonica cv. Asemandi through genetic trans-formation mediated by Agrobacterium tumefaciens. The transformation was conducted using Agrobacterium vector with the strain of Agl-1 containing activation tag construct. The result of experiment showed that it has been obtained 17 independent line (304 plants) transgenic Asemandi containing activation tag construct. These starter lines will be used as materials to develop several generations of stabil rice mutant through selfing.
    @article{AtmitriSisharmini09p49,
    title = {{Development of Activation Tagging Mutants Population: I. Agrobacterium-mediated Transform-ation of Tropical Japonica Rice of Local Sulawesi cv. Asemandi}},
    author = {Atmitri Sisharmini and Aniversari Apriana and Wening Enggarini and Kurniawan R. Trijatmiko},
    journal = {Jurnal AgroBiogen},
    pages = {49 - 56},
    volume = {5},
    number = {2},
    year = {2009},
    abstract = {The rice transformation technology is not only provides valuable methods for the introduction of useful genes into rice plant to improve important agronomic traits, but also helps in studying gene function and regulation based on rice genome sequence information. Knockout of genes by insertional mutagenesis is a straightforward method to identify gene functions. One of the methods to develop rice mutants is through genetic transformation mediated by Agrobacterium using activation tagging by Ac-Ds system. A study was done with an objective to obtain mutant rice of local tropical japonica cv. Asemandi through genetic trans-formation mediated by Agrobacterium tumefaciens. The transformation was conducted using Agrobacterium vector with the strain of Agl-1 containing activation tag construct. The result of experiment showed that it has been obtained 17 independent line (304 plants) transgenic Asemandi containing activation tag construct. These starter lines will be used as materials to develop several generations of stabil rice mutant through selfing.},
    keywords = {genetic transformation, rice cv, asemandi, agrobacterium tumefaciens, activation tagging},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_5_2_2009_49-56.pdf},
    note = {Pengembangan Populasi Mutan Penanda Aktivasi: I. Transformasi Padi Japonica Tropis Lokal Sulawesi cv. Asemandi dengan bantuan Agrobacterium tumefaciens}
    }
  8. Chaerani, Nurul Hidayatun, and Dwinita W. Utami. 2009. Development of Multiplex Sets of Microsatellite DNA Markers for Analysis of Genetic Diversity in Rice and Soybean. Jurnal agrobiogen 5 (2):57-64.
    [BibTeX] [Abstract] [PDF: Development of Multiplex Sets of Microsatellite DNA Markers for Analysis of Genetic Diversity in Rice and Soybean ]
    Detection of multiplex microsatellite markers in a single capillary array on a laser detection system is traditionally conducted with specific primers that are labelled with fluorescent dyes. An alternative method using fluorescent labels that are appended to 5′ end of universal primer M13 instead of to the specific primers offers flexibility in designning multiplex panels and a less expensive method. Allele size range of microsatellite loci that can be grouped in multiplex panels can be accurately estimated by pooling and analyzing DNA samples from several genotypes simultaneously. This paper describes the procedure in development of microsatellite multiplex panels using M13 fluorescentlylabelled and estimation of allele size range based on pooled DNA strategies. Two multiplex panels of PCR amplification products for rice consisting of 15 loci and three panels for soybean consisting of 10 loci have been designed. The panels have been applied to 50 accessions of rice and soybean with fairly good results. Further characterization of allele size range, however, is required prior to the application of these panels to diverse genotypes. The procedure described here should be applicable in the development of multiplex panels of other species.
    @article{Chaerani09p57,
    title = {{Development of Multiplex Sets of Microsatellite DNA Markers for Analysis of Genetic Diversity in Rice and Soybean}},
    author = {Chaerani and Nurul Hidayatun and Dwinita W. Utami},
    journal = {Jurnal AgroBiogen},
    pages = {57 - 64},
    volume = {5},
    number = {2},
    year = {2009},
    abstract = {Detection of multiplex microsatellite markers in a single capillary array on a laser detection system is traditionally conducted with specific primers that are labelled with fluorescent dyes. An alternative method using fluorescent labels that are appended to 5' end of universal primer M13 instead of to the specific primers offers flexibility in designning multiplex panels and a less expensive method. Allele size range of microsatellite loci that can be grouped in multiplex panels can be accurately estimated by pooling and analyzing DNA samples from several genotypes simultaneously. This paper describes the procedure in development of microsatellite multiplex panels using M13 fluorescentlylabelled and estimation of allele size range based on pooled DNA strategies. Two multiplex panels of PCR amplification products for rice consisting of 15 loci and three panels for soybean consisting of 10 loci have been designed. The panels have been applied to 50 accessions of rice and soybean with fairly good results. Further characterization of allele size range, however, is required prior to the application of these panels to diverse genotypes. The procedure described here should be applicable in the development of multiplex panels of other species.},
    keywords = {microsatellite markers, multiplex panels, fluorescently labelled m13 primer, rice, soybean},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_5_2_2009_57-64.pdf},
    note = {Pengembangan Set Multipleks Penanda DNA Mikrosatelit untuk Analisis Variasi Genetik Padi dan Kedelai}
    }
  9. Rahmawati, Dewi and Nurita Toruan-Mathius. 2009. Genetic Diversity of Acremonium Associated with Agarwood Plant as Analyzed using the RAPD Technique. Jurnal agrobiogen 5 (2):4-11.
    [BibTeX] [Abstract] [PDF: Genetic Diversity of Acremonium Associated with Agarwood Plant as Analyzed using the RAPD Technique ]
    Agarwood or gaharu is a plant that has a high economic value in Asia, due to its use for production of incense and traditional medicines. The agarwood formation occurs in the trunk and roots of trees that have been infected by a fungus, such as Acremonium spp. Various fungi were associated with the agarwood formation. Acremonium is generally considered as highly polyphyletic, contains distantly related fungi. A study was done to identify genetic diversities in 10 isolates of Acremonium spp. from four different areas in Indonesia that are associated with Aquilaria and Gyrinops verstigii using the Random Amplified Polymorphic DNA (RAPD) technique. Eight RAPD primers, i.e., OPA 02, OPB 04, OPB 07, OPB 17, OPC 11, OPD 03, OPD 05, and OPE 07 were used in the analyses. The results indicated that similarity index values of the genetic variation ranged from 0.21 to 0.97. Based on the Nei and Li’s similarity coefficients, these values indicating the presence of high degree of genetic variability. The lowest degree of genetic similarity were found between isolates F (Acremonium spp., which is associated with G. verstigii from Mataram, Nusa Tenggara Barat), and LM2 from south coastal area of West Sumatra. The highest genetic similarity value (0.97) was found between isolates Sr2 and Sr4 from Sorong, Papua. Results from the cluster analysis indicated that the isolates could be grouped into two major clusters that were associated with their geographical locations.
    @article{DewiRahmawati09p4,
    title = {{Genetic Diversity of Acremonium Associated with Agarwood Plant as Analyzed using the RAPD Technique}},
    author = {Dewi Rahmawati and Nurita Toruan-Mathius},
    journal = {Jurnal AgroBiogen},
    pages = {4 - 11},
    volume = {5},
    number = {2},
    year = {2009},
    abstract = {Agarwood or gaharu is a plant that has a high economic value in Asia, due to its use for production of incense and traditional medicines. The agarwood formation occurs in the trunk and roots of trees that have been infected by a fungus, such as Acremonium spp. Various fungi were associated with the agarwood formation. Acremonium is generally considered as highly polyphyletic, contains distantly related fungi. A study was done to identify genetic diversities in 10 isolates of Acremonium spp. from four different areas in Indonesia that are associated with Aquilaria and Gyrinops verstigii using the Random Amplified Polymorphic DNA (RAPD) technique. Eight RAPD primers, i.e., OPA 02, OPB 04, OPB 07, OPB 17, OPC 11, OPD 03, OPD 05, and OPE 07 were used in the analyses. The results indicated that similarity index values of the genetic variation ranged from 0.21 to 0.97. Based on the Nei and Li's similarity coefficients, these values indicating the presence of high degree of genetic variability. The lowest degree of genetic similarity were found between isolates F (Acremonium spp., which is associated with G. verstigii from Mataram, Nusa Tenggara Barat), and LM2 from south coastal area of West Sumatra. The highest genetic similarity value (0.97) was found between isolates Sr2 and Sr4 from Sorong, Papua. Results from the cluster analysis indicated that the isolates could be grouped into two major clusters that were associated with their geographical locations.},
    keywords = {agarwood, genetic diversity, acremonium spp, rapd},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_5_2_2009_65-70.pdf},
    note = {Analisis Keragaman Genetik Acremonium yang Berasosiasi dengan Tanaman Gaharu Menggunakan Teknik Random Amplified Polymorphic DNA (RAPD)}
    }
  10. Ambarwati, Dinar A., Ida H. Somantri, Dwinita W. Utami, Aniversari Apriana, and Sugiono Moeljopawiro. 2009. Kultur Anter Padi untuk Mendapatkan Galur-galur Tahan Penyakit Blas. Jurnal agrobiogen 5 (2):71-77.
    [BibTeX] [Abstract] [PDF: Kultur Anter Padi untuk Mendapatkan Galur-galur Tahan Penyakit Blas ]
    Penyakit blas pada padi yang disebabkan oleh cendawan Pyricularia grisea, merupakan salah satu kendala dalam produksi beras. Sumber gen ketahanan terhadap penyakit blas dijumpai pada spesies padi liar Oryza rufipogon. Populasi silang ganda (BC2F3) turunan IR64 dan O. rufipogon mempunyai QTL untuk sifat ketahanan terhadap penyakit blas. Untuk mempercepat perolehan tanaman homosigot dari populasi tersebut, dilakukan kultur anter pada dua media induksi kalus: I1 (N6 + NAA 2 mg/l + kinetin 0,5 mg/l + sukrosa 60 g/l + putresin 0,16 g/l) dan I2 (N6 + 2,4-D 2 mg/l + sukrosa 50 g/l) dan dua media regenerasi: R1 (MS + NAA 0,5 mg/l + kinetin 2 mg/l + sukrosa 40 g/l + putresin 0,16 g/l) dan R2 (MS + NAA 1 mg/l + kinetin 2 mg/l + sukrosa 30 g/l). Kultur anter dilakukan pada sembilan genotipe, di mana tiga genotipe (149-16, 343, 337-13) memberikan respon terbaik dalam produksi planlet hijau setelah dikulturkan pada media regenerasi R1. Dari 208 planlet hasil regenerasi diperoleh 42 planlet haploid ganda dari genotipe 149-16, 11 planlet haploid ganda dari genotipe 343, and 44 planlet haploid ganda dari genotipe 337-13. Skrining ketahanan blas di rumah kaca pada populasi haploid ganda menghasilkan 46 tanaman tahan terhadap ras 001, 33 tanaman tahan terhadap ras 033, and 79 tanaman tahan terhadap ras 173. Sebanyak 28 tanaman bersifat tahan, baik terhadap ras 001, 033, maupun 173 seperti halnya O. rufipogon. Galur-galur homosigot ini akan diuji di lapang untuk ketahanannya terhadap penyakit blas dan karakter agronominya.
    @article{DinarAmbarwati09p71,
    title = {{Kultur Anter Padi untuk Mendapatkan Galur-galur Tahan Penyakit Blas}},
    author = {A. Dinar Ambarwati and Ida H. Somantri and Dwinita W. Utami and Aniversari Apriana and Sugiono Moeljopawiro},
    journal = {Jurnal AgroBiogen},
    pages = {71 - 77},
    volume = {5},
    number = {2},
    year = {2009},
    abstract = {Penyakit blas pada padi yang disebabkan oleh cendawan Pyricularia grisea, merupakan salah satu kendala dalam produksi beras. Sumber gen ketahanan terhadap penyakit blas dijumpai pada spesies padi liar Oryza rufipogon. Populasi silang ganda (BC2F3) turunan IR64 dan O. rufipogon mempunyai QTL untuk sifat ketahanan terhadap penyakit blas. Untuk mempercepat perolehan tanaman homosigot dari populasi tersebut, dilakukan kultur anter pada dua media induksi kalus: I1 (N6 + NAA 2 mg/l + kinetin 0,5 mg/l + sukrosa 60 g/l + putresin 0,16 g/l) dan I2 (N6 + 2,4-D 2 mg/l + sukrosa 50 g/l) dan dua media regenerasi: R1 (MS + NAA 0,5 mg/l + kinetin 2 mg/l + sukrosa 40 g/l + putresin 0,16 g/l) dan R2 (MS + NAA 1 mg/l + kinetin 2 mg/l + sukrosa 30 g/l). Kultur anter dilakukan pada sembilan genotipe, di mana tiga genotipe (149-16, 343, 337-13) memberikan respon terbaik dalam produksi planlet hijau setelah dikulturkan pada media regenerasi R1. Dari 208 planlet hasil regenerasi diperoleh 42 planlet haploid ganda dari genotipe 149-16, 11 planlet haploid ganda dari genotipe 343, and 44 planlet haploid ganda dari genotipe 337-13. Skrining ketahanan blas di rumah kaca pada populasi haploid ganda menghasilkan 46 tanaman tahan terhadap ras 001, 33 tanaman tahan terhadap ras 033, and 79 tanaman tahan terhadap ras 173. Sebanyak 28 tanaman bersifat tahan, baik terhadap ras 001, 033, maupun 173 seperti halnya O. rufipogon. Galur-galur homosigot ini akan diuji di lapang untuk ketahanannya terhadap penyakit blas dan karakter agronominya.},
    keywords = {kultur anter, ir64, oryza rufipogon, ketahanan blas},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_5_2_2009_71-77.pdf},
    note = {Rice Anther Culture to Develop Double Haploid Population and Blast Resistant Lines}
    }
  11. Achmad, Elis N. Herliyana, and Ficky R. Agustian. 2009. Phylogenetic Relationship in White Edible Mushroom Pleurotus spp. Using Isoenzyme Analysis. Jurnal agrobiogen 5 (2):78-83.
    [BibTeX] [Abstract] [PDF: Phylogenetic Relationship in White Edible Mushroom Pleurotus spp. Using Isoenzyme Analysis ]
    Pleurotus spp. is an edible mushroom commonly found on stem of wide leaf trees or other wooden plants in the forest. A number of Pleurotus species are found in Indonesia, and some of them have been cultivated. An accurate technique is needed to identify the species of Pleurotus correctly; one of the method is the isoenzyme technique. Apart from its simplicity, cheapness and quickness, this method also gives accurate information on phylogenetic relationship among the Pleurotus spp. The technique was used to determine phylogenetic relationship in 6 isolates of Pleurotus spp., i.e., Pleurotus sp.8, Pleurotus sp.6, Pleurotus sp.1, Pleurotus sp.7, and Pleurotus sp.9, using the GOT System. Results of the analysis indicated that all the Pleurotus isolates tested produced two bands with similar thickness, except for Pleurotus sp.1 that produced one band that move to the cathode (-). Another isolate of Pleurotus spp. produced bands tend to move to the anode (+). The genetic distances between Pleurotus sp.8 was similar to that of Pleurotus sp.9, while that of Pleurotus sp.6 was similar to Pleurotus sp.7. Genetic distances of Pleurotus sp.8 or Pleurotus sp.9 was similar to Pleurotus sp.6 or Pleurotus sp.7, with the longest distance on Pleurotus sp.1. Pleurotus sp.1 showed a different migration distance, where one of the isoenzym band tend to move to the cathode (-). This indicated that Pleurotus sp.1 has different phylogenetic relationship with the other Pleurotus spp.
    @article{Achmad09p78,
    title = {{Phylogenetic Relationship in White Edible Mushroom Pleurotus spp. Using Isoenzyme Analysis}},
    author = {Achmad and Elis N. Herliyana and Ficky R. Agustian},
    journal = {Jurnal AgroBiogen},
    pages = {78 - 83},
    volume = {5},
    number = {2},
    year = {2009},
    abstract = {Pleurotus spp. is an edible mushroom commonly found on stem of wide leaf trees or other wooden plants in the forest. A number of Pleurotus species are found in Indonesia, and some of them have been cultivated. An accurate technique is needed to identify the species of Pleurotus correctly; one of the method is the isoenzyme technique. Apart from its simplicity, cheapness and quickness, this method also gives accurate information on phylogenetic relationship among the Pleurotus spp. The technique was used to determine phylogenetic relationship in 6 isolates of Pleurotus spp., i.e., Pleurotus sp.8, Pleurotus sp.6, Pleurotus sp.1, Pleurotus sp.7, and Pleurotus sp.9, using the GOT System. Results of the analysis indicated that all the Pleurotus isolates tested produced two bands with similar thickness, except for Pleurotus sp.1 that produced one band that move to the cathode (-). Another isolate of Pleurotus spp. produced bands tend to move to the anode (+). The genetic distances between Pleurotus sp.8 was similar to that of Pleurotus sp.9, while that of Pleurotus sp.6 was similar to Pleurotus sp.7. Genetic distances of Pleurotus sp.8 or Pleurotus sp.9 was similar to Pleurotus sp.6 or Pleurotus sp.7, with the longest distance on Pleurotus sp.1. Pleurotus sp.1 showed a different migration distance, where one of the isoenzym band tend to move to the cathode (-). This indicated that Pleurotus sp.1 has different phylogenetic relationship with the other Pleurotus spp.},
    keywords = {pleurotus spp, phylogenic, isoenzyme technique},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_5_2_2009_78-83.pdf},
    note = {Hubungan Kekerabatan Jamur Pelapuk Putih Pleurotus spp. Dengan Analisis Isoenzim}
    }
  12. Hutami, Sri. 2009. Utilization of Cell Suspension in In Vitro Culture. Jurnal agrobiogen 5 (2):84-92.
    [BibTeX] [Abstract] [PDF: Utilization of Cell Suspension in In Vitro Culture ]
    Cell suspension culture could be defined as a process that allows rapidly dividing homogenous suspension of cells to grow in liquid nutrient media. There are two main types of suspension cultures: (1) Batch cultures in which cells are nurtured in a fixed volume of medium until growth ceases and (2) Continuous cultures in which cell growth is maintained by continuous replenishment of sterile nutrient media. Plant cell suspension cultures are mostly used for the biochemical investigation of cell physiology, growth, metabolism, protoplast fusion, transformation and for large scale production of seed by bioreactor and production of secondary metabolites. Contamination is one of the largest problems when dealing with cell cultures. Differences between the products of cell suspension culture and whole plant are frequently observed. These phenomena’s may be resulted from lack of differentiation and organization and cell cultureinduced variation. Utilization of cell suspension culture in Indonesia is still limited, some of them for mass production of plantation seed with bioreactor system and for production of secondary metabolites. The success of this study give the opportunity for mass production of seeds from other plants and also production of secondary metabolites.
    @article{SriHutami09p84,
    title = {{Utilization of Cell Suspension in In Vitro Culture}},
    author = {Sri Hutami},
    journal = {Jurnal AgroBiogen},
    pages = {84 - 92},
    volume = {5},
    number = {2},
    year = {2009},
    abstract = {Cell suspension culture could be defined as a process that allows rapidly dividing homogenous suspension of cells to grow in liquid nutrient media. There are two main types of suspension cultures: (1) Batch cultures in which cells are nurtured in a fixed volume of medium until growth ceases and (2) Continuous cultures in which cell growth is maintained by continuous replenishment of sterile nutrient media. Plant cell suspension cultures are mostly used for the biochemical investigation of cell physiology, growth, metabolism, protoplast fusion, transformation and for large scale production of seed by bioreactor and production of secondary metabolites. Contamination is one of the largest problems when dealing with cell cultures. Differences between the products of cell suspension culture and whole plant are frequently observed. These phenomena's may be resulted from lack of differentiation and organization and cell cultureinduced variation. Utilization of cell suspension culture in Indonesia is still limited, some of them for mass production of plantation seed with bioreactor system and for production of secondary metabolites. The success of this study give the opportunity for mass production of seeds from other plants and also production of secondary metabolites.},
    keywords = {cell suspension culture, seed secondary metabolites},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_5_2_2009_84.pdf},
    note = {Penggunaan Suspensi Sel dalam Kultur In Vitro}
    }

2008

  1. Tasma, Made I., Ahmad Warsun, and Asadi. 2008. Pembentukan dan Karakterisasi Populasi F2 untuk Pemetaan QTL Karakter Ketahanan Tanaman Kedelai terhadap Keracunan Aluminium. Jurnal agrobiogen 4 (1):1-8.
    [BibTeX] [Abstract] [PDF: Pembentukan dan Karakterisasi Populasi F2 untuk Pemetaan QTL Karakter Ketahanan Tanaman Kedelai terhadap Keracunan Aluminium ]
    Keracunan aluminium merupakan salah satu kendala utama dalam budidaya kedelai pada lahan masam. Pembentukan populasi F2 merupakan langkah awal yang menentukan keberhasilan program pemuliaan tanaman. Tujuan penelitian ini untuk membentuk dan mengkarakterisasi populasi F2 hasil persilangan tetua toleran dan tetua peka keracunan Al. Pembentukan populasi dilakukan menggunakan bantuan marka SSR. Dengan marka SSR populasi dapat dibentuk dengan cepat, akurat, and efisien. Skrining genotipa kedelai pada tanah masam kahat hara menghasilkan dua genotipa toleran dan dua peka. Empat persilangan tunggal dibuat untuk mendapatkan benih F1. Tanaman F1 dan F2 diidentifikasi menggunakam marka SSR Satt_070. Dua populasi (B3462 X B3293 dan B3462 X B3442) dipilih berdasarkan superiotas fenotipa pada lahan masam dan karakteristik molekuler pasangan tetua. Karakterisasi kedua populasi di lapang menunjukkan transgresiveness luas untuk karakter reproduksi seperti jumlah polong dan berat 100 biji. Ini mengindikasikan bahwa karakter penting lain selain karakter ketahanan terhadap keracunan Al potensial untuk dipetakan dari populasi ini. Metoda pembentukan populasi ini akan sangat bermanfaat bagi pemulia tanaman khususnya pemulia kedelai untuk meningkatkan efisiensi program pemuliaan ketahanan terhadap keracunan Al.
