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Genetic Diversity of 50 Soybean Accessions Based on Ten Microsatellite Markers. Chaerani, Nurul Hidayatun, and Dwinita W. Utami. 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. Penelitian ini bertujuan mengidentifikasi keragaman genetik plasma nutfah kedelai untuk melengkapi pangkalan data karakter konvensional yang sudah ada sebagai dasar pengelolaan plasma nutfah secara efisien dan diskriminasi varietas-varietas unggul nasional secara akurat, serta identifikasi calon tetua persilangan yang potensial. Lima puluh aksesi kedelai yang terdiri dari 12 varietas unggul nasional, 32 varietas lokal, dan 6 aksesi introduksi dianalisis berdasarkan penanda DNA mikrosatelit menggunakan metode deteksi semi-otomatik. Sebanyak 86 alel terdeteksi dengan jumlah alel per lokus berkisar antara 4 sampai 16. Alel-alel jarang terdeteksi sebanyak 53% yang diperlihatkan oleh 68% genotipe. Rata-rata nilai keinformatifan penanda mikrosatelit, yang diukur berdasarkan keragaman gen (D...

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

DNA Fingerprinting of Indonesian 88 Sweet PotatoGermplasm Based on Eight SSR Markers. Nurul Hidayatun, Chaerani, and Dwinita W. Utami. 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.

<p>Marker assisted back crossing (MABC) is a molecular tool that can help breeders in reducing backcrossed generation. However, effectiveness of this method still needs further approval using actual phenotypic performances. The International Rice Research Institute had developed Ciherang near isogenic line (NIL) of submergence tolerance, Sub1. The study aimed  to evaluate phenotypic performances of Ciherang Sub1 NIL in the greenhouse and field conditions. The study was conducted  in ten locations using five submergence-tolerant varieties and a control treatment under normal conditions. The results showed that the average grain yields and some agronomic traits of Ciherang Sub1 were not significantly different compared with those of Ciherang (recurrent parent). However, under 10- and 15-days of submergence. Ciherang Sub1 was significantly different to Ciherang. The survival rate of Ciherang Sub1 was higher than Ciherang after 14-days submerged in the greenhouse tank experiment. Response of Ciherang Sub1 to brown planthopper biotype 1, 2 and 3, Xanthomonas oryzae pathotype III, IV and VIII, and rice tungro virus inocula from Subang, Magelang and Lanrang were also comparable with its recurrent parent. Quality and physico-chemical properties of rice (milled rice) of Ciherang Sub1 were not different with those of Ciherang. Similarity level of phenotypic traits of Ciherang Sub1 compared to Ciherang was more than 87.5%. This finding proved that a single backcross method can produce progeny identic with its parent. This MABC line can be recommended to farmers in flood-prone area where the Ciherang is preferred. </p>

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Development of Multiplex Sets of Microsatellite DNA Markers for Analysis of Genetic Diversity in Rice andSoybean. Chaerani, Nurul Hidayatun, and Dwinita W. Utami. 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.Key words: Microsatellite markers, multiplex panels, fluorescently labelled M13 primer, rice, soybean. PENDAHULUANMikrosatelit, atau juga dikenal sebagai SSR (simple sequence repeat), adalah utasan DNA yang terdiri atas beberapa kali pengulangan basa sepanjang 1 sampai 8 pasang (Bredemeijer et al. 1998, Narvel et al. 2000. Daerah pengapit sebuah mikrosatelit biasanya terkonservasi pada individu-individu dalam spesies yang sama sehingga dimungkinkan untuk merancang primer yang komplementer dengan daerah pengapit ini untuk amplifikasi mikrosatelit dengan teknik polymerase chain reaction (PCR). Variasi dalam jumlah pengulangan basa terlihat sebagai produk PCR yang berbeda panjangnya dan dikenal sebagai polimorfisme. Daerah yang teramplifikasi oleh primer dinyatakan sebagai lokus dan variasi panjang produk PCR sebagai alel (Narvel et al. 2000). Hak Cipta © 2009, BB-BiogenMetode-metode yang digunakan untuk mendeteksi produk PCR mikrosatelit adalah elektroforesis pada gel poliakrilamid terdenaturasi, gel agarose, dan menggunakan mesin genetic analyzer berbasis sistem deteksi laser yang otomatis. Deteksi fragmen mikrosatelit pada genetic analyzer memerlukan pelabelan salah satu dari sepasang primer pada ujung 5' dengan salah satu dari tiga warna fluoresen (Diwan dan Cregan 1997, Bredemeijer et al. 1998, Narvel et al. 2000. Amplifikasi PCR dengan primer berlabel fluoresen menghasilkan sejumlah kopi alel yang semuanya berlabel warna pada salah satu ujungnya. Label warna mengeluarkan emisi fluoresen pada panjang gelombang tertentu yang kemudian dideteksi oleh genetic analyzer berdasarkan sinar laser yang ditembakkannya...

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