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<p class="p1">Accuracy is an important issue for plant germplasm identification, especially forvarietal 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 &lt;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 detected. Furthermore, the presence of two soybean accessions with different names but having the same molecular identity was also identified.</p>

We developed nine new microsatellite markers for rice blast (Magnaporthe grisea) population studies. These markers were used in addition to nine microsatellite markers previously developed by our group for mapping purpose. Altogether, the 18 markers were used in multiplex PCR (polymerase chain reaction) to characterize six populations from different geographical origins. The average number of alleles per locus across populations ranged from 1.2 to 7 and the total number of alleles detected from 2 to 19. Based on this large range of polymorphism, this set of markers is expected to be useful for different kind of population studies at different geographical scales.

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...

ABSTRAK Profil marka molekuler atau sidik jari DNA dapat digunakan dalam kegiatan identifikasi varietas, pengawasan kemurnian genetika plasma nutfah, dan pelengkap dokumen perolehan hak kekayaaan intelektual. Analisis sidik jari DNA tanaman kedelai di BB Biogen-Balitbangtan telah dilakukan sejak tahun 2004 dengan menggunakan marka simple sequence repeat (SSR) yang diautomatisasi dengan mesin genetic analyzer CEQ 8000 berbasis sistem elektroferesis kapiler. Metode ini telah menghasilkan profil sidik jari DNA dari sebagian besar varietas yang diuji, namun set markanya belum pernah dikembangkan untuk mengidentifikasi varietas secara efisien. Tujuan penelitian adalah mengembangkan set marka SSR untuk identifikasi varietas unggul kedelai Indonesia. Penelitian menggunakan 42 varietas unggul kedelai yang dianalisis dengan 14 marka SSR berflouresen yang bersifat acak. Sebanyak 168 alel diperoleh dari analisis polimorfisme dengan rerata nilai polymorphic information content (PIC) tiap lokusnya sebesar 0,7337. Berdasarkan parameter tingkat reproduksi marka, nilai PIC, jumlah alel jarang, frekuensi alel dominan, dan tingkat keberhasilan deteksi fragmen SSR oleh genetic analyzer, teridentifikasi lima marka SSR, yaitu Satt414, Satt147, Satt308, Satt009, dan Satt516, sebagai set marka identifikasi. Set marka identifikasi ini dapat digunakan untuk menyusun identitas (ID) dari 42 varietas unggul kedelai Indonesia.Kata kunci: Sidik jari DNA, set marka identifikasi, kedelai, SSR. ABSTRACTProfile 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 ICABIOGRAD-IAARD 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.

Abstract. Nugraha Y, Utami DW, Rosdianti I, Ardie SW, Ghulammahdi M, Suwarno, Aswidinnoor H. 2016. Markers-traits association for iron toxicity tolerance in selected Indonesian rice varieties. . Ferrous iron toxicity is a mineral disorder frequently occurring under flooded soils condition where rice is cultivated. Here we study identification the Single Nucleotide Polymorphism (SNPs) markers associated with iron toxicity tolerance characters. The phenotypical data was collected from exploiting of twenty-four rice genotypes that were grown under Yoshida + 0.2% agar solution with treatment of 400 mg. L -1 Fe 2+ and control conditions. The same genotypes were grown in iron toxicity acute and control sites at Taman Bogo, Lampung Province, Indonesia. The Principle Component Analysis (PCA) of the phenotypic data showed that 18 rice genotypes were selected representing grouping of related characters to iron toxicity condition. The genotyping of selected genotypes was carried out using multiplexes of 384 SNPs Golden Gate Illumina© assay. We identified, TBGI380435 which located on 14.45 Mbp of chromosome 9 was associated to leaf bronzing and relative shoot weight characters in the greenhouse experiment. The marker was associated with heavy metal transport detoxification (HTDT). The results are expected to assist in locating the potential candidate genes or Fe toxicity tolerance and to allow for precise marker-assisted selection. This research will serve for rice improvement through marker-assisted breeding and genomic selection in Indonesia.

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

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