    @article{MadeTasma08p1,
    title = {{Pembentukan dan Karakterisasi Populasi F2 untuk Pemetaan QTL Karakter Ketahanan Tanaman Kedelai terhadap Keracunan Aluminium}},
    author = {I. Made Tasma and Ahmad Warsun and Asadi},
    journal = {Jurnal AgroBiogen},
    pages = {1 - 8},
    volume = {4},
    number = {1},
    year = {2008},
    abstract = {Keracunan aluminium merupakan salah satu kendala utama dalam budidaya kedelai pada lahan masam. Pembentukan populasi F2 merupakan langkah awal yang menentukan keberhasilan program pemuliaan tanaman. Tujuan penelitian ini untuk membentuk dan mengkarakterisasi populasi F2 hasil persilangan tetua toleran dan tetua peka keracunan Al. Pembentukan populasi dilakukan menggunakan bantuan marka SSR. Dengan marka SSR populasi dapat dibentuk dengan cepat, akurat, and efisien. Skrining genotipa kedelai pada tanah masam kahat hara menghasilkan dua genotipa toleran dan dua peka. Empat persilangan tunggal dibuat untuk mendapatkan benih F1. Tanaman F1 dan F2 diidentifikasi menggunakam marka SSR Satt_070. Dua populasi (B3462 X B3293 dan B3462 X B3442) dipilih berdasarkan superiotas fenotipa pada lahan masam dan karakteristik molekuler pasangan tetua. Karakterisasi kedua populasi di lapang menunjukkan transgresiveness luas untuk karakter reproduksi seperti jumlah polong dan berat 100 biji. Ini mengindikasikan bahwa karakter penting lain selain karakter ketahanan terhadap keracunan Al potensial untuk dipetakan dari populasi ini. Metoda pembentukan populasi ini akan sangat bermanfaat bagi pemulia tanaman khususnya pemulia kedelai untuk meningkatkan efisiensi program pemuliaan ketahanan terhadap keracunan Al.},
    keywords = {populasi, pemetaan molekuler , kedelai, keracunan aluminium},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_4_1_2008_1-8.pdf},
    note = {Development and Characterization of F2 Population for Molecular Mapping of Aluminum-Toxicity Tolerant QTL in Soybean}
    }
  2. Santoso, Tri J., Sri H. Hidayat, M. Herman, H. Aswidinnoor, and Sudarsono. 2008. Identities and Genetic Diversities of Begomoviruses Associated with Leaf Curl Disease of Tomato Based on the Polymerace Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) Technique. Jurnal agrobiogen 4 (1):9-17.
    [BibTeX] [Abstract] [PDF: Identities and Genetic Diversities of Begomoviruses Associated with Leaf Curl Disease of Tomato Based on the Polymerace Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) Technique ]
    Begomoviruses, members of the Geminivirus, are considered as emerging plant viruses. This was due to the increasing incidences and severities of the diseases in a number of economically important crops, including tomato. Genetic diversities of the Begomovirus isolates infecting tomato (Lycopersicon esculentum) of several areas in Indonesia were analyzed by using Polymerase Chain ReactionRestriction Fragment Length Polymorphism (PCR-RFLP) technique. A 1500 base pairs of PCR fragments amplified by using degenerate primers for Begomovirus was digested using four restriction enzymes, i.e., DraI, EcoRI, RsaI, and PstI. The pattern of RE digested fragments of 8 Begomovirus isolates and the predicted RFLP fragments of the Begomovirus isolates in the GeneBank database were used to determine the genetic identities and diversities among the isolates. Positive results of the PCR amplifications proved that diseased tomato plant samples collected from 8 locations in Java and Sumatra were infected with at least one Begomovirus isolate. The PCR amplification products, which were digested using the four restriction enzymes indicated the presence of polimorfisms among the DNA fragments of the Begomovirus isolates. Identifications of the Begomovirus indicated that the Brastagi, Bogor, Sragen, Ketep, and Boyolali isolates were Tomato Leaf Curl Virus (ToLCV); the isolates from Malang and Blitar isolates were Ageratum Yellow Vein Virus (AYVV), while one isolate from Kaliurang was Tomato Yellow Leaf Curl Virus (TYLCV). Results of the phylogenetic analysis of the 8 Begomovirus isolates based on Begomoviruses from the DNA database indicated that they belonged to three different groups. Dalam dasawarsa terakhir ini di berbagai daerah di Indonesia dilaporkan muncul serangan penyakit keriting daun pada tanaman tomat dan cabai. Hasil penelitian yang dilakukan menunjukkan bahwa penyakit tersebut disebabkan oleh infeksi Begomovirus dari kelompok geminivirus dan famili Geminiviridae (Aidawati et al. 2005, Hidayat et al. 1999). Penurunan hasil akibat serangan penyakit keriting daun pada tanaman di daerah Bogor, Jawa Barat dan sekitarnya dilaporkan dapat mencapai 50-70% (Sudiono et al. 2001). Di Indonesia, kejadian penyakit keriting akibat infeksi Begomovirus pada pertanaman tomat dapat mencapai 90-100%. Infeksi penyakit keriting daun ini dilaporkan dapat menyebabkan penurunan hasil hingga 50-100% (AVRDC Centerpoint Newsletter-spring 2003 issue) dibandingkan dengan tanaman tomat sehat. Selain tanaman tomat, Begomovirus juga menginfeksi beberapa tanaman lain, seperti kacang-kacangan, mentimun, cabai, and ubi kayu baik di daerah tropis maupun subtropis (Polkela et al. 2005, Rodriguez et al. 2006).
    @article{Santoso08p9,
    title = {{Identities and Genetic Diversities of Begomoviruses Associated with Leaf Curl Disease of Tomato Based on the Polymerace Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) Technique}},
    author = {Tri J. Santoso and Sri H. Hidayat and M. Herman and H. Aswidinnoor and Sudarsono},
    journal = {Jurnal AgroBiogen},
    pages = {9 - 17},
    volume = {4},
    number = {1},
    year = {2008},
    abstract = {Begomoviruses, members of the Geminivirus, are considered as emerging plant viruses. This was due to the increasing incidences and severities of the diseases in a number of economically important crops, including tomato. Genetic diversities of the Begomovirus isolates infecting tomato (Lycopersicon esculentum) of several areas in Indonesia were analyzed by using Polymerase Chain ReactionRestriction Fragment Length Polymorphism (PCR-RFLP) technique. A 1500 base pairs of PCR fragments amplified by using degenerate primers for Begomovirus was digested using four restriction enzymes, i.e., DraI, EcoRI, RsaI, and PstI. The pattern of RE digested fragments of 8 Begomovirus isolates and the predicted RFLP fragments of the Begomovirus isolates in the GeneBank database were used to determine the genetic identities and diversities among the isolates. Positive results of the PCR amplifications proved that diseased tomato plant samples collected from 8 locations in Java and Sumatra were infected with at least one Begomovirus isolate. The PCR amplification products, which were digested using the four restriction enzymes indicated the presence of polimorfisms among the DNA fragments of the Begomovirus isolates. Identifications of the Begomovirus indicated that the Brastagi, Bogor, Sragen, Ketep, and Boyolali isolates were Tomato Leaf Curl Virus (ToLCV); the isolates from Malang and Blitar isolates were Ageratum Yellow Vein Virus (AYVV), while one isolate from Kaliurang was Tomato Yellow Leaf Curl Virus (TYLCV). Results of the phylogenetic analysis of the 8 Begomovirus isolates based on Begomoviruses from the DNA database indicated that they belonged to three different groups. Dalam dasawarsa terakhir ini di berbagai daerah di Indonesia dilaporkan muncul serangan penyakit keriting daun pada tanaman tomat dan cabai. Hasil penelitian yang dilakukan menunjukkan bahwa penyakit tersebut disebabkan oleh infeksi Begomovirus dari kelompok geminivirus dan famili Geminiviridae (Aidawati et al. 2005, Hidayat et al. 1999). Penurunan hasil akibat serangan penyakit keriting daun pada tanaman di daerah Bogor, Jawa Barat dan sekitarnya dilaporkan dapat mencapai 50-70% (Sudiono et al. 2001). Di Indonesia, kejadian penyakit keriting akibat infeksi Begomovirus pada pertanaman tomat dapat mencapai 90-100%. Infeksi penyakit keriting daun ini dilaporkan dapat menyebabkan penurunan hasil hingga 50-100% (AVRDC Centerpoint Newsletter-spring 2003 issue) dibandingkan dengan tanaman tomat sehat. Selain tanaman tomat, Begomovirus juga menginfeksi beberapa tanaman lain, seperti kacang-kacangan, mentimun, cabai, and ubi kayu baik di daerah tropis maupun subtropis (Polkela et al. 2005, Rodriguez et al. 2006).},
    keywords = {begomovirus, tomato leaf curl, genetic diversity, pcr-rflp technique},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_4_1_2008_9-17.pdf},
    note = {Identitas dan Keragaman Genetik Begomovirus yang Berasosiasi dengan Penyakit Keriting pada Tomat Berdasarkan Teknik Polymerase Chain Reaction (PCR)Restriction Fragment Length Polymorphism (RFLP)}
    }
  3. Purnamaningsih, Ragapadmi and Ika Mariska. 2008. Testing of New Rice Clones Derived from In Vitro Selection for Tolerance to Al and Low pH by using Solution Culture. Jurnal agrobiogen 4 (1):18-23.
    [BibTeX] [Abstract] [PDF: Testing of New Rice Clones Derived from In Vitro Selection for Tolerance to Al and Low pH by using Solution Culture ]
    Rice productivity in acid soil is very low because of low pH, low availability of N, P, K, Ca, Mg, Mo, toxicity of Al and Mn. Development of Al tolerant varieties could increase rice productivity in acid soil. Somaclonal variation and in vitro selection method can be used to develop new Al tolerance varieties. A rapid screening method is needed to select a large number of new genotypes or new inbred lines in plant breeding, such as solution culture methods to evalu-ate Altolerant rice. This methods was used to know the response to Al in the seedling stage, root development, and pH changing. In this experiment solution culture method was used to evaluate the new genotypes derived from somaclonal variation and in vitro selection methods. These new genotypes have been tested the tolerance characteristic by using AlCl36H2O at 6 concentrations (0, 100, 200, 300, 400, and 500 ppm). Yoshida solution with two Al concentration were used to tested these genotypes. Measurement of Al tolerance was based on root development by using Relative Root Length (RRL), the relativity of root length at 45 ppm and 0 ppm. Almost all of the genotypes have RRLs higher than 0.7, which means that there was a positive correlation between the in vitro method and solution culture method. In this experiment pH changes were not applicable to measure the tolerance of the rice genotypes to Al and low pH.
    @article{RagapadmiPurnamaningsih08p18,
    title = {{Testing of New Rice Clones Derived from In Vitro Selection for Tolerance to Al and Low pH by using Solution Culture}},
    author = {Ragapadmi Purnamaningsih and Ika Mariska},
    journal = {Jurnal AgroBiogen},
    pages = {18 - 23},
    volume = {4},
    number = {1},
    year = {2008},
    abstract = {Rice productivity in acid soil is very low because of low pH, low availability of N, P, K, Ca, Mg, Mo, toxicity of Al and Mn. Development of Al tolerant varieties could increase rice productivity in acid soil. Somaclonal variation and in vitro selection method can be used to develop new Al tolerance varieties. A rapid screening method is needed to select a large number of new genotypes or new inbred lines in plant breeding, such as solution culture methods to evalu-ate Altolerant rice. This methods was used to know the response to Al in the seedling stage, root development, and pH changing. In this experiment solution culture method was used to evaluate the new genotypes derived from somaclonal variation and in vitro selection methods. These new genotypes have been tested the tolerance characteristic by using AlCl36H2O at 6 concentrations (0, 100, 200, 300, 400, and 500 ppm). Yoshida solution with two Al concentration were used to tested these genotypes. Measurement of Al tolerance was based on root development by using Relative Root Length (RRL), the relativity of root length at 45 ppm and 0 ppm. Almost all of the genotypes have RRLs higher than 0.7, which means that there was a positive correlation between the in vitro method and solution culture method. In this experiment pH changes were not applicable to measure the tolerance of the rice genotypes to Al and low pH.},
    keywords = {rice, aluminum, in vitro selection, somaclonal variation, solution culture testing},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_4_1_2008_18-23.pdf},
    note = {Pengujian Nomor-nomor Harapan Padi Tahan Al dan pH Rendah Hasil Seleksi In Vitro dengan Kultur Hara}
    }
  4. Richana, Nur, Tun T. Irawadi, Anwar Nur, and Khaswar Syamsu. 2008. Isolation and Identification of Xylanase Producing Bacteria and Characterization of Its Enzyme Properties. Jurnal agrobiogen 4 (1):24-34.
    [BibTeX] [Abstract] [PDF: Isolation and Identification of Xylanase Producing Bacteria and Characterization of Its Enzyme Properties ]
    Xylanase is an extracellular enzyme produced by microorganisms. This enzyme is able to hydrolise xylane (hemicellulose) to produce xylooligosaccharide and xylose. Thermoalkaliphilic xylanase is an agent that can be used as a substitute in the pulp whitening process instead of chlorine. A study was done to isolate, identificate of bacteria and characterize xylanase. The isolation of xylanase producing bacteria has been done from soil and waste of starch industry. Colonies which produced clearing zone were presumed as xylanolytic bacteria and chosen for further screening. Identification of potential isolate in xylanase production was done using 16S ribosomal RNA sequencing. Isolate Bacillus pumilus RXA-III5 originated from lime or alkaline soil was more potential isolate in xylanase production than other 24 isolates. Precipitation of xylanase, that was done using ammonium sulphate followed by dialyzes produced xylanase of a higher specific activity (267.1 U.mg-1) than that using acetone (131.1 U.mg-1) and ethanol (186.65 U.mg-1). Xylanase was done at purification produced three fractions of xylanase. Xylanase characteristics consist of pH and temperature (9 and 50oC), Km and Vmaks value 6 mg.ml-1 and 0.2 mol.minute-1, respectively. The Fe2+ was the strongest activetor and Mg2+ was the strongest inhibitor activity. This enzyme was detected as a cellulose-free xylanase. Xylanase is a prospective agent for bio-bleaching of paper.
    @article{NurRichana08p24,
    title = {{Isolation and Identification of Xylanase Producing Bacteria and Characterization of Its Enzyme Properties}},
    author = {Nur Richana and Tun T. Irawadi and Anwar Nur and Khaswar Syamsu},
    journal = {Jurnal AgroBiogen},
    pages = {24 - 34},
    volume = {4},
    number = {1},
    year = {2008},
    abstract = {Xylanase is an extracellular enzyme produced by microorganisms. This enzyme is able to hydrolise xylane (hemicellulose) to produce xylooligosaccharide and xylose. Thermoalkaliphilic xylanase is an agent that can be used as a substitute in the pulp whitening process instead of chlorine. A study was done to isolate, identificate of bacteria and characterize xylanase. The isolation of xylanase producing bacteria has been done from soil and waste of starch industry. Colonies which produced clearing zone were presumed as xylanolytic bacteria and chosen for further screening. Identification of potential isolate in xylanase production was done using 16S ribosomal RNA sequencing. Isolate Bacillus pumilus RXA-III5 originated from lime or alkaline soil was more potential isolate in xylanase production than other 24 isolates. Precipitation of xylanase, that was done using ammonium sulphate followed by dialyzes produced xylanase of a higher specific activity (267.1 U.mg-1) than that using acetone (131.1 U.mg-1) and ethanol (186.65 U.mg-1). Xylanase was done at purification produced three fractions of xylanase. Xylanase characteristics consist of pH and temperature (9 and 50oC), Km and Vmaks value 6 mg.ml-1 and 0.2 mol.minute-1, respectively. The Fe2+ was the strongest activetor and Mg2+ was the strongest inhibitor activity. This enzyme was detected as a cellulose-free xylanase. Xylanase is a prospective agent for bio-bleaching of paper.},
    keywords = {isolation, identification, bacteria, xylanase},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_4_1_2008_24-34.pdf},
    note = {Isolasi Identifikasi Bakteri Penghasil Xilanase serta Karakterisasi Enzimnya}
    }
  5. Hidayat, Topik and Adi Pancoro. 2008. Molecular Phylogenetic Studies in Providing Basic Knowledge to Improve Quality of Genetic Resources of Orchid. Jurnal agrobiogen 4 (1):35-40.
    [BibTeX] [Abstract] [PDF: Molecular Phylogenetic Studies in Providing Basic Knowledge to Improve Quality of Genetic Resources of Orchid ]
    Early information resulted from molecular phylogenetic studies of many important ornamental crops is often less attention to many growers and farmers. Phylogenetics is one of the most preferable method in systematics to reconstruct evolutionary relationships of groups of biological organisms in order to understand their biodiversities. This has been revolutionized by DNA sequences data. In this method, a group of organisms that shares many identical characteristics are considered to be closely related; deriving from a common ancestor and is assumed to have similar genetic patterns and biochemical properties. By these basic principles, molecular phylogenetics plays important roles in revealing a basic knowledge on pattern of relationships to which genetic resources can be improved. Over the past decade, botanists have done several thousand phylogenetic analyses based on molecular data of economically and horticulturally important crops. Orchids are the best example for this. There is no doubt that most orchid plants had played roles in horticulture and hybridization. At present, many infrageneric and intergeneric hybrids are available commercially. Successful hybridization can be achieved if two or more individual plants understudy are closely related in respect to their genetics and evolution.
    @article{TopikHidayat08p35,
    title = {{Molecular Phylogenetic Studies in Providing Basic Knowledge to Improve Quality of Genetic Resources of Orchid}},
    author = {Topik Hidayat and Adi Pancoro},
    journal = {Jurnal AgroBiogen},
    pages = {35 - 40},
    volume = {4},
    number = {1},
    year = {2008},
    abstract = {Early information resulted from molecular phylogenetic studies of many important ornamental crops is often less attention to many growers and farmers. Phylogenetics is one of the most preferable method in systematics to reconstruct evolutionary relationships of groups of biological organisms in order to understand their biodiversities. This has been revolutionized by DNA sequences data. In this method, a group of organisms that shares many identical characteristics are considered to be closely related; deriving from a common ancestor and is assumed to have similar genetic patterns and biochemical properties. By these basic principles, molecular phylogenetics plays important roles in revealing a basic knowledge on pattern of relationships to which genetic resources can be improved. Over the past decade, botanists have done several thousand phylogenetic analyses based on molecular data of economically and horticulturally important crops. Orchids are the best example for this. There is no doubt that most orchid plants had played roles in horticulture and hybridization. At present, many infrageneric and intergeneric hybrids are available commercially. Successful hybridization can be achieved if two or more individual plants understudy are closely related in respect to their genetics and evolution.},
    keywords = {hybridization, molecular phylogenetics, orchid subtribe aeridinae, quality of genetic resources},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_4_1_2008_35-40.pdf},
    note = {Kajian Filogenetika Molekuler dan Peranannya dalam Menyediakan Informasi Dasar untuk Meningkatkan Kualitas Sumber Genetik Anggrek}
    }
  6. Yunita, Rossa and Endang G. Lestari. 2008. In Vitro Propagation of Artemisia annua. Jurnal agrobiogen 4 (1):41-44.
    [BibTeX] [Abstract] [PDF: In Vitro Propagation of Artemisia annua ]
    Artemisinin, an anti-malarial medicine isolated from the annual wormwood Artemisia annua, has a marked activity against chloroquine-resistant and chloroquine-sensitive strains of Plasmodium falciparum. This compound is useful for treatment of cerebral malaria. An in vitro propagation system for A. annua has been developed. Shoots were induced by culturing seeds of A. annua on a MS medium containing BAP (0, 0.1, 0.3, 0.5 mg/l). Shoots were also formed on each seedling cultured on the same medium. Root formations were obtained from shoots that were subcultured on a MS medium containing IBA (0, 1.0, 1.5, 2 mg/l). The results showed that MS medium supplemented with BAP 0.3 mg/l was the best medium for induction and multiplication of the shoots, while the MS medium supplemented with IBA (1 mg/l) was good for root formations.
    @article{RossaYunita08p41,
    title = {{In Vitro Propagation of Artemisia annua}},
    author = {Rossa Yunita and Endang G. Lestari},
    journal = {Jurnal AgroBiogen},
    pages = {41 - 44},
    volume = {4},
    number = {1},
    year = {2008},
    abstract = {Artemisinin, an anti-malarial medicine isolated from the annual wormwood Artemisia annua, has a marked activity against chloroquine-resistant and chloroquine-sensitive strains of Plasmodium falciparum. This compound is useful for treatment of cerebral malaria. An in vitro propagation system for A. annua has been developed. Shoots were induced by culturing seeds of A. annua on a MS medium containing BAP (0, 0.1, 0.3, 0.5 mg/l). Shoots were also formed on each seedling cultured on the same medium. Root formations were obtained from shoots that were subcultured on a MS medium containing IBA (0, 1.0, 1.5, 2 mg/l). The results showed that MS medium supplemented with BAP 0.3 mg/l was the best medium for induction and multiplication of the shoots, while the MS medium supplemented with IBA (1 mg/l) was good for root formations.},
    keywords = {artemisia annua, micropropagation},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_4_1_2008_41-44.pdf},
    note = {Perbanyakan Tanaman Artemisia annua secara In Vitro}
    }
  7. Haryuningtyas, Dyah and Wayan T. Artama. 2008. Sequence Analysis of $\beta$-Tubulin Isotype 1 Gene from Benzimidazole Resistant Strains of Haemonchus contortus, A Parasitic Nematode of Sheep in Indonesia.. Jurnal agrobiogen 4 (2):45-50.
    [BibTeX] [Abstract] [PDF: Sequence Analysis of $\beta$-Tubulin Isotype 1 Gene from Benzimidazole Resistant Strains of Haemonchus contortus, A Parasitic Nematode of Sheep in Indonesia. ]
    Benzimidazole (BZ) resistance to gastrointestinal nematodes in small ruminants (sheep and goat) has become a significant problem worldwide. Evidences of anthelmintic resistance to albendazole in Indonesia has been reported from some government owned farms in West Java, Central Java, and Yogyakarta. Previous study on the sheep parasite H. contortus had shown that the BZ resistance was related to selection for individuals in a population possesing a spesific $\beta$-tubulin isotype 1 gene. The study is aimed to determine mutation on coding region of central part of $\beta$-tubulin isotype 1 gene of H. contortus resistant strain from Indonesia. Seven H. contortus worms were isolated from four BZ resistant sheep from two government farms (SPTD Trijaya, Kuningan, West Java, and UPTD Pelayanan Kesehatan Hewan, Bantul, Yogyakarta), and from a BZ susceptible sheep from Cicurug, Sukabumi, West Java. DNA was extracted individually from female H. contortus worms. A fragment of 520 bp $\beta$-tubulin isotype 1 gene exon 3, 4, 5 was amplified using the PCR technique and then sequenced. The results showed that a single mutation occurred in codon 200 (from phenilalanine to tyrosine) had caused benzimidazole resistance in H. contortus from SPTD Trijaya, Kuningan, West Java. Mutation in $\beta$-tubulin isotype 1 gene of H. contortus from UPTD Pelayanan Kesehatan Hewan, Yogyakarta, occurred in codon 198 (from glutamate to glycine), codon 201 (from cystein to stop codon), and codon 202 (from isoleucyne to stop codon).
    @article{DyahHaryuningtyas08p45,
    title = {{Sequence Analysis of $\beta$-Tubulin Isotype 1 Gene from Benzimidazole Resistant Strains of Haemonchus contortus, A Parasitic Nematode of Sheep in Indonesia.}},
    author = {Dyah Haryuningtyas and Wayan T. Artama},
    journal = {Jurnal AgroBiogen},
    pages = {45 - 50},
    volume = {4},
    number = {2},
    year = {2008},
    abstract = {Benzimidazole (BZ) resistance to gastrointestinal nematodes in small ruminants (sheep and goat) has become a significant problem worldwide. Evidences of anthelmintic resistance to albendazole in Indonesia has been reported from some government owned farms in West Java, Central Java, and Yogyakarta. Previous study on the sheep parasite H. contortus had shown that the BZ resistance was related to selection for individuals in a population possesing a spesific $\beta$-tubulin isotype 1 gene. The study is aimed to determine mutation on coding region of central part of $\beta$-tubulin isotype 1 gene of H. contortus resistant strain from Indonesia. Seven H. contortus worms were isolated from four BZ resistant sheep from two government farms (SPTD Trijaya, Kuningan, West Java, and UPTD Pelayanan Kesehatan Hewan, Bantul, Yogyakarta), and from a BZ susceptible sheep from Cicurug, Sukabumi, West Java. DNA was extracted individually from female H. contortus worms. A fragment of 520 bp $\beta$-tubulin isotype 1 gene exon 3, 4, 5 was amplified using the PCR technique and then sequenced. The results showed that a single mutation occurred in codon 200 (from phenilalanine to tyrosine) had caused benzimidazole resistance in H. contortus from SPTD Trijaya, Kuningan, West Java. Mutation in $\beta$-tubulin isotype 1 gene of H. contortus from UPTD Pelayanan Kesehatan Hewan, Yogyakarta, occurred in codon 198 (from glutamate to glycine), codon 201 (from cystein to stop codon), and codon 202 (from isoleucyne to stop codon).},
    keywords = {haemonchus contortus, benzimidazole resistance, isotype 1 $\beta$-tubulin gene, mutation},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_4_2_2008_45-50.pdf},
    note = {Analisis Sekuen Gen Tubulin-$\beta$ Isotipe 1 Cacing Haemonchus contortus Isolat Resisten terhadap Benzimidazole pada Domba di Indonesia}
    }
  8. Prasetiyono, Joko, Hajrial Aswidinnoor, Sugiono Moeljopawiro, Didy Sopandie, and Masdiar Bustamam. 2008. Identification of Polymorphic Markers for Breeding of Rice Tolerant to Phosphorus Defficiency. Jurnal agrobiogen 4 (1):51-58.
    [BibTeX] [Abstract] [PDF: Identification of Polymorphic Markers for Breeding of Rice Tolerant to Phosphorus Defficiency ]
    Information on polymorphisms among rice parents are very important in rice breeding for tolerance to phosphorus defficiency. A study was conducted at the Molecular Biology Laboratory, Indonesian Center Agricultural Biotechnology and Genetic Resources (ICABIOGRAD) from October 2006 to July 2007 to identify polymorphism markers from 6 rice genotypes. The rice genotypes, i.e., Dodokan, Situ Bagendit, Batur, Kasalath, NIL-C443, and K36-5-1-1 were analyzed for polymorphisms using 496 SSR markers, which cover the rice genomes. Seven of the 496 markers were used as foreground and recombinant selection markers, and the rests (489 markers) were used as background selection markers. PCR amplifications were separated on a 5% polyacrylamide gel and colored by the silver staining method. Three different markers among the seven foreground and recombinant selection markers were selected from each crossing, which are tightly linked with Pup1 gene and have a distance less than 5 cM. These markers are Dodokan vs Kasalath (RM277, SSR3, RM519), Dodokan vs NIL-C443 (RM277, SSR3, RM519), Dodokan vs K36-5-1-1 (RM277, SSR3, RM519), Situ Bagendit vs Kasalath (RM28102, SSR3, RM519), Situ Bagendit vs NILC443 (RM28102, SSR3, RM519), Situ Bagendit vs K36-5-1-1 (RM511, SSR3, RM519), Batur vs Kasalath (RM277, RM1261, RM519), Batur vs NIL-C443 (RM277, RM1261, RM519), and Batur vs K36-5-1-1 (RM28102, SSR3). Variations in background selection primers were found in each chromosome and in each parent combinations. Primers on chromosome 4, 5, and 12 showed the lowest polymorphisms; more primers are needed for these chromosomes.
    @article{JokoPrasetiyono08p51,
    title = {{Identification of Polymorphic Markers for Breeding of Rice Tolerant to Phosphorus Defficiency}},
    author = {Joko Prasetiyono and Hajrial Aswidinnoor and Sugiono Moeljopawiro and Didy Sopandie and Masdiar Bustamam},
    journal = {Jurnal AgroBiogen},
    pages = {51 - 58},
    volume = {4},
    number = {1},
    year = {2008},
    abstract = {Information on polymorphisms among rice parents are very important in rice breeding for tolerance to phosphorus defficiency. A study was conducted at the Molecular Biology Laboratory, Indonesian Center Agricultural Biotechnology and Genetic Resources (ICABIOGRAD) from October 2006 to July 2007 to identify polymorphism markers from 6 rice genotypes. The rice genotypes, i.e., Dodokan, Situ Bagendit, Batur, Kasalath, NIL-C443, and K36-5-1-1 were analyzed for polymorphisms using 496 SSR markers, which cover the rice genomes. Seven of the 496 markers were used as foreground and recombinant selection markers, and the rests (489 markers) were used as background selection markers. PCR amplifications were separated on a 5% polyacrylamide gel and colored by the silver staining method. Three different markers among the seven foreground and recombinant selection markers were selected from each crossing, which are tightly linked with Pup1 gene and have a distance less than 5 cM. These markers are Dodokan vs Kasalath (RM277, SSR3, RM519), Dodokan vs NIL-C443 (RM277, SSR3, RM519), Dodokan vs K36-5-1-1 (RM277, SSR3, RM519), Situ Bagendit vs Kasalath (RM28102, SSR3, RM519), Situ Bagendit vs NILC443 (RM28102, SSR3, RM519), Situ Bagendit vs K36-5-1-1 (RM511, SSR3, RM519), Batur vs Kasalath (RM277, RM1261, RM519), Batur vs NIL-C443 (RM277, RM1261, RM519), and Batur vs K36-5-1-1 (RM28102, SSR3). Variations in background selection primers were found in each chromosome and in each parent combinations. Primers on chromosome 4, 5, and 12 showed the lowest polymorphisms; more primers are needed for these chromosomes.},
    keywords = {microsatellite markers, rice breeding, phosphorus defficiency},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_4_2_2008_51-58.pdf},
    note = {Identifikasi Marka Polimorfik untuk Pemuliaan Padi Toleran Defisiensi Fosfor}
    }
  9. Hadiarto, Toto and Fumio Nanba. 2008. Interaction of AtMEK1-EXGT in Arabidopsis thaliana after Wounding. Jurnal agrobiogen 4 (2):59-64.
    [BibTeX] [Abstract] [PDF: Interaction of AtMEK1-EXGT in Arabidopsis thaliana after Wounding ]
    Protein interactions occur within cellular level of stimulated plant cells to relay signals from receptors to production of response. AtMEK1-EXGT interaction had been detected in nontreated Arabidopsis. In this research, interaction between AtMEK1, a mitogen-activated protein kinase kinase of Arabidopsis thaliana, and EXGT, endoxyloglucan transferase, after the plant was wounded was examined using co-immunoprecipitation and in vitro phosphorylation assay. The results demonstrated that EXGT interact with AtMEK1 soon after and 10 minutes after wounding. In addition, AtMEK1 phosphorylation activity increased when increased level of EXGT was incorporated into the reaction mixture. These indicate that EXGT amplifies wound-caused phosphorylation activity of AtMEK1. The results elucidate part of the AtMEKK1-AtMEK1-AtMPK4 cascade which is stimulated by wounding. How the complex interaction between EXGT, AtMEK1 and AtMPK4 fits within the cascade is remained to be uncovered.
    @article{TotoHadiarto08p59,
    title = {{Interaction of AtMEK1-EXGT in Arabidopsis thaliana after Wounding}},
    author = {Toto Hadiarto and Fumio Nanba},
    journal = {Jurnal AgroBiogen},
    pages = {59 - 64},
    volume = {4},
    number = {2},
    year = {2008},
    abstract = {Protein interactions occur within cellular level of stimulated plant cells to relay signals from receptors to production of response. AtMEK1-EXGT interaction had been detected in nontreated Arabidopsis. In this research, interaction between AtMEK1, a mitogen-activated protein kinase kinase of Arabidopsis thaliana, and EXGT, endoxyloglucan transferase, after the plant was wounded was examined using co-immunoprecipitation and in vitro phosphorylation assay. The results demonstrated that EXGT interact with AtMEK1 soon after and 10 minutes after wounding. In addition, AtMEK1 phosphorylation activity increased when increased level of EXGT was incorporated into the reaction mixture. These indicate that EXGT amplifies wound-caused phosphorylation activity of AtMEK1. The results elucidate part of the AtMEKK1-AtMEK1-AtMPK4 cascade which is stimulated by wounding. How the complex interaction between EXGT, AtMEK1 and AtMPK4 fits within the cascade is remained to be uncovered.},
    keywords = {endoxyloglucan transferase, atmek1, mapk, wounding},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_4_2_2008_59-64.pdf},
    note = {Interaksi AtMEK1-EXGT pada Arabidopsis thaliana pada Saat Terjadi Pelukaan}
    }
  10. Roostika, Ika, Ragapadmi Purnamaningsih, and Arief V. Noviati. 2008. The Effect of Carbon Source and Culture Condition to the Growth of Pruatjan (Pimpinella pruatjan Molk.) Culture. Jurnal agrobiogen 4 (2):65-69.
    [BibTeX] [Abstract] [PDF: The Effect of Carbon Source and Culture Condition to the Growth of Pruatjan (Pimpinella pruatjan Molk.) Culture ]
    Pruatjan (Pimpinella pruatjan Molk.) is an Indonesian medicinal plant which is categorized as endangered plant and included in Appendix I based on CITES. The in vitro conservation techniques have been studied. However, the storage period was very short (4 months) when plant growth retardant and media dilution were applied. Beside that, the residual effect of growth retardant was strong enough so that it needed more than 4 months for recovery. Thus, the use of certain carbon source may prolong the preservation period with shorter time for recovery. The objective of the study was to know the effects of carbon sources (sucrose and mannitol) and culture conditions (culture room and growth chamber) to the growth of pruatjan cultures. This application was hoped to prolong preservation period of pruatjan longer than 4 months and to cut the recovery period after presservation. The study was conducted at Tissue Culture Laboratory in Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development from August 2006 to July 2007. The activities included propagation of in vitro shoot grown in vitro as explants source, preservation of in vitro shoots of pruatjan, and regeneration of the cultures after preservation. The experiment was designed as factorial in Randomized Completely Block Design with 6 replications. The DKW basal media containing 1 ppm BA, 0.2 ppm thidiazuron, and 100 ppm arginine were supplemented with mannitol or sucrose at the level of 1, 2, 3, 4, and 5%. The observed variables were total number of leaves, number of shoot, and number of wilt leaves. The result revealed that pruatjan cultures could be stored longer than 4 months. Generally, the effect of mannitol or sucrose was more dominant than that of cultures condition. The mannitol (1-5%) strongly inhibited the growth of pruatjan cultures so that only a few cultures survived at 7 months preservation period and needed about 1 month for recovery. On the contrary, the effect of sucrose (at the same level) was better than mannitol. The 2.5% sucrose optimally inhibited pruatjan cultures. At that condition, the cultures could be stored for 10 months without morphological changes so that they could recover spontaneously.
    @article{IkaRoostika08p65,
    title = {{The Effect of Carbon Source and Culture Condition to the Growth of Pruatjan (Pimpinella pruatjan Molk.) Culture}},
    author = {Ika Roostika and Ragapadmi Purnamaningsih and Arief V. Noviati},
    journal = {Jurnal AgroBiogen},
    pages = {65 - 69},
    volume = {4},
    number = {2},
    year = {2008},
    abstract = {Pruatjan (Pimpinella pruatjan Molk.) is an Indonesian medicinal plant which is categorized as endangered plant and included in Appendix I based on CITES. The in vitro conservation techniques have been studied. However, the storage period was very short (4 months) when plant growth retardant and media dilution were applied. Beside that, the residual effect of growth retardant was strong enough so that it needed more than 4 months for recovery. Thus, the use of certain carbon source may prolong the preservation period with shorter time for recovery. The objective of the study was to know the effects of carbon sources (sucrose and mannitol) and culture conditions (culture room and growth chamber) to the growth of pruatjan cultures. This application was hoped to prolong preservation period of pruatjan longer than 4 months and to cut the recovery period after presservation. The study was conducted at Tissue Culture Laboratory in Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development from August 2006 to July 2007. The activities included propagation of in vitro shoot grown in vitro as explants source, preservation of in vitro shoots of pruatjan, and regeneration of the cultures after preservation. The experiment was designed as factorial in Randomized Completely Block Design with 6 replications. The DKW basal media containing 1 ppm BA, 0.2 ppm thidiazuron, and 100 ppm arginine were supplemented with mannitol or sucrose at the level of 1, 2, 3, 4, and 5%. The observed variables were total number of leaves, number of shoot, and number of wilt leaves. The result revealed that pruatjan cultures could be stored longer than 4 months. Generally, the effect of mannitol or sucrose was more dominant than that of cultures condition. The mannitol (1-5%) strongly inhibited the growth of pruatjan cultures so that only a few cultures survived at 7 months preservation period and needed about 1 month for recovery. On the contrary, the effect of sucrose (at the same level) was better than mannitol. The 2.5% sucrose optimally inhibited pruatjan cultures. At that condition, the cultures could be stored for 10 months without morphological changes so that they could recover spontaneously.},
    keywords = {pimpinella pruatjan molk, carbon sources, culture conditions},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_4_2_2008_65-69.pdf},
    note = {Pengaruh Sumber Karbon dan Kondisi Inkubasi terhadap Pertumbuhan Kultur In Vitro Purwoceng (Pimpinella pruatjan Molk.)}
    }
  11. Tasliah, Reflinur, and Masdiar Bustamam. 2008. Genetic Diversity of Rice Blast Fungus Pyricularia oryzae Based on a Specific Primer Pot-2 (Rep-PCR). Jurnal agrobiogen 4 (2):70-76.
    [BibTeX] [Abstract] [PDF: Genetic Diversity of Rice Blast Fungus Pyricularia oryzae Based on a Specific Primer Pot-2 (Rep-PCR) ]
    Rice blast (Pyricularia oryzae) is one of the most important diseases of rice. It can be very destructive in the field, when the environmental conditions are favourable. Information on genetic diversity of this pathogen could assist plant breeders in determining strategy for a successful control of the disease. This study was conducted to analyze genetic diversity in P. oryzae isolates by a pair of Pot-2 primers using the rep-PCR technique. These primers were designed from a transposon element of the entire blast fungus genomic DNA. DNA samples were extracted from 212 isolates of P. oryzae collected from two endemic areas of the disease in Indonesia, i.e., Tamanbogo, Lampung, and Sukabumi, West Java, as well as from some non-endemic areas in North Sumatra and West Sumatra). Results of the study indicated that the 212 isolates could clustered into 21 haplotypes. The most dominant haplotypes as indicated by their highest frequency of haplotypes were haplotype Pot 2-019 (54.46%) followed by haplotype Pot 2-021 (14.73%) and haplotipe Pot 2-016 (6.25%). Regardless of origins of the P. oryzae isolates, we found 6 haplotypes from Tamanbogo (out of 117 samples), 13 haplotypes from Sukabumi (out of 77 samples), and 11 haplotypes from North Sumatra and West Sumatra (out of 18 isolates). It seems that genetic diversity of the P. oryzae isolates was not affected by the total number of samples/isolates, but rather by place of the origin and rice genotypes from which the isolates were collected.
    @article{Tasliah08p70,
    title = {{Genetic Diversity of Rice Blast Fungus Pyricularia oryzae Based on a Specific Primer Pot-2 (Rep-PCR)}},
    author = {Tasliah and Reflinur and Masdiar Bustamam},
    journal = {Jurnal AgroBiogen},
    pages = {70 - 76},
    volume = {4},
    number = {2},
    year = {2008},
    abstract = {Rice blast (Pyricularia oryzae) is one of the most important diseases of rice. It can be very destructive in the field, when the environmental conditions are favourable. Information on genetic diversity of this pathogen could assist plant breeders in determining strategy for a successful control of the disease. This study was conducted to analyze genetic diversity in P. oryzae isolates by a pair of Pot-2 primers using the rep-PCR technique. These primers were designed from a transposon element of the entire blast fungus genomic DNA. DNA samples were extracted from 212 isolates of P. oryzae collected from two endemic areas of the disease in Indonesia, i.e., Tamanbogo, Lampung, and Sukabumi, West Java, as well as from some non-endemic areas in North Sumatra and West Sumatra). Results of the study indicated that the 212 isolates could clustered into 21 haplotypes. The most dominant haplotypes as indicated by their highest frequency of haplotypes were haplotype Pot 2-019 (54.46%) followed by haplotype Pot 2-021 (14.73%) and haplotipe Pot 2-016 (6.25%). Regardless of origins of the P. oryzae isolates, we found 6 haplotypes from Tamanbogo (out of 117 samples), 13 haplotypes from Sukabumi (out of 77 samples), and 11 haplotypes from North Sumatra and West Sumatra (out of 18 isolates). It seems that genetic diversity of the P. oryzae isolates was not affected by the total number of samples/isolates, but rather by place of the origin and rice genotypes from which the isolates were collected.},
    keywords = {genetic diversity, pyricularia oryzae, pot-2 primer, rep-pcr},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_4_2_2008_70-76.pdf},
    note = {Keragaman Genetik Isolat Cendawan Pyricularia oryzae Menggunakan Primer Pot-2 (Rep-PCR)}
    }
  12. Pabendon, Marcia B., M. Azrai, M. J. Mejaya, and Sutrisno. 2008. Genetic Diversity of QPM and Normal Maize Inbreds as Revealed by SSR Markers and Its Relationship with the Hybrid Performance. Jurnal agrobiogen 4 (2):77-82.
    [BibTeX] [Abstract] [PDF: Genetic Diversity of QPM and Normal Maize Inbreds as Revealed by SSR Markers and Its Relationship with the Hybrid Performance ]
    Information on genetic divergence of inbred lines and performance of the hybrids developed from the lines is a great value in maize hybrid program. A study was conducted to evaluate genetic diversity of six QPM and five normal maize inbred lines, to determine the relationship between genetic distance based on SSR markers and the grain yield of single cross hybrid, and to get information promising hybrid from the single cross of QPM hybrid. Twenty four polymorphic primers that covered the 10 maize chromosomes were used to fingerprint the lines, detecting in 94 alleles (average of 3.9 and a range of 2-6 alleles per locus). Genetic divergences were determined using the Jaccard’s similarity coefficient, and a dendrogram was constructed using the UPGMA. Cluster analysis divided the inbreds into two clusters that were confirmed by principal coordinate analysis. Two promising QPM hybrids that are crossed from different heterotic group were found. The estimated value of simple correlations (r) of GDs with the gain yield of single cross hybrid was negatif (-0.07). There is a need to conduct more field trials to obtain more accurate correlations, particularly in a practical utility for predicting maize hybrid performance for grain yield.
    @article{Pabendon08p77,
    title = {{Genetic Diversity of QPM and Normal Maize Inbreds as Revealed by SSR Markers and Its Relationship with the Hybrid Performance}},
    author = {Marcia B. Pabendon and M. Azrai and M. J. Mejaya and Sutrisno},
    journal = {Jurnal AgroBiogen},
    pages = {77 - 82},
    volume = {4},
    number = {2},
    year = {2008},
    abstract = {Information on genetic divergence of inbred lines and performance of the hybrids developed from the lines is a great value in maize hybrid program. A study was conducted to evaluate genetic diversity of six QPM and five normal maize inbred lines, to determine the relationship between genetic distance based on SSR markers and the grain yield of single cross hybrid, and to get information promising hybrid from the single cross of QPM hybrid. Twenty four polymorphic primers that covered the 10 maize chromosomes were used to fingerprint the lines, detecting in 94 alleles (average of 3.9 and a range of 2-6 alleles per locus). Genetic divergences were determined using the Jaccard's similarity coefficient, and a dendrogram was constructed using the UPGMA. Cluster analysis divided the inbreds into two clusters that were confirmed by principal coordinate analysis. Two promising QPM hybrids that are crossed from different heterotic group were found. The estimated value of simple correlations (r) of GDs with the gain yield of single cross hybrid was negatif (-0.07). There is a need to conduct more field trials to obtain more accurate correlations, particularly in a practical utility for predicting maize hybrid performance for grain yield.},
    keywords = {maize, qpm and normal inbreds, ssr, genetic distance, hybrid performance},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_4_2_2008_77-82.pdf},
    note = {Keragaman Genetik Inbrida Jagung QPM dan Normal Berbasis Marka Mikrosatelit dan Hubungannya dengan Penampilan Hibrida}
    }
  13. Hutami, Sri. 2008. Browning Problems in Tissue Culture. Jurnal agrobiogen 4 (2):83-88.
    [BibTeX] [Abstract] [PDF: Browning Problems in Tissue Culture ]
    Several tropical plant species contain high concentrations of phenolic compounds, which become oxidised when their cells are wounded or when the plant parts become senescences. In tissue culture, the phenolic compounds usually leach into the medium from the cut surfaces of explants. The phenolic compounds caused the culture medium turns to dark brown in colour due to oxidation. This is detrimental to the culture, because it causes the isolated tissue fails to grow. The browning of tissue culture and the medium can often be prevented by one of the several different approaches, such as by removing the phenolic compounds produced, modifying the redox potential, inactivating phenolase enzymes, reducing phenolase activity and substrate availability, as well as pre-treatments by soaking and preconditioning on a basal medium.
    @article{SriHutami08p83,
    title = {{Browning Problems in Tissue Culture}},
    author = {Sri Hutami},
    journal = {Jurnal AgroBiogen},
    pages = {83 - 88},
    volume = {4},
    number = {2},
    year = {2008},
    abstract = {Several tropical plant species contain high concentrations of phenolic compounds, which become oxidised when their cells are wounded or when the plant parts become senescences. In tissue culture, the phenolic compounds usually leach into the medium from the cut surfaces of explants. The phenolic compounds caused the culture medium turns to dark brown in colour due to oxidation. This is detrimental to the culture, because it causes the isolated tissue fails to grow. The browning of tissue culture and the medium can often be prevented by one of the several different approaches, such as by removing the phenolic compounds produced, modifying the redox potential, inactivating phenolase enzymes, reducing phenolase activity and substrate availability, as well as pre-treatments by soaking and preconditioning on a basal medium.},
    keywords = {browning, phenolic compounds, tissue culture},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_4_2_2008_83.pdf},
    note = {Masalah Pencoklatan pada Kultur Jaringan}
    }

2007

  1. Damayanti, Diani, Sudarsono, Ika Mariska, and M. Herman. 2007. Papaya Regeneration by In Vitro Culture. Jurnal agrobiogen 3 (2):49-54.
    [BibTeX] [Abstract] [PDF: Papaya Regeneration by In Vitro Culture ]
    A study was conducted in the Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development to optimize papaya regeneration systems through in vitro culture. Four steps were done, i.e., callus induction, callus regeneration, root formation, and acclimatization. Explant materials used were immature embryos of papaya cv. Burung. Immature papaya embryos were cultured on different media. The best medium for embryogenic callus development was ½ MS + 10 mg/l 2.4-D + 60% sucrose + 143 mg/l adenine sulphate + 50 mg/l myo inositol + 400 mg/l glutamine, while that for callus embryo regeneration was MS + 0.5 mg/l GA3 + 0.1 mg/l kinetin + Morel and Wetmore Vitamin. Using this medium, the average of shoot formation was three shoots per explant of embriogenic callus, and the percentage of regenerated callus was 80%. The color of shoot derived from this treatment was green. Eighty percent of plants formed a complete root development using ½ MS + 0.5 mg/l paclobutrazol media. Media hull of rice and compost was the best medium for papaya plant acclimatization. The percentage of survival on that acclimatization step was 65%.
    @article{DianiDamayanti07p49,
    title = {{Papaya Regeneration by In Vitro Culture}},
    author = {Diani Damayanti and Sudarsono and Ika Mariska and M. Herman},
    journal = {Jurnal AgroBiogen},
    pages = {49 - 54},
    volume = {3},
    number = {2},
    year = {2007},
    abstract = {A study was conducted in the Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development to optimize papaya regeneration systems through in vitro culture. Four steps were done, i.e., callus induction, callus regeneration, root formation, and acclimatization. Explant materials used were immature embryos of papaya cv. Burung. Immature papaya embryos were cultured on different media. The best medium for embryogenic callus development was ½ MS + 10 mg/l 2.4-D + 60% sucrose + 143 mg/l adenine sulphate + 50 mg/l myo inositol + 400 mg/l glutamine, while that for callus embryo regeneration was MS + 0.5 mg/l GA3 + 0.1 mg/l kinetin + Morel and Wetmore Vitamin. Using this medium, the average of shoot formation was three shoots per explant of embriogenic callus, and the percentage of regenerated callus was 80%. The color of shoot derived from this treatment was green. Eighty percent of plants formed a complete root development using ½ MS + 0.5 mg/l paclobutrazol media. Media hull of rice and compost was the best medium for papaya plant acclimatization. The percentage of survival on that acclimatization step was 65%.},
    keywords = {papaya, callus induction, callus regeneration, in vitro culture},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_3_2_2007_49-54.pdf},
    note = {Regenerasi Pepaya melalui Kultur In Vitro}
    }
  2. Roostika, Ika, Ragapadmi Purnamaningsih, Ireng Darwati, and Ika Mariska. 2007. Manipulasi Kultur In Vitro pada Tanaman Purwoceng untuk Produksi Metabolit Sekunder. Jurnal agrobiogen 3 (2):55-59.
    [BibTeX] [Abstract] [PDF: Manipulasi Kultur In Vitro pada Tanaman Purwoceng untuk Produksi Metabolit Sekunder ]
    Purwoceng (Pimpinella pruatjan Molk. atau Pimpinella alpina KDS.) adalah tanaman obat langka yang dapat dimanfaatkan sebagai bahan obat afrodisik, diuretik, and tonik. Kultur in vitro tidak hanya dapat digunakan untuk konservasi dan perbanyakan tanaman, melainkan dapat juga diterapkan untuk produksi metabolit sekunder. Melalui teknik ini, produksi metabolit sekunder tidak bergantung kepada sumber tanaman di lapang. Penelitian ini dilakukan dengan tujuan untuk meningkatkan kadar stigmasterol melalui kultur in vitro dengan menggunakan prekursor asam mevalonat. Penelitian dibagi menjadi dua tahap, yaitu induksi kalus dan manipulasi kultur in vitro untuk meningkatkan kadar stigmasterol. Pada tahap induksi kalus, terdapat 16 perlakuan yang merupakan kombinasi perlakuan 2,4-D dan pikloram masing-masing pada taraf 0,5; 1,0; 1,5; dan 2,0 ppm. Untuk meningkatkan kadar stigmasterol, digunakan asam mevalonat pada taraf 0, 250, 500, and 750 ppm dengan masa inkubasi selama 4 dan 6 minggu. Kandungan stigmasterol dianalisis menggunakan GC-MS. Hasil penelitian menunjukkan bahwa media P2 (DKW + 2,4-D 0,5 ppm + pikloram 1,0 ppm) adalah media terbaik untuk induksi kalus. Eksplan daun lebih baik daripada eksplan petiol. Hasil analisis GC-MS menunjukkan bahwa kandungan stigmasterol tertinggi (0,0356 ppm) diperoleh dari kalus dengan masa inkubasi 4 minggu pada media dengan penambahan asam mevalonat 250 ppm. Peningkatan taraf asam mevalonat tidak mampu meningkatkan kandungan stigmasterol. Kadar tersebut mirip dengan kandungan stigmasterol pada planlet dari Gunung Putri (0,0365 ppm) dan Dieng (0,0414 ppm). Dibandingkan dengan kadarnya dalam akar tanaman dari lapang, kandungan tersebut sekitar 10-100 kali lipat lebih tinggi.
    @article{IkaRoostika07p55,
    title = {{Manipulasi Kultur In Vitro pada Tanaman Purwoceng untuk Produksi Metabolit Sekunder}},
    author = {Ika Roostika and Ragapadmi Purnamaningsih and Ireng Darwati and Ika Mariska},
    journal = {Jurnal AgroBiogen},
    pages = {55 - 59},
    volume = {3},
    number = {2},
    year = {2007},
    abstract = {Purwoceng (Pimpinella pruatjan Molk. atau Pimpinella alpina KDS.) adalah tanaman obat langka yang dapat dimanfaatkan sebagai bahan obat afrodisik, diuretik, and tonik. Kultur in vitro tidak hanya dapat digunakan untuk konservasi dan perbanyakan tanaman, melainkan dapat juga diterapkan untuk produksi metabolit sekunder. Melalui teknik ini, produksi metabolit sekunder tidak bergantung kepada sumber tanaman di lapang. Penelitian ini dilakukan dengan tujuan untuk meningkatkan kadar stigmasterol melalui kultur in vitro dengan menggunakan prekursor asam mevalonat. Penelitian dibagi menjadi dua tahap, yaitu induksi kalus dan manipulasi kultur in vitro untuk meningkatkan kadar stigmasterol. Pada tahap induksi kalus, terdapat 16 perlakuan yang merupakan kombinasi perlakuan 2,4-D dan pikloram masing-masing pada taraf 0,5; 1,0; 1,5; dan 2,0 ppm. Untuk meningkatkan kadar stigmasterol, digunakan asam mevalonat pada taraf 0, 250, 500, and 750 ppm dengan masa inkubasi selama 4 dan 6 minggu. Kandungan stigmasterol dianalisis menggunakan GC-MS. Hasil penelitian menunjukkan bahwa media P2 (DKW + 2,4-D 0,5 ppm + pikloram 1,0 ppm) adalah media terbaik untuk induksi kalus. Eksplan daun lebih baik daripada eksplan petiol. Hasil analisis GC-MS menunjukkan bahwa kandungan stigmasterol tertinggi (0,0356 ppm) diperoleh dari kalus dengan masa inkubasi 4 minggu pada media dengan penambahan asam mevalonat 250 ppm. Peningkatan taraf asam mevalonat tidak mampu meningkatkan kandungan stigmasterol. Kadar tersebut mirip dengan kandungan stigmasterol pada planlet dari Gunung Putri (0,0365 ppm) dan Dieng (0,0414 ppm). Dibandingkan dengan kadarnya dalam akar tanaman dari lapang, kandungan tersebut sekitar 10-100 kali lipat lebih tinggi.},
    keywords = {kultur in vitro, metabolit sekunder, pimpinella pruatjan molk},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_3_2_2007_55-59.pdf},
    note = {In Vitro Culture Manipulation on Pruatjan for Secondary Metabolite Production}
    }
  3. Sukmadjaja, Deden, Novianti Sunarlim, Endang G. Lestari, Ika Roostika, and Tintin Suhartini. 2007. Isolation and Culture Techniques of Rice Protoplasts. Jurnal agrobiogen 3 (3):60-65.
    [BibTeX] [Abstract] [PDF: Isolation and Culture Techniques of Rice Protoplasts ]
    Protoplast fusion or somatic hybridization technology is an alternative technology for production hybrids of plants that are difficult to be produced by conventional methods due to their sexual incompatibility. An experiment was conducted to develop techniques for isolation, purification, and culture of rice protoplasts of cultivar IR64 and a wild rice species (Oryza officinalis). Optimization of protoplast isolation and purification methods from both rice genotypes were successfully done. The highest protoplast density was obtained by digesting embryonic callus or stems of young seedling in an enzyme solution containing of 2% cellulose, 0.1% pectolyase, 0.5% macerozyme, 0.5% driselase, 5 mM ES, and 13% mannitol in CPW solution. The protoplast digestion was done for three hours by soaking in the enzyme solution followed by shaking at 50 rpm under a room temperature. Purification of the protoplasts were done by separating them from plant debris using a 25% sucrose solution. Protoplast regeneration was not successful using although different media compositions and conditions. Growth process from cell division to cell aggregate was only successful on IR64 protoplast culture on a medium that contained AgNO3.
    @article{DedenSukmadjaja07p60,
    title = {{Isolation and Culture Techniques of Rice Protoplasts}},
    author = {Deden Sukmadjaja and Novianti Sunarlim and Endang G. Lestari and Ika Roostika and Tintin Suhartini},
    journal = {Jurnal AgroBiogen},
    pages = {60 - 65},
    volume = {3},
    number = {3},
    year = {2007},
    abstract = {Protoplast fusion or somatic hybridization technology is an alternative technology for production hybrids of plants that are difficult to be produced by conventional methods due to their sexual incompatibility. An experiment was conducted to develop techniques for isolation, purification, and culture of rice protoplasts of cultivar IR64 and a wild rice species (Oryza officinalis). Optimization of protoplast isolation and purification methods from both rice genotypes were successfully done. The highest protoplast density was obtained by digesting embryonic callus or stems of young seedling in an enzyme solution containing of 2% cellulose, 0.1% pectolyase, 0.5% macerozyme, 0.5% driselase, 5 mM ES, and 13% mannitol in CPW solution. The protoplast digestion was done for three hours by soaking in the enzyme solution followed by shaking at 50 rpm under a room temperature. Purification of the protoplasts were done by separating them from plant debris using a 25% sucrose solution. Protoplast regeneration was not successful using although different media compositions and conditions. Growth process from cell division to cell aggregate was only successful on IR64 protoplast culture on a medium that contained AgNO3.},
    keywords = {protoplasts, isolation and culture, cultivated and wild rices},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_3_2_2007_60-65.pdf},
    note = {Teknik Isolasi dan Kultur Protoplas Tanaman Padi}
    }
  4. Herman, M.. 2007. Eleven Years Global Development of Bt Corn and Its Status. Jurnal agrobiogen 3 (2):73-79.
    [BibTeX] [Abstract] [PDF: Eleven Years Global Development of Bt Corn and Its Status ]
    Major insect pests of corn are the Asian corn borer, the European corn borer, and the corn root worm. The value of crop losses due to the insect pests in America is $2.6 billion, Asia $1.6 billion, Africa $0.8 billion, and Europe $0.6 billion. Prior to the use of Bt corn, farmers used a lot of insecticides to control the insect pests. Following introduction of the Bt corn in 1996, this crop has been grown over 21 million hectares by millions of farmers from 13 countries in North America, Latin America, Asia, Africa and Europe. Globally, the farmers had been benefited by grownt the Bt corn. The benefits varies, dependent on countries and level of the corn borer infestations. In 2001, the US farmers gained $125 million benefit from growing the crop. In 2002, farmers in Spain gained 11-15 million benefit from the Bt corn alone. During the period of 2003-2005, corn farmers in the Philippines gained $8 million from the Bt corn. Bt corn has not been grown commercially in Indonesia, although Bt corn MON810 has been declared as save to release in the environment by the Indonesian Biosafety Committee. In 2001-2002, farmers in South Sulawesi with had grown Bt cotton, this was the first time Bt crop in the country since the placement and implementation of the biosafety regulation by the Indonesian Government in 1998.
    @article{Herman07p73,
    title = {{Eleven Years Global Development of Bt Corn and Its Status}},
    author = {M. Herman},
    journal = {Jurnal AgroBiogen},
    pages = {73 - 79},
    volume = {3},
    number = {2},
    year = {2007},
    abstract = {Major insect pests of corn are the Asian corn borer, the European corn borer, and the corn root worm. The value of crop losses due to the insect pests in America is $2.6 billion, Asia $1.6 billion, Africa $0.8 billion, and Europe $0.6 billion. Prior to the use of Bt corn, farmers used a lot of insecticides to control the insect pests. Following introduction of the Bt corn in 1996, this crop has been grown over 21 million hectares by millions of farmers from 13 countries in North America, Latin America, Asia, Africa and Europe. Globally, the farmers had been benefited by grownt the Bt corn. The benefits varies, dependent on countries and level of the corn borer infestations. In 2001, the US farmers gained $125 million benefit from growing the crop. In 2002, farmers in Spain gained 11-15 million benefit from the Bt corn alone. During the period of 2003-2005, corn farmers in the Philippines gained $8 million from the Bt corn. Bt corn has not been grown commercially in Indonesia, although Bt corn MON810 has been declared as save to release in the environment by the Indonesian Biosafety Committee. In 2001-2002, farmers in South Sulawesi with had grown Bt cotton, this was the first time Bt crop in the country since the placement and implementation of the biosafety regulation by the Indonesian Government in 1998.},
    keywords = {corn borers, bt corn, global status},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_3_2_2007_73-79.pdf},
    note = {Sebelas Tahun Perkembangan Jagung Bt dan Statusnya secara Global}
    }
  5. Leunufna, Semuel. 2007. Cryopreservation Technique for Conservation of Plant Germplasm: Its Possible Use in Indonesia. Jurnal agrobiogen 3 (2):80-88.
    [BibTeX] [Abstract] [PDF: Cryopreservation Technique for Conservation of Plant Germplasm: Its Possible Use in Indonesia ]
    Increasing rate of plant germplasm lost in Indonesia has promoted the implementation of various methods for their conservation. Cryopreservation is a technique applicable for a long-term preservation (base collection) of plants possessing non-orthodox (recalcitrant and semi-recalcitrant) seeds and those propagated vegetatively. The technique can be used as an alternative method for orthodox seed plants preservation in the ex situ conservation system. Although field and in vitro collection methods can be applied for the non-orthodox seed plants, a number of disadvantages possesed by these methods, especially in the tropics or the developing countries, deny their use for the establishment of a long-term germplasm collection. Successful implementation of the cryopreservation technique is supported by the development of protocols, which are able to provide a high recovery rate for species understudy, using vitrification based methods which are simple, economical, applicable to complex organs, and able to implement a high number of explants per experiment. The availability of infrastructures including in vitro culture laboratories, continue supply of liquid nitrogen is highly supporting the use of cryopreservation technique in Indonesia.
    @article{SemuelLeunufna07p80,
    title = {{Cryopreservation Technique for Conservation of Plant Germplasm: Its Possible Use in Indonesia}},
    author = {Semuel Leunufna},
    journal = {Jurnal AgroBiogen},
    pages = {80 - 88},
    volume = {3},
    number = {2},
    year = {2007},
    abstract = {Increasing rate of plant germplasm lost in Indonesia has promoted the implementation of various methods for their conservation. Cryopreservation is a technique applicable for a long-term preservation (base collection) of plants possessing non-orthodox (recalcitrant and semi-recalcitrant) seeds and those propagated vegetatively. The technique can be used as an alternative method for orthodox seed plants preservation in the ex situ conservation system. Although field and in vitro collection methods can be applied for the non-orthodox seed plants, a number of disadvantages possesed by these methods, especially in the tropics or the developing countries, deny their use for the establishment of a long-term germplasm collection. Successful implementation of the cryopreservation technique is supported by the development of protocols, which are able to provide a high recovery rate for species understudy, using vitrification based methods which are simple, economical, applicable to complex organs, and able to implement a high number of explants per experiment. The availability of infrastructures including in vitro culture laboratories, continue supply of liquid nitrogen is highly supporting the use of cryopreservation technique in Indonesia.},
    keywords = {cryopreservation technique, long term preservation plant germplasm},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_3_2_2007_80-88.pdf},
    note = {Kriopreservasi untuk Konservasi Plasma Nutfah Tanaman: Peluang Pemanfaatannya di Indonesia}
    }
  6. Lestari, Puji, Dwi N. Susilowati, and Eny I. Riyanti. 2007. Effect of Indole Acetic Acid Produced by Azospirillum sp. On Rice Root Growth Development. Jurnal agrobiogen 3 (2):66-72.
    [BibTeX] [Abstract] [PDF: Effect of Indole Acetic Acid Produced by Azospirillum sp. On Rice Root Growth Development ]
    Free-living bacteria of the genus Azospirillum live in close association with rice roots. This bacteria produced indole acetic acid (IAA), a plant growth hormon, to the environment. IAA was isolated from cultures of Azospirillum strains and investigated for its effect on root development and plant height of rice variety IR64 in vitro. Rice cultures of variety IR64 were grown in vitro and inoculated with cultures of Azospirilllum. Production of IAA by the bacterium during its growth period in rice culture medium containing different levels of nitrogen was observed. Results of the experiment showed that strains Azospirillum Az15 and Az44 had a high ability to produce IAA, i.e., 57.93 $\mu$g/ml at 12 days after incubation (DAI) and 40.42 $\mu$g/ml at 7 DAI, respectively. The IAA production pattern of Azospirillum Az15 and Az44 in the liquid medium were fluctuative until the end of the incubation period, while that of the strain Az7 was linier. Strain Az7 gave a better effect on the root development and plant height than strains Az15 and Az44. Treatment combination of strain Az7 and 100% nitrogen gave highest root development. High level of nitrogen increased IAA content in the uninoculated culture, while low IAA content on the inoculated one. Inoculation the culture with strain Az7 together with 50% nitrogen application resulted in the IAA content, root dry weight, root length, fiber root number, and plant height as high as those on cultures containing 100% nitrogen (1 mM NH4NO3) without inoculation. Inoculation of rice culture with Azospirillum is expected to reduce nitrogen application on rice IR64 by the IAA production as indicated by significant changes in the root growth and development. A higher concentrations of IAA tend to give better effects on the root growth and development of rice IR64.
    @article{PujiLestari07p66,
    title = {{Effect of Indole Acetic Acid Produced by Azospirillum sp. On Rice Root Growth Development}},
    author = {Puji Lestari and Dwi N. Susilowati and Eny I. Riyanti},
    journal = {Jurnal AgroBiogen},
    pages = {66 - 72},
    volume = {3},
    number = {2},
    year = {2007},
    abstract = {Free-living bacteria of the genus Azospirillum live in close association with rice roots. This bacteria produced indole acetic acid (IAA), a plant growth hormon, to the environment. IAA was isolated from cultures of Azospirillum strains and investigated for its effect on root development and plant height of rice variety IR64 in vitro. Rice cultures of variety IR64 were grown in vitro and inoculated with cultures of Azospirilllum. Production of IAA by the bacterium during its growth period in rice culture medium containing different levels of nitrogen was observed. Results of the experiment showed that strains Azospirillum Az15 and Az44 had a high ability to produce IAA, i.e., 57.93 $\mu$g/ml at 12 days after incubation (DAI) and 40.42 $\mu$g/ml at 7 DAI, respectively. The IAA production pattern of Azospirillum Az15 and Az44 in the liquid medium were fluctuative until the end of the incubation period, while that of the strain Az7 was linier. Strain Az7 gave a better effect on the root development and plant height than strains Az15 and Az44. Treatment combination of strain Az7 and 100% nitrogen gave highest root development. High level of nitrogen increased IAA content in the uninoculated culture, while low IAA content on the inoculated one. Inoculation the culture with strain Az7 together with 50% nitrogen application resulted in the IAA content, root dry weight, root length, fiber root number, and plant height as high as those on cultures containing 100% nitrogen (1 mM NH4NO3) without inoculation. Inoculation of rice culture with Azospirillum is expected to reduce nitrogen application on rice IR64 by the IAA production as indicated by significant changes in the root growth and development. A higher concentrations of IAA tend to give better effects on the root growth and development of rice IR64.},
    keywords = {azospirillum, indole acetic acid, nitrogen fertilization, rice plant},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_3_2_2007_66-72.pdf},
    note = {Pengaruh Hormon Asam Indol Asetat yang Dihasilkan Azospirillum sp. Terhadap Perkembangan Akar Padi}
    }
  7. Utami, Dwinita W., Dinar A. Ambarwati, Aniversari Apriana, Atmitri Sisharmini, Ida Hanarida, Didier Tharreau, and Santosa. 2007. Resistance Spectrum of Double Haploid Lines Derived from IR64 and Wild Rice Species, Oryza rufipogon Contained the Blast Resistance QTL (Pir). Jurnal agrobiogen 3 (1):1-8.
    [BibTeX] [Abstract] [PDF: Resistance Spectrum of Double Haploid Lines Derived from IR64 and Wild Rice Species, Oryza rufipogon Contained the Blast Resistance QTL (Pir) ]
    This study was initiated to determine the spectrum resistance of the candidate durable blast resistance variety contained the QTL (quantitative trait locus), Pir1 and 2. This QTL was mapped on chromosome 2 detected using the advanced backcross population (BC5) from the wild rice species Oryza rufipogon to IR64. Pir (1 and 2) also established on double haploid (DH) population derived from the selected lines of BC2F3 population, progenies from the same parents. The DH lines were developed to speed up the fixation process of the recessive alleles in the selected lines. Near isogenic lines with different blast resistance genes and combination were used in this study comparing to the DH population on their resistance spectrum using the known avr gene isolates both on green house and field screening. The determination of the resistance spectrum will useful on the prediction of durability of blast resistance gene in DH population. The results of spectrum resistance test in green house and field showed that Pir1and Pir2 segregated on 1 : 1 proportion related with specific respond to blast avr gene PH14 and CM28 resistance. Pir1 was identic to Pi33 or Pi25 and Pir2 to Pitq5 on spectrum resistance.
    @article{Utami07p1,
    title = {{Resistance Spectrum of Double Haploid Lines Derived from IR64 and Wild Rice Species, Oryza rufipogon Contained the Blast Resistance QTL (Pir)}},
    author = {Dwinita W. Utami and A. Dinar Ambarwati and Aniversari Apriana and Atmitri Sisharmini and Ida Hanarida and Didier Tharreau and Santosa},
    journal = {Jurnal AgroBiogen},
    pages = {1 - 8},
    volume = {3},
    number = {1},
    year = {2007},
    abstract = {This study was initiated to determine the spectrum resistance of the candidate durable blast resistance variety contained the QTL (quantitative trait locus), Pir1 and 2. This QTL was mapped on chromosome 2 detected using the advanced backcross population (BC5) from the wild rice species Oryza rufipogon to IR64. Pir (1 and 2) also established on double haploid (DH) population derived from the selected lines of BC2F3 population, progenies from the same parents. The DH lines were developed to speed up the fixation process of the recessive alleles in the selected lines. Near isogenic lines with different blast resistance genes and combination were used in this study comparing to the DH population on their resistance spectrum using the known avr gene isolates both on green house and field screening. The determination of the resistance spectrum will useful on the prediction of durability of blast resistance gene in DH population. The results of spectrum resistance test in green house and field showed that Pir1and Pir2 segregated on 1 : 1 proportion related with specific respond to blast avr gene PH14 and CM28 resistance. Pir1 was identic to Pi33 or Pi25 and Pir2 to Pitq5 on spectrum resistance.},
    keywords = {double haploid lines, ir64, oryza rufipogon},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_3_1_2007_1-8.pdf},
    note = {Spektrum Ketahanan Galur Haploid Ganda Turunan IR64 dan Oryza rufipogon yang mengandung QTL Ketahanan terhadap Penyakit Blas (Pir)}
    }
  8. Sutoro, Abdul Bari, Subandi, and Sudirman Yahya. 2007. Genetic Parameter of Secondary Traits of Corn in Bisma Population under Different Fertilizer Application. II. Genetic Variance and Correlation of Secondary Traits. Jurnal agrobiogen 3 (1):9-14.
    [BibTeX] [Abstract] [PDF: Genetic Parameter of Secondary Traits of Corn in Bisma Population under Different Fertilizer Application. II. Genetic Variance and Correlation of Secondary Traits ]
    The magnitute of secondary traits of corn could affect the corn yield. Genetic parameter value of secondary traits are important in plant breeding, especially in selection program. Genetic parameter could be used for estimation of correlated response by involving value of genetic correlation and genetic variance. Value of genetic parameter is different among population and environment. Genetic parameter of secondary traits on Bisma population under 3 different level of fertilizer application were studied in Bogor. Result of the study showed that addtive genetic variance of ASI, chlorofil, seed number, amount of green leaves and LAI at flowering stage greater than dominant variance. Conversely, additive genetic variance of green leaf number and LAI at maturing stage, and leaf senescene are lower than dominant variance. ASI has greatest heritability among secondary traits under three level of fertilizer application. Positive genetic correlation was found between grain yield under low fertileizer application and ASI under high level fertilizer application or between grain yield under high level of fertilizer application and ASI under low level fertilizer application.
    @article{Sutoro07p9,
    title = {{Genetic Parameter of Secondary Traits of Corn in Bisma Population under Different Fertilizer Application. II. Genetic Variance and Correlation of Secondary Traits}},
    author = {Sutoro and Abdul Bari and Subandi and Sudirman Yahya},
    journal = {Jurnal AgroBiogen},
    pages = {9 - 14},
    volume = {3},
    number = {1},
    year = {2007},
    abstract = {The magnitute of secondary traits of corn could affect the corn yield. Genetic parameter value of secondary traits are important in plant breeding, especially in selection program. Genetic parameter could be used for estimation of correlated response by involving value of genetic correlation and genetic variance. Value of genetic parameter is different among population and environment. Genetic parameter of secondary traits on Bisma population under 3 different level of fertilizer application were studied in Bogor. Result of the study showed that addtive genetic variance of ASI, chlorofil, seed number, amount of green leaves and LAI at flowering stage greater than dominant variance. Conversely, additive genetic variance of green leaf number and LAI at maturing stage, and leaf senescene are lower than dominant variance. ASI has greatest heritability among secondary traits under three level of fertilizer application. Positive genetic correlation was found between grain yield under low fertileizer application and ASI under high level fertilizer application or between grain yield under high level of fertilizer application and ASI under low level fertilizer application.},
    keywords = {secondary trait, genetic variance, corn},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_3_1_2007_9-14.pdf},
    note = {Parameter Genetik Jagung Populasi Bisma pada Pemupukan yang Berbeda. II. Ragam dan Korelasi Genetik Karakter Sekunder}
    }
  9. Susilowati, Dwi N., Ratih D. Hastuti, and Erny Yuniarti. 2007. Isolation and Characterization of Actinomycetes Producing Antibacterial Compound into Enteropatogenik Escherichia coli K1.1, Pseudomonas pseudomallei 02 05 and Listeria monocytogenes 5407. Jurnal agrobiogen 3 (1):15-23.
    [BibTeX] [Abstract] [PDF: Isolation and Characterization of Actinomycetes Producing Antibacterial Compound into Enteropatogenik Escherichia coli K1.1, Pseudomonas pseudomallei 02 05 and Listeria monocytogenes 5407 ]
    The resistance of bacterial pathogens to some antibacterial agents and side effects of the antibacterial usage demanded discovery of new effective, safe, and active antibacterial compounds. Some pathogenic bacteria, such as enteropathogen Escherichia coli (EPEC) that cause diarrhoea on children and infants, Pseudomonas pseudomallei that cause melioidosis on human and animal, and Listeria monocytogenes that cause listeriosis on newly born babies mortality and death of pregnant woman. Actinomycetes is the largest bacterial group that produce antibiotics. More than 10,000 antibacterial compounds had been discovered, two-third of them were produced by this bacterial group. A study was done to isolate and characterize Actinomycetes producing antibacterial compounds effective against EPEC K1.1 and P. pseudomallei 02 05. Soil samples were taken from 39 locations in Indonesia and 115 actinomycetes isolates were obtained. Two of the isolates, i.e., isolate A3.5 that was effective against P. pseudomallei 02 05 and isolate F6.1 that was effective against EPEC K1.1 evaluated further. The isolate A3.5 had an optimum time 72 hours to produce antibacterial compound, while F6.1 took 96 hours. The antibacterial compounds produced by both isolates were dissolve in the a 70% ethyl acetate solution, but not in a 40oC warm methanol solution because it is very dissolved. The antibacterial compound extracted from the isolate A3.5 had a similar effectiveness to antibiotics bacithracyn 10 unit and neomycin 30 g. On the other hand, the antibacterial compound extracted from isolate F6.1 had a similar effectiveness to antibiotics colistin 10 g and doxyciclin 30 g. Further identification of the isolates suggested that both of them belongs to the genera Streptomyces.
    @article{Susilowati07p15,
    title = {{Isolation and Characterization of Actinomycetes Producing Antibacterial Compound into Enteropatogenik Escherichia coli K1.1, Pseudomonas pseudomallei 02 05 and Listeria monocytogenes 5407}},
    author = {Dwi N. Susilowati and Ratih D. Hastuti and Erny Yuniarti},
    journal = {Jurnal AgroBiogen},
    pages = {15 - 23},
    volume = {3},
    number = {1},
    year = {2007},
    abstract = {The resistance of bacterial pathogens to some antibacterial agents and side effects of the antibacterial usage demanded discovery of new effective, safe, and active antibacterial compounds. Some pathogenic bacteria, such as enteropathogen Escherichia coli (EPEC) that cause diarrhoea on children and infants, Pseudomonas pseudomallei that cause melioidosis on human and animal, and Listeria monocytogenes that cause listeriosis on newly born babies mortality and death of pregnant woman. Actinomycetes is the largest bacterial group that produce antibiotics. More than 10,000 antibacterial compounds had been discovered, two-third of them were produced by this bacterial group. A study was done to isolate and characterize Actinomycetes producing antibacterial compounds effective against EPEC K1.1 and P. pseudomallei 02 05. Soil samples were taken from 39 locations in Indonesia and 115 actinomycetes isolates were obtained. Two of the isolates, i.e., isolate A3.5 that was effective against P. pseudomallei 02 05 and isolate F6.1 that was effective against EPEC K1.1 evaluated further. The isolate A3.5 had an optimum time 72 hours to produce antibacterial compound, while F6.1 took 96 hours. The antibacterial compounds produced by both isolates were dissolve in the a 70% ethyl acetate solution, but not in a 40oC warm methanol solution because it is very dissolved. The antibacterial compound extracted from the isolate A3.5 had a similar effectiveness to antibiotics bacithracyn 10 unit and neomycin 30 g. On the other hand, the antibacterial compound extracted from isolate F6.1 had a similar effectiveness to antibiotics colistin 10 g and doxyciclin 30 g. Further identification of the isolates suggested that both of them belongs to the genera Streptomyces.},
    keywords = {actinomycetes, antibacterial compound, escherichia coli k1, 1, pseudomonas pseudomallei 02 05, listeria monocytogenes 5407},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_3_1_2007_15-23.pdf},
    note = {Isolasi dan Karakterisasi Aktinomisetes Penghasil Antibakteri Enteropatogen Escherichia coli K1.1, Pseudomonas pseudomallei 02 05, and Listeria monocytogenes 5407}
    }
  10. Kadir, Abdul, Surjono H. Sutjahjo, Gustav A. Wattimena, and Ika Mariska. 2007. The Effect of Gamma Irradiation on Calli Growth and Patchouly Planlet Variation. Jurnal agrobiogen 3 (1):24-31.
    [BibTeX] [Abstract] [PDF: The Effect of Gamma Irradiation on Calli Growth and Patchouly Planlet Variation ]
    This research was objected to study the effect of gamma irradiation on growth of calli and plantlet and phenotypic variation of patchouly plantlet. Research was conducted at the Tissue Culture Laboratory of Center for Agricultural Biotechnology and Genetic Resources Research and Development, Bogor. Gamma irradiation treatment was done at the Centre for Research and Development of Isotop and Radiation Technology, BATAN, Jakarta. The treatment consisted of 5 level of irradiation i.e. 0 (control), 5, 10, 15, and 20 Gy of gamma irradiation. The result showed that gamma irradiation of 20 Gy decrease calli quality index and increased percentage of calli death and inhibited calli growth at 30, 60 and 90 days after irradiation, also decrese number of shoots. Gamma irradiation of 5 Gy and 10 Gy increased growth planlet compared 15 Gy and 20 Gy, meanwhile gamma irradiation at 20 Gy induced high frequency of phenotypic variation of patchouly plantlet.
    @article{AbdulKadir07p24,
    title = {{The Effect of Gamma Irradiation on Calli Growth and Patchouly Planlet Variation}},
    author = {Abdul Kadir and Surjono H. Sutjahjo and Gustav A. Wattimena and Ika Mariska},
    journal = {Jurnal AgroBiogen},
    pages = {24 - 31},
    volume = {3},
    number = {1},
    year = {2007},
    abstract = {This research was objected to study the effect of gamma irradiation on growth of calli and plantlet and phenotypic variation of patchouly plantlet. Research was conducted at the Tissue Culture Laboratory of Center for Agricultural Biotechnology and Genetic Resources Research and Development, Bogor. Gamma irradiation treatment was done at the Centre for Research and Development of Isotop and Radiation Technology, BATAN, Jakarta. The treatment consisted of 5 level of irradiation i.e. 0 (control), 5, 10, 15, and 20 Gy of gamma irradiation. The result showed that gamma irradiation of 20 Gy decrease calli quality index and increased percentage of calli death and inhibited calli growth at 30, 60 and 90 days after irradiation, also decrese number of shoots. Gamma irradiation of 5 Gy and 10 Gy increased growth planlet compared 15 Gy and 20 Gy, meanwhile gamma irradiation at 20 Gy induced high frequency of phenotypic variation of patchouly plantlet.},
    keywords = {gamma irradiation, calli of patchouli, phenotypic variation},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_3_1_2007_24-31.pdf}
    }
  11. Sianipar, Nesti F., Gustav A. Wattimena, Hajrial Aswidinnoor, Maggy Thenawidjaya S, Nurita Toruan-Mathius, and Gale Ginting. 2007. Morphological Characterization on Abnormalities of Oilpalm (Elaeis guineensis Jacq) Embryo Somatic Generated from Leaf Explant. Jurnal agrobiogen 3 (1):32-39.
    [BibTeX] [Abstract] [PDF: Morphological Characterization on Abnormalities of Oilpalm (Elaeis guineensis Jacq) Embryo Somatic Generated from Leaf Explant ]
    Somatic embryogenesis is the development of somatic cells to form a structure alike zygotic embryo direct or indirectly. Somatic embryos from young leaf explants could be induced from primary callus formed surrounding the palm-leaf rib. Embryogenic callus will develop to be somatic embryos which grew nonuniformly. Embryo somatic growth pattern of globular, asymmetric heart shape, and cotyledon ary stage produced different morphological variation. Morphological variability of in vitro somatic embryos could be due to high application of growth regulator 2,4-D at the beginning of initiation, subculture frequency, loaded cells, and polysomic cells from certain tissues. From the three clones used, which were clone 638, 636, and 558, there were different variation at each step of development stages, grouping morphologically into normal and abnormal based on the development of somatic embryos. The percentage of abnormality from the three clone used was clone 27% (638), 30% (636), and 46% (558). The normal somatic embryos at globular stage were round and bipolar shaped; while the abnormal embryos were oval and no bipolar. At heart-shape stage, the normal somatic embryos had symmetrical polarized surface; while the abnormal embryos had asymmetrical polarized surface. At the cotyledon stage, the normal embryos had monocot-tyledon; the abnormal ones were more than one cotyledon.
    @article{Sianipar07p32,
    title = {{Morphological Characterization on Abnormalities of Oilpalm (Elaeis guineensis Jacq) Embryo Somatic Generated from Leaf Explant}},
    author = {Nesti F. Sianipar and Gustav A. Wattimena and Hajrial Aswidinnoor and Maggy Thenawidjaya S and Nurita Toruan-Mathius and Gale Ginting},
    journal = {Jurnal AgroBiogen},
    pages = {32 - 39},
    volume = {3},
    number = {1},
    year = {2007},
    abstract = {Somatic embryogenesis is the development of somatic cells to form a structure alike zygotic embryo direct or indirectly. Somatic embryos from young leaf explants could be induced from primary callus formed surrounding the palm-leaf rib. Embryogenic callus will develop to be somatic embryos which grew nonuniformly. Embryo somatic growth pattern of globular, asymmetric heart shape, and cotyledon ary stage produced different morphological variation. Morphological variability of in vitro somatic embryos could be due to high application of growth regulator 2,4-D at the beginning of initiation, subculture frequency, loaded cells, and polysomic cells from certain tissues. From the three clones used, which were clone 638, 636, and 558, there were different variation at each step of development stages, grouping morphologically into normal and abnormal based on the development of somatic embryos. The percentage of abnormality from the three clone used was clone 27% (638), 30% (636), and 46% (558). The normal somatic embryos at globular stage were round and bipolar shaped; while the abnormal embryos were oval and no bipolar. At heart-shape stage, the normal somatic embryos had symmetrical polarized surface; while the abnormal embryos had asymmetrical polarized surface. At the cotyledon stage, the normal embryos had monocot-tyledon; the abnormal ones were more than one cotyledon.},
    keywords = {elaeis guineensis, somatic abnormality, morphology},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_3_1_2007_32-39.pdf},
    note = {Karakterisasi secara Morfologi Abnormalitas Embrio Somatik Kelapa Sawit (Elaeis guineensis Jacq) dari Eksplan Daun}
    }
  12. Bahagiawati and Sutrisno. 2007. Application of Genetically Modified Crops: Status, Regulation, and Detection Method in Indonesia. Jurnal agrobiogen 3 (1):40-48.
    [BibTeX] [Abstract] [PDF: Application of Genetically Modified Crops: Status, Regulation, and Detection Method in Indonesia ]
    Global area of transgenic crop was increase tremendously. The number of country accepting of planting and/or marketing the transgenic crops and its derivative products also become more numberous. However, due to existing controversy on the benefit and risk, the application of transgenic crops was governed by regulations to protect the consumer and environment from its unwanted effects. There are some international conventions that managing and controlling the uses of these crops, one of them was Cartagena protocol that Indonesia ratified in 2004. Indonesia also launched a regulation upon labelling package food derived from transgenic crops in 1999. To implement either the Cartagena protocol and labelling regulation, Indonesia needs to increase its capacity to detect the present of the transgenic crop product either in raw, and proceesed food. This review will discuss about the development of the application of transgenic crop and its product globally, and list of transgenic crops that have been accepted and approved as safe for human consumption and environment. The regulations upon the application of transgenic crop in Indonesia also be informed. Some metodologies to detect the presence of the genetically modified food that are generally use in some countries also be discussed in this review.
    @article{Bahagiawati07p40,
    title = {{Application of Genetically Modified Crops: Status, Regulation, and Detection Method in Indonesia}},
    author = {Bahagiawati and Sutrisno},
    journal = {Jurnal AgroBiogen},
    pages = {40 - 48},
    volume = {3},
    number = {1},
    year = {2007},
    abstract = {Global area of transgenic crop was increase tremendously. The number of country accepting of planting and/or marketing the transgenic crops and its derivative products also become more numberous. However, due to existing controversy on the benefit and risk, the application of transgenic crops was governed by regulations to protect the consumer and environment from its unwanted effects. There are some international conventions that managing and controlling the uses of these crops, one of them was Cartagena protocol that Indonesia ratified in 2004. Indonesia also launched a regulation upon labelling package food derived from transgenic crops in 1999. To implement either the Cartagena protocol and labelling regulation, Indonesia needs to increase its capacity to detect the present of the transgenic crop product either in raw, and proceesed food. This review will discuss about the development of the application of transgenic crop and its product globally, and list of transgenic crops that have been accepted and approved as safe for human consumption and environment. The regulations upon the application of transgenic crop in Indonesia also be informed. Some metodologies to detect the presence of the genetically modified food that are generally use in some countries also be discussed in this review.},
    keywords = {transgenic crop, regulation, detection method, laboratory},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_3_1_2007_40-48.pdf},
    note = {Application of Genetically Modified Crops: Status, Regulation and Detection Method in Indonesia}
    }

2006

  1. Santoso, T. J., D. W. Utami, and E. M. Septiningsih. 2006. DNA Fingerprinting Analysis of Soybean Germplasm using SSR Markers. Jurnal agrobiogen 2 (1):1-7.
    [BibTeX] [Abstract] [PDF: DNA Fingerprinting Analysis of Soybean Germplasm using SSR Markers ]
    Accuracy is an important issue for plant germplasm identification, especially for varietal conformation, registration, and plant protection. A study was conducted to determine genetic variation in 96 soybean accessions based on variation in size and number alelles using fluorescently-labeled SSR (Simple Sequence Repeat) markers on a capillary-electrophoresis DNA analyzer. This technology can be used to measure sizes of DNA fragments accurately and the genotyping protocol can be automated in a high-throughput manner. In addition, the germplasm as a whole can be further analyzed to measure the amount of genetic diversity and to identify agronomically-important genes or alleles for variety improvement. Results of the study indicated that nearly all the soyben accessions tested showed unique DNA fingerprints or genetic identities. The rare alleles (frequency <5\%) that might have the potential in the variety improvement program had also been detected. Identification of the 96 soybean accessions using 10 SSR markers had detected 116 alleles, ranging between 7-19 alleles per locus, with the value of PIC (Polymorphism Information Content), reflecting the value of frequency and allele variation) 0.703. The tendency for clustering together of the allelles in certain groups of the improved soyben varieties indicating that there were close genetic relationships among them. In addition, molecular differences between two accessions having the same names but with different number of registrations were de-tected. Furthermore, the presence of two soybean accessions with different names but having the same molecular identity was also identified.
    @article{Santoso06p1,
    abstract = "Accuracy is an important issue for plant germplasm identification, especially for varietal conformation, registration, and plant protection. A study was conducted to determine genetic variation in 96 soybean accessions based on variation in size and number alelles using fluorescently-labeled SSR (Simple Sequence Repeat) markers on a capillary-electrophoresis DNA analyzer. This technology can be used to measure sizes of DNA fragments accurately and the genotyping protocol can be automated in a high-throughput manner. In addition, the germplasm as a whole can be further analyzed to measure the amount of genetic diversity and to identify agronomically-important genes or alleles for variety improvement. Results of the study indicated that nearly all the soyben accessions tested showed unique DNA fingerprints or genetic identities. The rare alleles (frequency <5\%) that might have the potential in the variety improvement program had also been detected. Identification of the 96 soybean accessions using 10 SSR markers had detected 116 alleles, ranging between 7-19 alleles per locus, with the value of PIC (Polymorphism Information Content), reflecting the value of frequency and allele variation) 0.703. The tendency for clustering together of the allelles in certain groups of the improved soyben varieties indicating that there were close genetic relationships among them. In addition, molecular differences between two accessions having the same names but with different number of registrations were de-tected. Furthermore, the presence of two soybean accessions with different names but having the same molecular identity was also identified.",
    author = "Santoso, T. J. and Utami, D. W. and Septiningsih, E. M.",
    file = "http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_2_1_2006_01-07.pdf",
    institution = "Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumberdaya Genetik Pertanian",
    journal = "Jurnal AgroBiogen",
    keywords = "dna fingerprinting; soybean genetic diversity",
    note = "Analisis Sidik Jari DNA Plasma Nutfah Kedelai Menggunakan Markah SSR",
    number = "1",
    pages = "1--7",
    title = "{DNA Fingerprinting Analysis of Soybean Germplasm using SSR Markers}",
    volume = "2",
    year = "2006"
    }
  2. Rahmawati, Syamsidah. 2006. Development Status of Rice Genetic Improvement using Agrobacterium Transformation. Jurnal agrobiogen 2 (1):36-44.
    [BibTeX] [Abstract] [PDF: Development Status of Rice Genetic Improvement using Agrobacterium Transformation ]
    Genetic transformation of rice becomes an important research area in recent years. Rice is staple food for almost half of world population and has been extensively used as a plant model system for monocotyledonous plant. Compare to direct DNA transfer techniques (PEG, electroporation, and DNA bombardment), Agrobacterium tumefaciens-mediated transformation was considered to be more advantageous because it is easy to handle, integration and segregation pattern are more predictable, and the likelihood to get transgenic plant with low copy number is high, thus decreasing gene silencing phenomena. Various important genes have been introduced into rice genome via Agrobacterium transformation. A number of important factors affecting the Agrobacterium transformation and the application of this technique in the next future will be discussed.
    @article{SyamsidahRahmawati06p36,
    abstract = "Genetic transformation of rice becomes an important research area in recent years. Rice is staple food for almost half of world population and has been extensively used as a plant model system for monocotyledonous plant. Compare to direct DNA transfer techniques (PEG, electroporation, and DNA bombardment), Agrobacterium tumefaciens-mediated transformation was considered to be more advantageous because it is easy to handle, integration and segregation pattern are more predictable, and the likelihood to get transgenic plant with low copy number is high, thus decreasing gene silencing phenomena. Various important genes have been introduced into rice genome via Agrobacterium transformation. A number of important factors affecting the Agrobacterium transformation and the application of this technique in the next future will be discussed.",
    author = "Rahmawati, Syamsidah",
    file = "http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_2_1_2006_36-44.pdf",
    journal = "Jurnal AgroBiogen",
    keywords = "rice; genetic improvement",
    note = "Status Perkembangan Perbaikan Sifat Genetik Padi Menggunakan Transformasi Agrobacterium",
    number = "1",
    pages = "36--44",
    title = "{Development Status of Rice Genetic Improvement using Agrobacterium Transformation}",
    volume = "2",
    year = "2006"
    }
  3. Suryadi, Yadi, Ifa Manzila, Alina Akhdiya, and Etty Pratiwi. 2006. Production and Evaluation of Polyclonal Antibody for Detection of Photorhabdus spp. Toxin. Jurnal agrobiogen 2 (1):16-23.
    [BibTeX] [Abstract] [PDF: Production and Evaluation of Polyclonal Antibody for Detection of Photorhabdus spp. Toxin ]
    The research was aimed to produce and evaluate polyclonal antibody (PAb) for specific Photorhabdus spp. bacterial toxin detection. Photorhabdus spp. toxin of HJ isolates which was purified using Hi Prep. 16/60 Sephacryl S-200 HR column chromatography revealed three different peaks of polypeptides. The results showed that the protein concentration of crude antigen protein (supernatant) was 3,711 µg/µl, whilst fraction of protein was 1,95 x 10-2 µg/µl, respectively. The bioassay using Tenebrio molitor larvae-3 indicated that after 48 h application, the percentage of larvae mortality by crude antigen was lower (73\%) than by fraction antigen (93\%). Based upon NCM-ELISA test, PAb of fraction protein derived from HJ isolate reacted with Photorhabdus spp. antigen yielded stronger or darker violet color on membrane than that of crude protein. In addition, it was observed that PAb could differentiate specifically Photorhabdus spp. toxin with other bacterial filtrate such as Xanthomonas oryzae pv oryzae, X. campestris pv glycinea, Ralstonia solanacearum, Pseudomonas syringae pv glycinea and P. fluorescens, however it showed cross reaction with Escherichia coli. Further tests are needed in optimizing PAb-Photorhabdus spp. sensitivity to achieve effective concentration for detection of Photorhabdus spp. toxin as well as specificity test against other bacterial antigens.
    @article{YadiSuryadi06p16,
    abstract = "The research was aimed to produce and evaluate polyclonal antibody (PAb) for specific Photorhabdus spp. bacterial toxin detection. Photorhabdus spp. toxin of HJ isolates which was purified using Hi Prep. 16/60 Sephacryl S-200 HR column chromatography revealed three different peaks of polypeptides. The results showed that the protein concentration of crude antigen protein (supernatant) was 3,711 µg/µl, whilst fraction of protein was 1,95 x 10-2 µg/µl, respectively. The bioassay using Tenebrio molitor larvae-3 indicated that after 48 h application, the percentage of larvae mortality by crude antigen was lower (73\%) than by fraction antigen (93\%). Based upon NCM-ELISA test, PAb of fraction protein derived from HJ isolate reacted with Photorhabdus spp. antigen yielded stronger or darker violet color on membrane than that of crude protein. In addition, it was observed that PAb could differentiate specifically Photorhabdus spp. toxin with other bacterial filtrate such as Xanthomonas oryzae pv oryzae, X. campestris pv glycinea, Ralstonia solanacearum, Pseudomonas syringae pv glycinea and P. fluorescens, however it showed cross reaction with Escherichia coli. Further tests are needed in optimizing PAb-Photorhabdus spp. sensitivity to achieve effective concentration for detection of Photorhabdus spp. toxin as well as specificity test against other bacterial antigens.",
    author = "Suryadi, Yadi and Manzila, Ifa and Akhdiya, Alina and Pratiwi, Etty",
    file = "http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_2_1_2006_16-23.pdf",
    journal = "Jurnal AgroBiogen",
    keywords = "photorhabdus spp; pab; ncm-elisa",
    note = "Produksi dan Evaluasi Antibodi Poliklonal untuk Deteksi Toksin Photorhabdus spp.",
    number = "1",
    pages = "16--23",
    title = "{Production and Evaluation of Polyclonal Antibody for Detection of Photorhabdus spp. Toxin}",
    volume = "2",
    year = "2006"
    }
  4. Enggarini, Wening and Erly Marwani. 2006. The Effects of Aluminum Stress on Organic Acid Content of Lycopersicon esculentum Mill. Cv. Intan Callus and Plantlet. Jurnal agrobiogen 2 (1):24-28.
    [BibTeX] [Abstract] [PDF: The Effects of Aluminum Stress on Organic Acid Content of Lycopersicon esculentum Mill. Cv. Intan Callus and Plantlet ]
    The purpose of this research was to evaluate the effects of Al stress on citric, malic and oxalic acid content of L. esculentum cv. Intan callus and plantlet, also aluminum content of L. esculentum plantlet. Callus was induced from cotyledone of L. esculentum on Murashige & Skoog (MS) media containing 10-7 M NAA and 10-6 kinetin. The callus was then transferred step wisely at 3 weeks interval to media containing 220, 275, 330, 385, 440, 550, 825, and 1100 µM AlCl3. The callus cultures on the control media and media with the addition of 550 µM AlCl3 were able to regenerate and produce shoots after 8 passages of subculture. The shoots from media with the addition of 550 µM AlCl3 were transferred into the media with addition of 825 µM AlCl3, then to the media with 1100 µM AlCl3. The High Pressure Liquid Chromatography (HPLC) analysis showed that Al stress callus and plantlets contained malic acid, but no citric and oxalic acid. The content of malic acid in callus decreased with increasing AlCl3 concentration from 0 to 385 µM. On the other hand, the content of malic acid in callus increased with increasing AlCl3 concentration from 440 µM to 1100 µM. Similarly, the content of malic acid in root increased with increasing concentration of AlCl3 from 550 µM to 1100 µM. The result of Neutron Activation Analysis showed that Al content in root decreased as the amount of AlCl3 increased in the media. These results suggested that L. esculentum callus and plantlet respond to the Al stress by producing higher amount of malic acid.
    @article{WeningEnggarini06p24,
    abstract = "The purpose of this research was to evaluate the effects of Al stress on citric, malic and oxalic acid content of L. esculentum cv. Intan callus and plantlet, also aluminum content of L. esculentum plantlet. Callus was induced from cotyledone of L. esculentum on Murashige \& Skoog (MS) media containing 10-7 M NAA and 10-6 kinetin. The callus was then transferred step wisely at 3 weeks interval to media containing 220, 275, 330, 385, 440, 550, 825, and 1100 µM AlCl3. The callus cultures on the control media and media with the addition of 550 µM AlCl3 were able to regenerate and produce shoots after 8 passages of subculture. The shoots from media with the addition of 550 µM AlCl3 were transferred into the media with addition of 825 µM AlCl3, then to the media with 1100 µM AlCl3. The High Pressure Liquid Chromatography (HPLC) analysis showed that Al stress callus and plantlets contained malic acid, but no citric and oxalic acid. The content of malic acid in callus decreased with increasing AlCl3 concentration from 0 to 385 µM. On the other hand, the content of malic acid in callus increased with increasing AlCl3 concentration from 440 µM to 1100 µM. Similarly, the content of malic acid in root increased with increasing concentration of AlCl3 from 550 µM to 1100 µM. The result of Neutron Activation Analysis showed that Al content in root decreased as the amount of AlCl3 increased in the media. These results suggested that L. esculentum callus and plantlet respond to the Al stress by producing higher amount of malic acid.",
    author = "Enggarini, Wening and Marwani, Erly",
    file = "http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_2_1_2006_24-28.pdf",
    journal = "Jurnal AgroBiogen",
    keywords = "aluminum; organic acid; lycopersicon esculentum",
    note = "Pengaruh Cekaman Aluminium terhadap Kandungan Asam Organik dalam Kalus dan Pinak Tomat (Lycopersicon esculentum Mill.)",
    number = "1",
    pages = "24--28",
    title = "{The Effects of Aluminum Stress on Organic Acid Content of Lycopersicon esculentum Mill. Cv. Intan Callus and Plantlet}",
    volume = "2",
    year = "2006"
    }
  5. Dewi, Iswari S., Bambang S. Purwoko, Hajrial Aswidinnoor, Ida H. Somantri, and M. A. Chozin. 2006. Plant Regeneration from Anther Culture of Several Accessions of Indica Rice Tolerant to Aluminum. Jurnal agrobiogen 2 (1):30-35.
    [BibTeX] [Abstract] [PDF: Plant Regeneration from Anther Culture of Several Accessions of Indica Rice Tolerant to Aluminum ]
    Anther culture provides the quick route in obtaining pure lines in a single generation from either green haploid plant that may be artificially or spontaneously doubled. Indica rice known as recalcitrant genotype because of its difficulty in regenerating sufficient number of green plantlets among the regenerated plants through anther culture. Whilst, research on studying anther culture ability has to be done to assure the success of rice breeding through anther culture. The objective of this research was to determine regeneration ability of five accessions of indica rice tolerance to aluminum through application of putrescine in anther culture. Completely randomized design with 15 replications was used in this research. Treatments consisted of five accessions of aluminum tolerance indica rice, ie. CT6510-24-1-3, Grogol, Hawara Bunar, Krowal, and Sigundil. Callus induction medium based on N6 medium + 10-3 M putrescine, while regeneration medium based on MS + 10-3 M putrescine. The results indicated that culture ability is controlled by the genotype. From this research, Grogol, Krowal and Sigundil were selected as accessions having good rice anther culture ability, and therefore can be used as parents for developing new rice varieties tolerance to aluminum through anther culture.
    @article{Dewi06p30,
    abstract = "Anther culture provides the quick route in obtaining pure lines in a single generation from either green haploid plant that may be artificially or spontaneously doubled. Indica rice known as recalcitrant genotype because of its difficulty in regenerating sufficient number of green plantlets among the regenerated plants through anther culture. Whilst, research on studying anther culture ability has to be done to assure the success of rice breeding through anther culture. The objective of this research was to determine regeneration ability of five accessions of indica rice tolerance to aluminum through application of putrescine in anther culture. Completely randomized design with 15 replications was used in this research. Treatments consisted of five accessions of aluminum tolerance indica rice, ie. CT6510-24-1-3, Grogol, Hawara Bunar, Krowal, and Sigundil. Callus induction medium based on N6 medium + 10-3 M putrescine, while regeneration medium based on MS + 10-3 M putrescine. The results indicated that culture ability is controlled by the genotype. From this research, Grogol, Krowal and Sigundil were selected as accessions having good rice anther culture ability, and therefore can be used as parents for developing new rice varieties tolerance to aluminum through anther culture.",
    author = "Dewi, Iswari S. and Purwoko, Bambang S. and Aswidinnoor, Hajrial and Somantri, Ida H. and Chozin, M. A.",
    file = "http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_2_1_2006_30-35.pdf",
    journal = "Jurnal AgroBiogen",
    keywords = "rice; subspecies indica; anther culture; plant",
    note = "Regenerasi Tanaman pada Kultur Antera Beberapa Aksesi Padi Indica Toleran Aluminium",
    number = "1",
    pages = "30--35",
    title = "{Plant Regeneration from Anther Culture of Several Accessions of Indica Rice Tolerant to Aluminum}",
    volume = "2",
    year = "2006"
    }
  6. Lestari, Puji, Kyujung Van, Moon Young Kim, and Suk-Ha Lee. 2006. Nodulasi dan Pertumbuhan Mutan Kedelai Penghasil Nodulsuper SS2-2 dalam Asosiasi Simbiotik dengan Bradyrhizobium japonicum. Jurnal agrobiogen 2 (1):8-15.
    [BibTeX] [Abstract] [PDF: Nodulasi dan Pertumbuhan Mutan Kedelai Penghasil Nodulsuper SS2-2 dalam Asosiasi Simbiotik dengan Bradyrhizobium japonicum ]
    Mutan kedelai penghasil nodulsuper menunjukkan kelemahan dalam kontrol autoregulasi pada nodulasi dan perbedaan fenotip dibandingkan dengan tipe liarnya. Studi untuk mengevaluasi karakter pertumbuhan dan nodulasi dari kedelai penghasil nodulsuper dalam asosiasinya dengan Bradyrhizobium japonicum dilakukan dalam penelitian ini. Tiga genotip kedelai, yaitu mutan kedelai penghasil nodulsuper SS2-2, tipe liarnya Sinpaldalkong 2 dan kedelai kontrol Jangyeobkong diinokulasi dengan B. japonicum USDA 110, kemudian ditumbuhkan di rumah kaca dalam kondisi terkontrol. Karakter nodulasi, fiksasi nitrogen (Acetylene Reduction Activity/ARA), pertumbuhan tanaman, dan hasil biji ditentukan untuk mengevaluasi asosiasi simbiotik antara B. japonicum dan kedelai nodulsuper. Kedelai yang diinokulasi dengan B. japonicum menunjukkan peningkatan jumlah dan berat kering nodul serta berat kering total tanaman dibandingkan dengan tanpa inokulasi. Tanaman SS2-2 yang diinokulasi menunjukkan jumlah nodul sekitar 20 kali lipat lebih tinggi daripada tipe liarnya. Inokulasi B. japonicum ternyata juga meningkatkan fiksasi nitrogen seiring dengan perkembangan nodul. Tanaman S2-2 lebih pendek dan menghasilkan fik-sasi nitrogen (ARA) lebih tinggi, tetapi spesifik ARA dan hasil biji lebih rendah dibandingkan dengan tipe liarnya. Berda-sarkan hasil evaluasi terhadap nodulasi dan pertumbuhan-nya, interaksi Rhizobium dan kedelai penghasil nodulsuper SS2-2 mempunyai respon asosiasi simbiotik lebih rendah dibandingkan kedelai penghasil nodul normal (kedelai yang tidak mendapat perlakuan mutasi).
    @article{PujiLestari06p8,
    abstract = "Mutan kedelai penghasil nodulsuper menunjukkan kelemahan dalam kontrol autoregulasi pada nodulasi dan perbedaan fenotip dibandingkan dengan tipe liarnya. Studi untuk mengevaluasi karakter pertumbuhan dan nodulasi dari kedelai penghasil nodulsuper dalam asosiasinya dengan Bradyrhizobium japonicum dilakukan dalam penelitian ini. Tiga genotip kedelai, yaitu mutan kedelai penghasil nodulsuper SS2-2, tipe liarnya Sinpaldalkong 2 dan kedelai kontrol Jangyeobkong diinokulasi dengan B. japonicum USDA 110, kemudian ditumbuhkan di rumah kaca dalam kondisi terkontrol. Karakter nodulasi, fiksasi nitrogen (Acetylene Reduction Activity/ARA), pertumbuhan tanaman, dan hasil biji ditentukan untuk mengevaluasi asosiasi simbiotik antara B. japonicum dan kedelai nodulsuper. Kedelai yang diinokulasi dengan B. japonicum menunjukkan peningkatan jumlah dan berat kering nodul serta berat kering total tanaman dibandingkan dengan tanpa inokulasi. Tanaman SS2-2 yang diinokulasi menunjukkan jumlah nodul sekitar 20 kali lipat lebih tinggi daripada tipe liarnya. Inokulasi B. japonicum ternyata juga meningkatkan fiksasi nitrogen seiring dengan perkembangan nodul. Tanaman S2-2 lebih pendek dan menghasilkan fik-sasi nitrogen (ARA) lebih tinggi, tetapi spesifik ARA dan hasil biji lebih rendah dibandingkan dengan tipe liarnya. Berda-sarkan hasil evaluasi terhadap nodulasi dan pertumbuhan-nya, interaksi Rhizobium dan kedelai penghasil nodulsuper SS2-2 mempunyai respon asosiasi simbiotik lebih rendah dibandingkan kedelai penghasil nodul normal (kedelai yang tidak mendapat perlakuan mutasi).",
    author = "Lestari, Puji and Van, Kyujung and Kim, Moon Young and Lee, Suk-Ha",
    file = "http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_2_1_2006_08-15.pdf",
    journal = "Jurnal AgroBiogen",
    keywords = "bradyrhizobium japonicum; fiksasi nitrogen; fenotip; kedelai nodulsuper",
    note = "Nodulation and Growth of a Supernodulating Soybean Mutant SS2-2 Symbiotically Associated with Bradyrhizobium japonicum",
    number = "1",
    pages = "8--15",
    title = "{Nodulasi dan Pertumbuhan Mutan Kedelai Penghasil Nodulsuper SS2-2 dalam Asosiasi Simbiotik dengan Bradyrhizobium japonicum}",
    volume = "2",
    year = "2006"
    }
  7. Damayanti, Buchari, Nurindah, H. Rijzaani, Dwinita W. Utami, B. Sahari, Bahagiawati, and A. Sari. 2006. Population Structure of Trichogrammatoidea armigera, Egg Parasitoid of Helicoverpa armigera Based on RAPDPCR Analysis. Jurnal agrobiogen 2 (2):52-58.
    [BibTeX] [Abstract] [PDF: Population Structure of Trichogrammatoidea armigera, Egg Parasitoid of Helicoverpa armigera Based on RAPDPCR Analysis ]
    Genetic structures of Trichogrammatoidea armigera (Hymenoptera: Trichogrammatidae), the egg parasitoid of Helicoverpa armigera (Lepidoptera: Noctuidae) were studied. Egg masses of H. armigera were collected from fields of several locations in West Java and East Java with different distances among them and two distinct cultural practices, i.e., monoculture and polyculture. Genetic relationships among T. armigera populations that emerged from the collected H. armigera eggs were analysed by the RAPD-PCR technique using four oligonucleotide primers. The four primers revealed 55 presumptive polymorphic loci that were used to estimate the population structures. The estimated values of Fixation Index (Fst) was 0.16, indicating that there was a division of the populations into subpopulations. This Fst value implied the present of reproductive isolation among the populations that might be due to their low migration rate (1.3 insect per generation). This low migration rate indicated the present of low level of gene flow among the populations. A dendrogram resulted from the NTSYS analysis indicated that the West Java and East Java populations of the egg parasitoid had quite wide genetic distances, while within each of the populations there was a subdivision of minor populations. This finding has an important implication on the program to release Trichogramma spp. as a biological control agent. The release of the parasitoid cannot be done randomly, because if we pick up a minor population, the starter or the released population will mate with the local population and multiply, thus the inundation will fail to control the target pest.
    @article{Damayanti06p52,
    title = {{Population Structure of Trichogrammatoidea armigera, Egg Parasitoid of Helicoverpa armigera Based on RAPDPCR Analysis}},
    author = {Buchari Damayanti and Nurindah and H Rijzaani and Dwinita W. Utami and B Sahari and Bahagiawati and A. Sari},
    journal = {Jurnal AgroBiogen},
    pages = {52 - 58},
    volume = {2},
    number = {2},
    year = {2006},
    abstract = {Genetic structures of Trichogrammatoidea armigera (Hymenoptera: Trichogrammatidae), the egg parasitoid of Helicoverpa armigera (Lepidoptera: Noctuidae) were studied. Egg masses of H. armigera were collected from fields of several locations in West Java and East Java with different distances among them and two distinct cultural practices, i.e., monoculture and polyculture. Genetic relationships among T. armigera populations that emerged from the collected H. armigera eggs were analysed by the RAPD-PCR technique using four oligonucleotide primers. The four primers revealed 55 presumptive polymorphic loci that were used to estimate the population structures. The estimated values of Fixation Index (Fst) was 0.16, indicating that there was a division of the populations into subpopulations. This Fst value implied the present of reproductive isolation among the populations that might be due to their low migration rate (1.3 insect per generation). This low migration rate indicated the present of low level of gene flow among the populations. A dendrogram resulted from the NTSYS analysis indicated that the West Java and East Java populations of the egg parasitoid had quite wide genetic distances, while within each of the populations there was a subdivision of minor populations. This finding has an important implication on the program to release Trichogramma spp. as a biological control agent. The release of the parasitoid cannot be done randomly, because if we pick up a minor population, the starter or the released population will mate with the local population and multiply, thus the inundation will fail to control the target pest.},
    keywords = {trichogrammatoidea armigera, egg parasitoid},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_2_2_2006_52-58.pdf},
    note = {Struktur Populasi Trichogrammatoidea armigera, Parasitoid Telur Helicoverpa armigera, Berdasarkan Analisis RAPD-PCR}
    }
  8. Sutoro, Abdul Bari, Subandi, and Sudirman Yahya. 2006. Genetic Parameters of Bisma Maize Population under Different Levels of Fertilizer Applications. I. Additivedominant variance of grain yield.. Jurnal agrobiogen 2 (2):60-67.
    [BibTeX] [Abstract] [PDF: Genetic Parameters of Bisma Maize Population under Different Levels of Fertilizer Applications. I. Additivedominant variance of grain yield. ]
    New maize varieties could be obtained through improvement of their plant populations. The method used in selection in the crop improvement was based on values of their genetic parameters. Bisma is one of the maize varieties that has a broad genetic background. New maize varieties could be obtained by improving their population through selection under different environmental conditions. Genetic parameter value were estimated by conducting an experiment under NCD II crossing at Bogor. Twenty seven sets, which were developed from three females and three males of S1 as parents of each set, were evaluated under three different fertilization schemes. Results of the experiment showed that the additive genetic variance was significantly different from zero, and so among the different levels of fertilizer applications. The dominant variances was not significant under the three different levels of fertilization applications. The additive genetic variance was lower under the low level of fertilizer application than that on the higher level of fertilization application. This might be due to the scale effect. To reduce effect of scale, the data were transformed by dividing the grand mean value. After the data transformation, the genetic variance under the low level of fertilizer application tended to be greater than that under the higher level of fertilizer application. There was a tendency that population improvement of Bisma variety could be achieved better under lower level of fertilizer applications than under the higher ones.
    @article{Sutoro06p60,
    title = {{Genetic Parameters of Bisma Maize Population under Different Levels of Fertilizer Applications. I. Additivedominant variance of grain yield.}},
    author = {Sutoro and Abdul Bari and Subandi and Sudirman Yahya},
    journal = {Jurnal AgroBiogen},
    pages = {60 - 67},
    volume = {2},
    number = {2},
    year = {2006},
    abstract = {New maize varieties could be obtained through improvement of their plant populations. The method used in selection in the crop improvement was based on values of their genetic parameters. Bisma is one of the maize varieties that has a broad genetic background. New maize varieties could be obtained by improving their population through selection under different environmental conditions. Genetic parameter value were estimated by conducting an experiment under NCD II crossing at Bogor. Twenty seven sets, which were developed from three females and three males of S1 as parents of each set, were evaluated under three different fertilization schemes. Results of the experiment showed that the additive genetic variance was significantly different from zero, and so among the different levels of fertilizer applications. The dominant variances was not significant under the three different levels of fertilization applications. The additive genetic variance was lower under the low level of fertilizer application than that on the higher level of fertilization application. This might be due to the scale effect. To reduce effect of scale, the data were transformed by dividing the grand mean value. After the data transformation, the genetic variance under the low level of fertilizer application tended to be greater than that under the higher level of fertilizer application. There was a tendency that population improvement of Bisma variety could be achieved better under lower level of fertilizer applications than under the higher ones.},
    keywords = {additive dominant variance, maize improvent},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_2_2_2006_60-67.pdf},
    note = {Parameter Genetik Jagung Populasi Bisma pada Pemupukan Berbeda. I. Ragam Aditif-Dominan Bobot Biji Jagung}
    }
  9. Roostika, Ika, Ireng Darwati, and Ika Mariska. 2006. Regenerasi Tanaman Purwoceng (Pimpinella pruatjan Molk): Proliferasi dan Enkapsulasi Tunas Aksilar. Jurnal agrobiogen 2 (2):68-73.
    [BibTeX] [Abstract] [PDF: Regenerasi Tanaman Purwoceng (Pimpinella pruatjan Molk): Proliferasi dan Enkapsulasi Tunas Aksilar ]
    Purwoceng (Pimpinella alpina KDS atau Pimpinella pruatjan Molk.) merupakan tanaman obat asli Indonesia yang terancam punah. Akarnya dapat dimanfaatkan sebagai obat afrodisiak, diuretik, and tonik. Teknik kultur in vitro merupakan teknologi alternatif yang dapat diterapkan untuk konservasi dan perbanyakan tanaman tersebut. Mikropropagasi telah dilakukan melalui jalur organogenesis dengan proliferasi tunas aksilar dan enkapsulasi. Penelitian dilakukan di Laboratorium Kultur Jaringan BB-Biogen, Bogor mulai tahun 2004 hingga 2005. Penelitian ini terbagi atas empat percobaan, yaitu (1) optimasi lingkungan tumbuh kultur, (2) optimasi formulasi media untuk proliferasi tunas aksilar dan enkapsulasi tunas aksilar, (3) induksi perakaran, and (4) aklimatisasi. Kondisi lingkungan kultur yang optimum adalah di growth chamber dengan suhu 9oC dan intensitas cahaya 1000 lux. Formulasi media terbaik untuk proliferasi tunas aksilar adalah media DKW dengan penambahan BA 4 ppm dengan eksplan berupa tunas tanpa daun. Penggunaan arginin 100 ppm lebih baik daripada glutamin 100 ppm dan modifikasi vitamin (mioinositol 100 ppm dan thiamine-HCl 1 ppm). Pada media yang sama, pertumbuhan tunas aksilar terenkapsulasi juga paling baik dan tunas tersebut dapat menembus kapsul alginat setelah 4 minggu dalam periode in vitro (85%). Penggunaan NAA 1,0 ppm menginduksi perakaran paling cepat (40 hari) dengan persentase perakaran paling tinggi (100%). Vermikulit bertekstur kasar paling baik untuk aklimatisasi tunas aksilar terenkapsulasi sedangkan arang sekam paling baik untuk aklimatisasi planlet.
    @article{IkaRoostika06p68,
    title = {{Regenerasi Tanaman Purwoceng (Pimpinella pruatjan Molk): Proliferasi dan Enkapsulasi Tunas Aksilar}},
    author = {Ika Roostika and Ireng Darwati and Ika Mariska},
    journal = {Jurnal AgroBiogen},
    pages = {68 - 73},
    volume = {2},
    number = {2},
    year = {2006},
    abstract = {Purwoceng (Pimpinella alpina KDS atau Pimpinella pruatjan Molk.) merupakan tanaman obat asli Indonesia yang terancam punah. Akarnya dapat dimanfaatkan sebagai obat afrodisiak, diuretik, and tonik. Teknik kultur in vitro merupakan teknologi alternatif yang dapat diterapkan untuk konservasi dan perbanyakan tanaman tersebut. Mikropropagasi telah dilakukan melalui jalur organogenesis dengan proliferasi tunas aksilar dan enkapsulasi. Penelitian dilakukan di Laboratorium Kultur Jaringan BB-Biogen, Bogor mulai tahun 2004 hingga 2005. Penelitian ini terbagi atas empat percobaan, yaitu (1) optimasi lingkungan tumbuh kultur, (2) optimasi formulasi media untuk proliferasi tunas aksilar dan enkapsulasi tunas aksilar, (3) induksi perakaran, and (4) aklimatisasi. Kondisi lingkungan kultur yang optimum adalah di growth chamber dengan suhu 9oC dan intensitas cahaya 1000 lux. Formulasi media terbaik untuk proliferasi tunas aksilar adalah media DKW dengan penambahan BA 4 ppm dengan eksplan berupa tunas tanpa daun. Penggunaan arginin 100 ppm lebih baik daripada glutamin 100 ppm dan modifikasi vitamin (mioinositol 100 ppm dan thiamine-HCl 1 ppm). Pada media yang sama, pertumbuhan tunas aksilar terenkapsulasi juga paling baik dan tunas tersebut dapat menembus kapsul alginat setelah 4 minggu dalam periode in vitro (85%). Penggunaan NAA 1,0 ppm menginduksi perakaran paling cepat (40 hari) dengan persentase perakaran paling tinggi (100%). Vermikulit bertekstur kasar paling baik untuk aklimatisasi tunas aksilar terenkapsulasi sedangkan arang sekam paling baik untuk aklimatisasi planlet.},
    keywords = {organogenesis, enkapsulasi, proliferasi tunas},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_2_2_2006_68-73.pdf},
    note = {Regeneration of Pruatjan (Pimpinella pruatjan Molk): Axillary Bud Proliferation and Encapsulation}
    }
  10. Purnamaningsih, Ragapadmi. 2006. Callus Induction and Plant Regeneration of Four Rice Varieties through In Vitro Culture. Jurnal agrobiogen 2 (2):74-80.
    [BibTeX] [Abstract] [PDF: Callus Induction and Plant Regeneration of Four Rice Varieties through In Vitro Culture ]
    A study was conducted at the Tissue Culture Laboratory of ICABIOGRAD, Bogor, to obtain an optimum medium formulation for calli regenerations of for rice varities (Ciherang, Cisadane, IR64, and T-309). The research activities were done in five steps, i.e., callus induction, callus regeneration, shoot multiplication, root formation, and plant acclimatization. The type of explants used in the study was embriozygotic explants. Five media formulations were used for the callus induction, while four media formulations were used for the callus regeneration. The results showed that the best medium formulation for induction of callus formation was MS + 2,4-D 2 mg/l + casein hidrolisat 3 mg/l, while the best medium formulation for callus regeneration was MS + BA 3 mg/l + thidiazuron 0,1 mg/l.
    @article{RagapadmiPurnamaningsih06p74,
    title = {{Callus Induction and Plant Regeneration of Four Rice Varieties through In Vitro Culture}},
    author = {Ragapadmi Purnamaningsih},
    journal = {Jurnal AgroBiogen},
    pages = {74 - 80},
    volume = {2},
    number = {2},
    year = {2006},
    abstract = {A study was conducted at the Tissue Culture Laboratory of ICABIOGRAD, Bogor, to obtain an optimum medium formulation for calli regenerations of for rice varities (Ciherang, Cisadane, IR64, and T-309). The research activities were done in five steps, i.e., callus induction, callus regeneration, shoot multiplication, root formation, and plant acclimatization. The type of explants used in the study was embriozygotic explants. Five media formulations were used for the callus induction, while four media formulations were used for the callus regeneration. The results showed that the best medium formulation for induction of callus formation was MS + 2,4-D 2 mg/l + casein hidrolisat 3 mg/l, while the best medium formulation for callus regeneration was MS + BA 3 mg/l + thidiazuron 0,1 mg/l.},
    keywords = {rice, callus induction, callus regeration, in vitro},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_2_2_2006_74-80.pdf},
    note = {Induksi Kalus dan Optimasi Regenerasi Empat Varietas Padi melalui Kultur In Vitro}
    }
  11. Hutami, Sri, Ika Mariska, and Yati Supriati. 2006. Improvement of Plant Genetic Variability through Somaclonal Variations. Jurnal agrobiogen 2 (2):81-88.
    [BibTeX] [Abstract] [PDF: Improvement of Plant Genetic Variability through Somaclonal Variations ]
    High genetic variability’s are important factors in the development of new crop varieties. In vitro techniques are applicable for development of crop variability that is not found in the gene pool. One of the in vitro techniques that can be used for this purpose is the somaclonal variation technique. Somaclonal variation may be derived from genetic variations in explants and genetic variations in tissue cultures. Variations in the explant may be obtained from cell mutations or polysomic mutations of a certain tissue. Genetic variations in tissue culture may be caused by ploidy of chromosomes (endomitosis fusion), changes of chromosom structures (crossings), as well as changes of genes and cytoplasms. Changes of genetic characters may be improved if anorganic compound was added into the medium. To improve the plant tolerances to biotic or abiotic factors, selection components may also be added to the medium. Research results showed that somaclonal variation in tissue culture can improve genetic variations in plants. The variation produced in tissue culture provide chances to develop new plant genotipes. Many selection components, such as Gamma-ray irradiation, Al contents and low pH, pure toxin or filtrate, polyethylene glycol (PEG), and plant growth regulators can be used to improve somaclonal variations in many plants to produce new genotipes.
    @article{SriHutami06p81,
    title = {{Improvement of Plant Genetic Variability through Somaclonal Variations}},
    author = {Sri Hutami and Ika Mariska and Yati Supriati},
    journal = {Jurnal AgroBiogen},
    pages = {81 - 88},
    volume = {2},
    number = {2},
    year = {2006},
    abstract = {High genetic variability's are important factors in the development of new crop varieties. In vitro techniques are applicable for development of crop variability that is not found in the gene pool. One of the in vitro techniques that can be used for this purpose is the somaclonal variation technique. Somaclonal variation may be derived from genetic variations in explants and genetic variations in tissue cultures. Variations in the explant may be obtained from cell mutations or polysomic mutations of a certain tissue. Genetic variations in tissue culture may be caused by ploidy of chromosomes (endomitosis fusion), changes of chromosom structures (crossings), as well as changes of genes and cytoplasms. Changes of genetic characters may be improved if anorganic compound was added into the medium. To improve the plant tolerances to biotic or abiotic factors, selection components may also be added to the medium. Research results showed that somaclonal variation in tissue culture can improve genetic variations in plants. The variation produced in tissue culture provide chances to develop new plant genotipes. Many selection components, such as Gamma-ray irradiation, Al contents and low pH, pure toxin or filtrate, polyethylene glycol (PEG), and plant growth regulators can be used to improve somaclonal variations in many plants to produce new genotipes.},
    keywords = {genetic variability, somaclonal variation},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_2_2_2006_81-88.pdf},
    note = {Peningkatan Keragaman Genetik Tanaman melalui Keragaman Somaklonal}
    }

2005

  1. Utami, D. W., S. Moeljopawiro, H. Aswidinnoor, A. Setiawan, and I. Hanarida. 2005. Blast (Pyricularia grisea) Resistance Genes on a Wildrice Oryza rufipogon Griff. And Rice Cultivar IR64. Jurnal agrobiogen 1 (1):1-6.
    [BibTeX] [Abstract] [PDF: Blast (Pyricularia grisea) Resistance Genes on a Wildrice Oryza rufipogon Griff. And Rice Cultivar IR64 ]
    Improvement of rice for durable resistance rice blast is difficult due to the complexity of the inheritance of resistance. As study was conducted to analyze blast resistance in rice using two different approaches, i.e., blast QTL mapping and comparison of resistance spectrum and genetic control. The blast QTL mapping was done using an interspesific population originated from backcrossing between a wild rice, Oryza rufipogon, and a cultivated rice, IR64. Comparison of resistance spectrum and genetic control was based on phenotypic reactions. Results of the experiment showed that based on the blast QTL mapping, genes Pirf2-1(t) and Pir2-3(t) were mapped on chromosome 2. Gene Pirf2-1(t) was isolated from chromosome 2 of O. rufipogon and coding for resistance to P. grisea race 001, while gene Pir2-3(t), which was isolated from rice cultivar IR64, was coding for resistance to P. grisea race 173. Based on the resistance spectrum, O. rufipogon has a non-race specific resistance. Gene Pirf2-1(t) on O. rufipogon contributed a dominant mode of resistance to blast which was affected by a duplicate epistasis. The other gene, Pir2-3(t) contributed an additive mode of resistance which was affected by a complementary epistasis.
    @article{Utami05p1,
    abstract = "Improvement of rice for durable resistance rice blast is difficult due to the complexity of the inheritance of resistance. As study was conducted to analyze blast resistance in rice using two different approaches, i.e., blast QTL mapping and comparison of resistance spectrum and genetic control. The blast QTL mapping was done using an interspesific population originated from backcrossing between a wild rice, Oryza rufipogon, and a cultivated rice, IR64. Comparison of resistance spectrum and genetic control was based on phenotypic reactions. Results of the experiment showed that based on the blast QTL mapping, genes Pirf2-1(t) and Pir2-3(t) were mapped on chromosome 2. Gene Pirf2-1(t) was isolated from chromosome 2 of O. rufipogon and coding for resistance to P. grisea race 001, while gene Pir2-3(t), which was isolated from rice cultivar IR64, was coding for resistance to P. grisea race 173. Based on the resistance spectrum, O. rufipogon has a non-race specific resistance. Gene Pirf2-1(t) on O. rufipogon contributed a dominant mode of resistance to blast which was affected by a duplicate epistasis. The other gene, Pir2-3(t) contributed an additive mode of resistance which was affected by a complementary epistasis.",
    author = "Utami, D. W. and Moeljopawiro, S. and Aswidinnoor, H. and Setiawan, A. and Hanarida, I.",
    file = "http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_1_1_2005_01-06.pdf",
    institution = "Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumberdaya Genetik Pertanian",
    journal = "Jurnal AgroBiogen",
    keywords = "blast; oryza rufipogon; ir64",
    note = "Gen Pengendali Sifat Ketahanan Penyakit Blas (Pyricularia grisea Sacc.) Pada Spesies Padi Liar Oryza rufipogon Griff. Dan Padi Budi Daya IR64",
    number = "1",
    pages = "1--6",
    title = "{Blast (Pyricularia grisea) Resistance Genes on a Wildrice Oryza rufipogon Griff. And Rice Cultivar IR64}",
    volume = "1",
    year = "2005"
    }
  2. Bahagiawati. 2005. Isolation and Purification of alpha-amylase Inhibitor from Common Bean, Phaseolus vulgaris, Seed. Jurnal agrobiogen 1 (1):7-12.
    [BibTeX] [Abstract] [PDF: Isolation and Purification of alpha-amylase Inhibitor from Common Bean, Phaseolus vulgaris, Seed ]
    Plant genetic engineering technologies enable of introducing insect resistance genes into crop plants. The cry genes, genes encoding for inhibitor of digestive enzymes of a target insect that were isolated from Bacillus thuringiensis can be used for this purpose. Seeds of common bean (Phaseolus vulgaris) contain a glycoprotein that inhibits activity of alpha-amylase of insects. A alpha-amylase inhibitor was purified from the common bean seeds. The purified alpha-amylase inhibitor was then fed to cowpea storage weevil, Callosobruchus maculatus. The results showed a lengthened larval development time inside the seed and caused mortality to the insect larvae. This experiment suggests that the alpha-amylase inhibitor gene from the common bean seeds could be used as a candidate gene for genetic engineering of plant resistance to bruchid insects.
    @article{Bahagiawati05p7,
    abstract = "Plant genetic engineering technologies enable of introducing insect resistance genes into crop plants. The cry genes, genes encoding for inhibitor of digestive enzymes of a target insect that were isolated from Bacillus thuringiensis can be used for this purpose. Seeds of common bean (Phaseolus vulgaris) contain a glycoprotein that inhibits activity of alpha-amylase of insects. A alpha-amylase inhibitor was purified from the common bean seeds. The purified alpha-amylase inhibitor was then fed to cowpea storage weevil, Callosobruchus maculatus. The results showed a lengthened larval development time inside the seed and caused mortality to the insect larvae. This experiment suggests that the alpha-amylase inhibitor gene from the common bean seeds could be used as a candidate gene for genetic engineering of plant resistance to bruchid insects.",
    author = "Bahagiawati",
    file = "http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_1_1_2005_07-12.pdf",
    institution = "Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumberdaya Genetik Pertanian",
    journal = "Jurnal AgroBiogen",
    keywords = "alpha-amylase inhibitor; common bean; storage",
    note = "Isolasi dan Purifikasi Inhibitor alpha-amilase dari Biji Kacang Phaseolus vulgaris",
    number = "1",
    pages = "7--12",
    title = "{Isolation and Purification of alpha-amylase Inhibitor from Common Bean, Phaseolus vulgaris, Seed}",
    volume = "1",
    year = "2005"
    }
  3. Roostika, I., N. Sunarlim, and I. Mariska. 2005. Micropropagation of Mangosteen (Garcinia mangostana L.). Jurnal agrobiogen 1 (1999):20-25.
    [BibTeX] [Abstract] [PDF: Micropropagation of Mangosteen (Garcinia mangostana L.) ]
    The conventional propagation of mangosteen plant is still facing some problems, such as the limited fruiting season and number of seedling, and slow growth of seedling. In vitro culture is an alternative technique to solve the problems. An experiment was done to obtain a suitable micropropagation technique for mangosteen plant through in vitro culture with high level of shoot multiplication and root formation, as well as high level of acclimated shoot or planlet growth. The treatments for shoot induction and axillary bud multiplication of mangosteen were three levels of BA (1, 3, and 5 mg/l) on the MS basal medium. The treatments for root induction were combinations between two kinds of basal medium (MS and WPM), two formulations of the media (full strength and ¼ strength), and two levels of IBA (5 and 10 mg/l). Root induction was also done ex situ by dipping the shoots in IBA solutions (100-200 ppm) for 1-2 hours, followed planting onto the best acclimation media. The acclimation was done using two different media (soil only and soil + compost) under two different environments (green house and incubation room + green house). Results of the experiment showed that the highest percentages of seed growth and number of shoots per seed was obtained on the basal medium containing 5 mg/l BA. The highest number of axillary bud multiplication was obtained on the medium with 3 mg/l BA. MS medium + 5 mg/l IBA promoted 75\% rooting. The plant acclimatization on soil + compost in the green house with 75\% shading promoted the fastest plant growth. During the acclimatization, up to 75\% of the shoots treated with dipping in 100 ppm IBA solution for one hour grew well. After four months, the roots of the plant developed secondary and tertiary roots.
    @article{Roostika05p20,
    abstract = "The conventional propagation of mangosteen plant is still facing some problems, such as the limited fruiting season and number of seedling, and slow growth of seedling. In vitro culture is an alternative technique to solve the problems. An experiment was done to obtain a suitable micropropagation technique for mangosteen plant through in vitro culture with high level of shoot multiplication and root formation, as well as high level of acclimated shoot or planlet growth. The treatments for shoot induction and axillary bud multiplication of mangosteen were three levels of BA (1, 3, and 5 mg/l) on the MS basal medium. The treatments for root induction were combinations between two kinds of basal medium (MS and WPM), two formulations of the media (full strength and ¼ strength), and two levels of IBA (5 and 10 mg/l). Root induction was also done ex situ by dipping the shoots in IBA solutions (100-200 ppm) for 1-2 hours, followed planting onto the best acclimation media. The acclimation was done using two different media (soil only and soil + compost) under two different environments (green house and incubation room + green house). Results of the experiment showed that the highest percentages of seed growth and number of shoots per seed was obtained on the basal medium containing 5 mg/l BA. The highest number of axillary bud multiplication was obtained on the medium with 3 mg/l BA. MS medium + 5 mg/l IBA promoted 75\% rooting. The plant acclimatization on soil + compost in the green house with 75\% shading promoted the fastest plant growth. During the acclimatization, up to 75\% of the shoots treated with dipping in 100 ppm IBA solution for one hour grew well. After four months, the roots of the plant developed secondary and tertiary roots.",
    author = "Roostika, I. and Sunarlim, N. and Mariska, I.",
    file = "http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_1_1_2005_20-25.pdf",
    institution = "Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumberdaya Genetik Pertanian",
    journal = "Jurnal AgroBiogen",
    keywords = "garcinia mangostana; micropropagation",
    note = "Mikropropagasi Tanaman Manggis (Garcinia mangostana)",
    number = "1999",
    pages = "20--25",
    title = "{Micropropagation of Mangosteen (Garcinia mangostana L.)}",
    volume = "1",
    year = "2005"
    }
  4. Azrai, M.. 2005. Application of Marker-Assisted Selection in Crop Breeding. Jurnal agrobiogen 1 (274):26-37.
    [BibTeX] [Abstract] [PDF: Application of Marker-Assisted Selection in Crop Breeding ]
    DNA-based technology has dramatically enhanced the efficiency of plant breeding, especially when selections are to be done under unfavourable conditions. Although significant strides have been made in crop improvement trough phenotypic selections for ergonomically important traits, this often encounters considerable difficulties, particularly those posed by genotype x environment interactions. Besides testing procedure may be many times difficult, unreliable or expensive due to the nature of the target traits (e.g. abiotic and biotic stresses) or the target environment. The most widespread use of Marker Assisted Selection (MAS) to date is to assist backcrossing of major gene already proven elite cultivars. If individual genes or Quantitative Trait Loci (QTL) significantly influencing specific target traits can be identified based on their linkage to molecular markers, the efficiency of incorporating the desired traits in elite germplasm could be greatly enhanced. By combining QTL approach with backcrossing, useful genes that control quantitative traits have been identified in plant germplasm that are not for agriculture and have successfully been transferred to danced breeding lines. Indonesian molecular breeders should have a research program on DNA marker work that leads to application of useful selection tools and valuable germplasm. As molecular breeders adopt more rigorous experimental guidelines and ambitious goals, they also need to integrate the growing body of knowledge from genomics and bioinformatics.
    @article{Azrai05p26,
    abstract = "DNA-based technology has dramatically enhanced the efficiency of plant breeding, especially when selections are to be done under unfavourable conditions. Although significant strides have been made in crop improvement trough phenotypic selections for ergonomically important traits, this often encounters considerable difficulties, particularly those posed by genotype x environment interactions. Besides testing procedure may be many times difficult, unreliable or expensive due to the nature of the target traits (e.g. abiotic and biotic stresses) or the target environment. The most widespread use of Marker Assisted Selection (MAS) to date is to assist backcrossing of major gene already proven elite cultivars. If individual genes or Quantitative Trait Loci (QTL) significantly influencing specific target traits can be identified based on their linkage to molecular markers, the efficiency of incorporating the desired traits in elite germplasm could be greatly enhanced. By combining QTL approach with backcrossing, useful genes that control quantitative traits have been identified in plant germplasm that are not for agriculture and have successfully been transferred to danced breeding lines. Indonesian molecular breeders should have a research program on DNA marker work that leads to application of useful selection tools and valuable germplasm. As molecular breeders adopt more rigorous experimental guidelines and ambitious goals, they also need to integrate the growing body of knowledge from genomics and bioinformatics.",
    author = "Azrai, M.",
    file = "http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_1_1_2005_26-37.pdf",
    institution = "Balai Penelitian Tanaman Serealia",
    journal = "Jurnal AgroBiogen",
    keywords = "dna markers; selection; crops breeding",
    note = "Pemanfaatan Markah Molekuler dalam Proses Seleksi Pemuliaan Tanaman",
    number = "274",
    pages = "26--37",
    title = "{Application of Marker-Assisted Selection in Crop Breeding}",
    volume = "1",
    year = "2005"
    }
  5. Listanto, E., Sutrisno, S. J. Pardal, and M. Herman. 2005. The Insertion of alpha-amylase Inhibitor Gene into the Binary Plasmid pCambia1301. Jurnal agrobiogen 1 (43):45-52.
    [BibTeX] [Abstract] [PDF: The Insertion of alpha-amylase Inhibitor Gene into the Binary Plasmid pCambia1301 ]
    The experiment was conducted at the Molecular Biology Laboratory of the Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, Bogor. The objective was to construct alpha-ai gene on a binary plasmid pCambia 1301. This experiment was carried out using construction method by ligation process between fragments of alpha-ai gene from pTA3 plasmid and pCambia 1301 on HindIII site. The result of ligant transformation into E. coli DH5alpha was 182 surviving colonies on YEP medium containing kanamycin. DNA samples were obtained from 60 randomly selected colonies. The restriction pattern was tested by digesting each DNA sample using HindIII showed colonies containing two fragments expected of sizes wich are 11.837 and 4.887 kb. Two colonies are predicted containing of alpha-ai gene on its the binary plasmid. Advanced tests using restriction enzymes BamHI and XbaI showed two directions (right and left) of alpha-ai gene. The right direction was shown by pCambia-alpha-ai1 from colony number 43. This plasmid showed expected fragments of sizes 13.485 and 3.219 kb when digested with BamHI and two fragments of sizes 15.421 and 1.303 kb when digested with XbaI. The left direction was shown pCambia-alpha-ai2 from colony number 58. This plasmid also demon-strated expected fragments of sizes 15.026 and 1.698 kb when digested with BamHI and two fragments of sizes 13.082 and 3.642 kb when digested with XbaI. Both pCambia-alpha-ai1 and pCambia-alpha-ai2 were transformed into A. tumefaciens LBA4404.
    @article{Listanto05p45,
    abstract = "The experiment was conducted at the Molecular Biology Laboratory of the Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, Bogor. The objective was to construct alpha-ai gene on a binary plasmid pCambia 1301. This experiment was carried out using construction method by ligation process between fragments of alpha-ai gene from pTA3 plasmid and pCambia 1301 on HindIII site. The result of ligant transformation into E. coli DH5alpha was 182 surviving colonies on YEP medium containing kanamycin. DNA samples were obtained from 60 randomly selected colonies. The restriction pattern was tested by digesting each DNA sample using HindIII showed colonies containing two fragments expected of sizes wich are 11.837 and 4.887 kb. Two colonies are predicted containing of alpha-ai gene on its the binary plasmid. Advanced tests using restriction enzymes BamHI and XbaI showed two directions (right and left) of alpha-ai gene. The right direction was shown by pCambia-alpha-ai1 from colony number 43. This plasmid showed expected fragments of sizes 13.485 and 3.219 kb when digested with BamHI and two fragments of sizes 15.421 and 1.303 kb when digested with XbaI. The left direction was shown pCambia-alpha-ai2 from colony number 58. This plasmid also demon-strated expected fragments of sizes 15.026 and 1.698 kb when digested with BamHI and two fragments of sizes 13.082 and 3.642 kb when digested with XbaI. Both pCambia-alpha-ai1 and pCambia-alpha-ai2 were transformed into A. tumefaciens LBA4404.",
    author = "Listanto, E. and Sutrisno and Pardal, S. J. and Herman, M.",
    file = "http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_1_2_2005_45-52.pdf",
    institution = "Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumberdaya Genetik Pertanian",
    journal = "Jurnal AgroBiogen",
    keywords = "alpha-amylase inhibitor gene; pcambia 1301; e; coli",
    note = "Penyisipan Gen Inhibitor alpha-amilase pada Plasmid Biner pCambia 1301",
    number = "43",
    pages = "45--52",
    title = "{The Insertion of alpha-amylase Inhibitor Gene into the Binary Plasmid pCambia1301}",
    volume = "1",
    year = "2005"
    }
  6. Pardal, S. J., G. A. Wattimena, H. Aswidinnoor, and M. Herman. 2005. Genetic Transformation of Soybean Using the Proteinase Inhibitor II Gene by the Particle Bombardment Technique. Jurnal agrobiogen 1 (2):53-61.
    [BibTeX] [Abstract] [PDF: Genetic Transformation of Soybean Using the Proteinase Inhibitor II Gene by the Particle Bombardment Technique ]
    An experiment was conducted at the Molecular Biology and Genetic Engineering Laboratory of BB-Biogen, Bogor with an objective to obtain transgenic soybean plants containing the proteinase inhibitor II (pinII) gene. The experiment consisted of three steps, i.e., optimalization of the soybean transformation technique using the gus gene; transformation of soybean using the pinII gene, and molecular analysis of the transformed soybean plants. Two type of explants (young embryo and cotyledon) were bombarded with pRQ6 plasmid containing the gus gene with the following treatment: Helium gas pressure (1100 psi and 1300 psi), shoot distance (5 and 7 cm), and number of bombardment (1x and 2x). The result of gus assay indicated that the best bombardment was done on young cotyledon explants with 1100 psi Helium pressure, shoot distance 5 cm, and 1x bombardment. Transformation of the soybean explant using the pinII gene (inside the pTWa plasmid) was conducted using the best bombardment treatment from the first activity. Two plants from c.v. Wilis (WP1, WP2) and three plants from c.v. Tidar (TP1, TP2, TP3) were recovered from regeneration and selection of the transformed explants. Molecular analysis of the regenerated plants using the PCR technique showed that only WP2 contained the pinII gene. This plant was fertile and will be used for further evaluation.
    @article{Pardal05p53,
    abstract = "An experiment was conducted at the Molecular Biology and Genetic Engineering Laboratory of BB-Biogen, Bogor with an objective to obtain transgenic soybean plants containing the proteinase inhibitor II (pinII) gene. The experiment consisted of three steps, i.e., optimalization of the soybean transformation technique using the gus gene; transformation of soybean using the pinII gene, and molecular analysis of the transformed soybean plants. Two type of explants (young embryo and cotyledon) were bombarded with pRQ6 plasmid containing the gus gene with the following treatment: Helium gas pressure (1100 psi and 1300 psi), shoot distance (5 and 7 cm), and number of bombardment (1x and 2x). The result of gus assay indicated that the best bombardment was done on young cotyledon explants with 1100 psi Helium pressure, shoot distance 5 cm, and 1x bombardment. Transformation of the soybean explant using the pinII gene (inside the pTWa plasmid) was conducted using the best bombardment treatment from the first activity. Two plants from c.v. Wilis (WP1, WP2) and three plants from c.v. Tidar (TP1, TP2, TP3) were recovered from regeneration and selection of the transformed explants. Molecular analysis of the regenerated plants using the PCR technique showed that only WP2 contained the pinII gene. This plant was fertile and will be used for further evaluation.",
    author = "Pardal, S. J. and Wattimena, G. A. and Aswidinnoor, H. and Herman, M.",
    file = "http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_1_2_2005_53-61.pdf",
    journal = "Jurnal AgroBiogen",
    keywords = "soybean transformation; pinii gene; particle",
    note = "Transformasi Genetik Kedelai dengan Gen Proteinase Inhibitor II Menggunakan Teknik Penembakan Partikel",
    number = "2",
    pages = "53--61",
    title = "{Genetic Transformation of Soybean Using the Proteinase Inhibitor II Gene by the Particle Bombardment Technique}",
    volume = "1",
    year = "2005"
    }
  7. Kosmiatin, M., A. Husni, and I. Mariska. 2005. In Vitro Germination and Micropropagation of Agarwood. Jurnal agrobiogen 1 (2):62-67.
    [BibTeX] [Abstract] [PDF: In Vitro Germination and Micropropagation of Agarwood ]
    Agarwood (Aquilaria malaccensis Lank) is one of the forest wood that are continously exploited. Currently, the Indonesian export of agarwood is decreasing because its population is endangered by excessive logging. Agarwood propagations need technology for reproduction of agarwood seedlings and their fungal inoculum. In vitro technique for germination of recalsitrant seeds and micropropagation are technologies that can be used for propagation of agarwood seedlings. An experiment was done to develop techniques for in vitro germination and micropropagation of agarwood. The in vitro germination was done using two different techniques. Firstly, sterile seeds were germinated on an MS medium + 50 mg/l PVP, 50 mg/l GA, and 1 mg/l BA or kinetin. Secondly, sterile seeds were germinated on basal medium of MS, ½ MS medium, MS medium without vitamins, as well as on MS medium without pyridoxine, nicotinic acid and WPM. Shoot initiations and multiplications were done on MS and ½ MS media containing 1, 3, or 5 mg/l BA. The explants used were cotyledone nodes, terminal shoots, single node with leaf, and sinle node without leaf. The results showed that the seed germination rate on the different media ranged from 7,14 to 50\%. The seed germination rate on the MS medium without vitamis was the highest. The best explants for shoot induction and multiplication was single node with leaf which was cultured on MS + 1 mg/l BA.
    @article{Kosmiatin05p62,
    abstract = "Agarwood (Aquilaria malaccensis Lank) is one of the forest wood that are continously exploited. Currently, the Indonesian export of agarwood is decreasing because its population is endangered by excessive logging. Agarwood propagations need technology for reproduction of agarwood seedlings and their fungal inoculum. In vitro technique for germination of recalsitrant seeds and micropropagation are technologies that can be used for propagation of agarwood seedlings. An experiment was done to develop techniques for in vitro germination and micropropagation of agarwood. The in vitro germination was done using two different techniques. Firstly, sterile seeds were germinated on an MS medium + 50 mg/l PVP, 50 mg/l GA, and 1 mg/l BA or kinetin. Secondly, sterile seeds were germinated on basal medium of MS, ½ MS medium, MS medium without vitamins, as well as on MS medium without pyridoxine, nicotinic acid and WPM. Shoot initiations and multiplications were done on MS and ½ MS media containing 1, 3, or 5 mg/l BA. The explants used were cotyledone nodes, terminal shoots, single node with leaf, and sinle node without leaf. The results showed that the seed germination rate on the different media ranged from 7,14 to 50\%. The seed germination rate on the MS medium without vitamis was the highest. The best explants for shoot induction and multiplication was single node with leaf which was cultured on MS + 1 mg/l BA.",
    author = "Kosmiatin, M. and Husni, A. and Mariska, I.",
    file = "http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_1_2_2005_62-67.pdf",
    institution = "Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumberdaya Genetik Pertanian",
    journal = "Jurnal AgroBiogen",
    keywords = "aquilaria malaccensis lank; in vitro germination",
    note = "Perkecambahan dan Perbanyakan Gaharu secara In Vitro",
    number = "2",
    pages = "62--67",
    title = "{In Vitro Germination and Micropropagation of Agarwood}",
    volume = "1",
    year = "2005"
    }
  8. Lestari, E. G. and R. Purnamaningsih. 2005. In Vitro Preservation of Daun Dewa using the Minimum Growth Preservation Method. Jurnal agrobiogen 1 (2):68-72.
    [BibTeX] [Abstract] [PDF: In Vitro Preservation of Daun Dewa using the Minimum Growth Preservation Method ]
    Daun dewa (Gynura Procumbens) is a medicinal crop commonly used to remedy cancer, diabetes, and dermatitis. It has a bright prospect for future used. Plant preservations through tissue culture is done to anticipate an urgent need. An experiment was carried out to in vitro preservation of Daun Dewa by the minimum growth and regeneration to examine viability of the culture after the preservation. Terminal shoots (±1 cm) were cultured on a ½ MS basic medium + paclobutrazol (0, 1, 2, 3, and 4 mg/l) or ABA (1, 2, and 5 mg/l). The trial was arranged in a, completely randomized with 10 replications. The results showed a three-month preservation of the culture on a medium containing ABA inhibited proliferation and expansion of the plant shoots. Increasing ABA concentrations up to 5 mg/l, according to the shoot-growth inhibition, resulted in the height of 0.6 cm. After three month preservation, the shoots were able to produce roots. After 12 month preservation, the optimum capacity of growth inhibition was shown on ½ MS medium + ABA (1, 3, and 5 mg/l). The application of paclobutrazol (1, 2, 3, and 4 mg/l) in the medium produced low multiplication level of shoots, the length of the shoots remains higher than those on ½ MS medium without paclobutrazol. Seven months after preservation, viability of the plants was still high when cultured on MS medium + 2 mg/l BA combined with paclobutrazol and ABA as previously given. In addition, the rooted culture could be directly acclimatized in the glasshouse. The lowest number of shoot and shortest shoot after 12 month preservation period was found on the medium containing 5 mg/l ABA and 4 mg/l paclobutrazol, this treatment produced two shoots of 4 cm long. The best medium for the explant regeneration after 7 month preservation was MS + 2 mg/l BA. The plant shoots produced roots directly after they were acclimatized in the glasshouse.
    @article{Lestari05p68,
    abstract = "Daun dewa (Gynura Procumbens) is a medicinal crop commonly used to remedy cancer, diabetes, and dermatitis. It has a bright prospect for future used. Plant preservations through tissue culture is done to anticipate an urgent need. An experiment was carried out to in vitro preservation of Daun Dewa by the minimum growth and regeneration to examine viability of the culture after the preservation. Terminal shoots (±1 cm) were cultured on a ½ MS basic medium + paclobutrazol (0, 1, 2, 3, and 4 mg/l) or ABA (1, 2, and 5 mg/l). The trial was arranged in a, completely randomized with 10 replications. The results showed a three-month preservation of the culture on a medium containing ABA inhibited proliferation and expansion of the plant shoots. Increasing ABA concentrations up to 5 mg/l, according to the shoot-growth inhibition, resulted in the height of 0.6 cm. After three month preservation, the shoots were able to produce roots. After 12 month preservation, the optimum capacity of growth inhibition was shown on ½ MS medium + ABA (1, 3, and 5 mg/l). The application of paclobutrazol (1, 2, 3, and 4 mg/l) in the medium produced low multiplication level of shoots, the length of the shoots remains higher than those on ½ MS medium without paclobutrazol. Seven months after preservation, viability of the plants was still high when cultured on MS medium + 2 mg/l BA combined with paclobutrazol and ABA as previously given. In addition, the rooted culture could be directly acclimatized in the glasshouse. The lowest number of shoot and shortest shoot after 12 month preservation period was found on the medium containing 5 mg/l ABA and 4 mg/l paclobutrazol, this treatment produced two shoots of 4 cm long. The best medium for the explant regeneration after 7 month preservation was MS + 2 mg/l BA. The plant shoots produced roots directly after they were acclimatized in the glasshouse.",
    author = "Lestari, E. G. and Purnamaningsih, R.",
    file = "http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_1_2_2005_68-72.pdf",
    institution = "Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumberdaya Genetik Pertanian",
    journal = "Jurnal AgroBiogen",
    keywords = "in vitro preservation; gynura procumbens",
    note = "Penyimpanan In Vitro Tanaman Obat Daun Dewa melalui Pertumbuhan Minimal",
    number = "2",
    pages = "68--72",
    title = "{In Vitro Preservation of Daun Dewa using the Minimum Growth Preservation Method}",
    volume = "1",
    year = "2005"
    }
  9. Noviati, A. V., S. Hutami, I. Mariska, and E. Sjamsudin. 2005. Preliminary Screening of Soybean Genotypes from In Vitro Selection for Aluminium and Acid Soil Tolerance. Jurnal agrobiogen 1 (2):73-75.
    [BibTeX] [Abstract] [PDF: Preliminary Screening of Soybean Genotypes from In Vitro Selection for Aluminium and Acid Soil Tolerance ]
    Aluminum toxicity is a major constraint to soybean production in acid soils. Since variabilities on Al tolerance in plants are very limited, mutation breeding, and in vitro selection were used to increase the variability. Three soyben genotypes were produced from cultivars Wilis and Sindoro that have been gamma irradiated and selected in vitro for their tolerance to Al on Al and low pH media. These genotypes and their original cultivars were then planted in a greenhouse in an acid soil on May 2001. The results showed that the plant performances were varied, some were shorter and more compact than the original. Based on the yield components, a number of plants from the genotypes showed higher than those of the control cultivars. These plants were considered more tolerant to Al than the original cultivars.
    @article{Noviati05p73,
    abstract = "Aluminum toxicity is a major constraint to soybean production in acid soils. Since variabilities on Al tolerance in plants are very limited, mutation breeding, and in vitro selection were used to increase the variability. Three soyben genotypes were produced from cultivars Wilis and Sindoro that have been gamma irradiated and selected in vitro for their tolerance to Al on Al and low pH media. These genotypes and their original cultivars were then planted in a greenhouse in an acid soil on May 2001. The results showed that the plant performances were varied, some were shorter and more compact than the original. Based on the yield components, a number of plants from the genotypes showed higher than those of the control cultivars. These plants were considered more tolerant to Al than the original cultivars.",
    author = "Noviati, A. V. and Hutami, S. and Mariska, I. and Sjamsudin, E.",
    file = "http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_1_2_2005_73-75.pdf",
    journal = "Jurnal AgroBiogen",
    keywords = "soybean; al tolerance; in vitro selection; acid",
    note = "Uji Pendahuluan Genotipe-genotipe Kedelai Hasil Seleksi In Vitro terhadap Cekaman Aluminium dan pH Rendah",
    number = "2",
    pages = "73--75",
    title = "{Preliminary Screening of Soybean Genotypes from In Vitro Selection for Aluminium and Acid Soil Tolerance}",
    volume = "1",
    year = "2005"
    }
  10. Bahagiawati. 2005. Effect of Bt Transgenic Plant on Biological Agent Population. Jurnal agrobiogen 1 (2):76-84.
    [BibTeX] [Abstract] [PDF: Effect of Bt Transgenic Plant on Biological Agent Population ]
    An alternative technique to improve plant resistance to insect pests is plant transformation using the genetic engineering technology. Several transgenic plants resistant to insect have been produced and commercially released to environment in some industrial and developing countries. Before release, transgenic plants need to be assessed for their potential risks to human health and environment. One of the environmental risk assessments is the potential risk to non-target insects, including the biocontrol insects. Laboratories, glasshouse, and field experiments have been conducting the study of the impact of transgenic plant resistance to insect, especially transgenic Bt plants to the population of predators and parasitoids. However the results were controversial. The objective of this review is to inform some of controversial results, and to suggest serial experiments need to be done to solve the problem. The impact of the transgenic plant resistance to insects depends on several factors, such as genes that are used to transform the plants, the kind of plant pests, and the kind and stages of the insect natural enemies. Results of the experiments were influenced by sites of the experiments (laboratory, glasshouse, or field) and contact of the natural enemies to the toxin. Some experiments showed that the transgenic Bt plants have no impact to the natural enemies population, and otherwise. Due to the controversial results, the experiment and assessment should be done in depth and carefully studied. A sequential experiments need to be adopted to avoid the misleading interpretation, and the assessment need to be based on a case by case study.
    @article{Bahagiawati05p76,
    abstract = "An alternative technique to improve plant resistance to insect pests is plant transformation using the genetic engineering technology. Several transgenic plants resistant to insect have been produced and commercially released to environment in some industrial and developing countries. Before release, transgenic plants need to be assessed for their potential risks to human health and environment. One of the environmental risk assessments is the potential risk to non-target insects, including the biocontrol insects. Laboratories, glasshouse, and field experiments have been conducting the study of the impact of transgenic plant resistance to insect, especially transgenic Bt plants to the population of predators and parasitoids. However the results were controversial. The objective of this review is to inform some of controversial results, and to suggest serial experiments need to be done to solve the problem. The impact of the transgenic plant resistance to insects depends on several factors, such as genes that are used to transform the plants, the kind of plant pests, and the kind and stages of the insect natural enemies. Results of the experiments were influenced by sites of the experiments (laboratory, glasshouse, or field) and contact of the natural enemies to the toxin. Some experiments showed that the transgenic Bt plants have no impact to the natural enemies population, and otherwise. Due to the controversial results, the experiment and assessment should be done in depth and carefully studied. A sequential experiments need to be adopted to avoid the misleading interpretation, and the assessment need to be based on a case by case study.",
    author = "Bahagiawati",
    file = "http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_1_2_2005_76-84.pdf",
    institution = "Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumberdaya Genetik Pertanian",
    journal = "Jurnal AgroBiogen",
    keywords = "transgenic bt plants; potential risks; impact to",
    note = "Dampak Tanaman Transgenik Bt terhadap Populasi Serangga Pengendali Hayati",
    number = "2",
    pages = "76--84",
    title = "{Effect of Bt Transgenic Plant on Biological Agent Population}",
    volume = "1",
    year = "2005"
    }
  11. Pabendon, Marcia B., M. Dahlan, Sutrisno, and M. L. C. George. 2005. Microsatellite Marker-based Genetic Characterization of Indonesian Maize Inbred Collections.. Jurnal agrobiogen 2 (2):45-51.
    [BibTeX] [Abstract] [PDF: Microsatellite Marker-based Genetic Characterization of Indonesian Maize Inbred Collections. ]
    Information on genetic relationships among available crop germplasm such as maize inbred lines, has important implications to breeding programs. A set of 26 maize inbreds togeher with six standard lines from CIMMYT (CML51, CML292, CML202, CML206, CML236, and CML396), was characterized using 26 SSR markers, which were coverage of the maize genomes. The objective of this study was to analyze genetic diversities among the Indonesian maize inbred collections. Polymorphism Information Content (PIC) value and the observed genetic distance indicated the existence of large variabilities among the inbreds. Cluster analysis based on 27% of the Jaccard’s similarity coefficient placed the inbreds into three groups. Genetic distances among all the possible pairs without the standard maize lines varied from 0.32 (KSX360F2-5-13-1v vs KSX2601F2-5-1-1-v) to 0.88 (PT963298-1-B-B-Bv vs Mr13). Cluster and Principal Coordinate Analysis of the genetic distances, revealed a clear differentiation of the inbred lines into groups according to their source populations. This clustering were consistent with those of the known pedigree records of the inbreds based on their morphological characters. These results support the use of morphological traits in the production of maize hybrids. The SSR markers proved to be effective to characterize, identify, and demonstrate genetic similarities among the maize inbred lines.
    @article{Pabendon05p45,
    title = {{Microsatellite Marker-based Genetic Characterization of Indonesian Maize Inbred Collections.}},
    author = {Marcia B. Pabendon and M. Dahlan and Sutrisno and M. L. C. George},
    journal = {Jurnal AgroBiogen},
    pages = {45 - 51},
    volume = {2},
    number = {2},
    year = {2005},
    abstract = {Information on genetic relationships among available crop germplasm such as maize inbred lines, has important implications to breeding programs. A set of 26 maize inbreds togeher with six standard lines from CIMMYT (CML51, CML292, CML202, CML206, CML236, and CML396), was characterized using 26 SSR markers, which were coverage of the maize genomes. The objective of this study was to analyze genetic diversities among the Indonesian maize inbred collections. Polymorphism Information Content (PIC) value and the observed genetic distance indicated the existence of large variabilities among the inbreds. Cluster analysis based on 27% of the Jaccard's similarity coefficient placed the inbreds into three groups. Genetic distances among all the possible pairs without the standard maize lines varied from 0.32 (KSX360F2-5-13-1v vs KSX2601F2-5-1-1-v) to 0.88 (PT963298-1-B-B-Bv vs Mr13). Cluster and Principal Coordinate Analysis of the genetic distances, revealed a clear differentiation of the inbred lines into groups according to their source populations. This clustering were consistent with those of the known pedigree records of the inbreds based on their morphological characters. These results support the use of morphological traits in the production of maize hybrids. The SSR markers proved to be effective to characterize, identify, and demonstrate genetic similarities among the maize inbred lines.},
    keywords = {maize inbreds, genetic similarity, microsatellite},
    file = {http://biogen.litbang.pertanian.go.id/terbitan/pdf/agrobiogen_2_2_2006_45-51.pdf},
    note = {Karakterisasi Kemiripan Genetik Koleksi Inbrida Jagung Berdasarkan Marka Mikrosatelit}
    }