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.

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

Identification and Application of PCR-based Marker toIdentify Rice Variety with High Palatability. Puji Lestari, Andari Risliawati, and Hee Jong Koh. To date, there has been no DNA fingerprint profile as unique identity of rice variety that has a high palatability (overall eating quality) in Indonesia, thus identification of premium varieties using molecular markers is considered to be important. This study aimed to establish DNA fingerprint profiles of indica and japonica rice varieties, and unique identities of rice varieties with high palatability using molecular markers associated with palatability. Total of 22 japonica and 24 indica rice varieties were evaluated their overall eating quality and tested using 20 molecular markers STS (sequence-tagged site) which were designed on the basis of japonica rice genome. To identify the genes functions, all these markers amplicons were cloned, transformed, sequenced and the sequences results were analyzed their homologous against the genome database. Ilpum (japonica) and Rojolele (indica) were identified to have the highest palatability compared to other varieties. DNA fingerprint profiles identified with the total STS markers were not able to differentiate each variety, however premium varieties of japonica and indica showed specific identities. A unique identity of Indonesian indica variety possessing high palatability, Rojolele was successfully developed using a markers set. DNA fingerprint profile in digital value system facilitates the identification of premium rice from other varieties. The fragments of the STS primers showed no any known-genes functions related to rice eating quality, therefore these markers are preferentially used for identification of premium rice with high palatability than differentiation of rice varieties based on the palatability. In this study, the unique identity of rice variety with high palatability is very usefull to evaluate the purity for germplasm protection. Keywords

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Development of Rice Core Collection. Tiur S. Silitonga and Andari Risliawati. Rice genetic resources have been collected from almost all of the district in the provinces of Indonesia. Presently, the collection of rice genetic resourses are totally 4.200 accessions. The purpose of these activities were to test, select and grouping of rice genetic resources to develop core collection. Various activities have been conducted such as characterization and selection of rice genetic resources to agronomic performance and yield, evaluation to brown plant hopper and grassy stunt virus and their resistance/tolerance to bacterial leaf blight, blast, and drought. Development core collection with various traits such as morphology and agronomy characteristics, yield component, seed quality, resistance to pest and diseases and tolerance to abiotic stresses will increase the use of rice genetic resources to create high yielding varieties with various traits. The availability of various rice varieties with traits needs could cover all the areas including lowland, upland, swampy areas, and marginal land areas with endemic attacked by pest and diseases. All rice genetic resources have been characterized to agronomic performance and yield in Sukamandi experimental farm, evaluated their resistance to brown plant hopper and bacterial leaf blight in Sukamandi and Cianjur, and drought tolerance in Jakenan, Central Java. The results of the experiment have developed core collection by grouping varieties with their traits such as 55 accession (accs.) of varieties with long panicle (>30 cm), 25 accs. short duration (<115 days), 32 accs. of dwarf plant (<115 cm), 25 accs. of short to medium duration (<130 days) with yielded 4.7-5.9 t/ha, 35 accs. have low to medium amylose content, 20 accs. resistant to brown plant hopper and grassy stunt virus, 33 accs. resistant to bacterial leaf blight, 23 accs. resistant to blast and 30 accs. tolerant to drought.Keywords: Rice genetic resources, core collection, utilization. ABSTRAKKoleksi plasma nutfah padi saat ini lebih dari 4.200 aksesi yang dikumpulkan dari hampir seluruh provinsi di Indonesia. Untuk meningkatkan pengelolaan dan pemanfaatan sumber daya genetik padi telah dilakukan pengujian, seleksi, dan pengelompokan varietas dalam bentuk koleksi inti. Tersedianya koleksi inti plasma nutfah padi dengan sifat agronomis, morfologis, komponen hasil terutama mutu gabah, kadar amilosa, dan ketahanan terhadap hama dan penyakit akan mempermudah pemanfaatannya dalam perakitan varietas unggul padi umur genjah, produksi tinggi, dengan mutu beras dan rasa nasi yang enak. Penelitian ini bertujuan untuk membentuk koleksi inti dengan cara menyeleksi dan mengelompokkan sumber daya genetik padi pada berbagai sifat penting seperti umur genjah, tanaman pendek, hasil tinggi, toleran terhadap cekaman biotik dan abiotik, bentuk beras, dan kadar amilosa. Tersedianya beragam varietas dalam koleksi inti dengan berbagai sifat yang diinginkan akan mempermudah akses dan pemanfaatan oleh para pengguna, terutama pemuli...

Pigmented rice is functional staple food that becomes popular because of its anthocyanin content which is beneficial for health. Studies on the diversity of the local variety of Indonesian pigmented rice accessions have been carried out, but are still limited to one region of germplasm origin. This study aimed to analyze the genetic diversity of local varieties of pigmented rice collections of the IAARD-ICABIOGRAD Gene Bank. A total of 93 pigmented rice accessions from 16 provinces in Indonesia were analyzed using 15 functional molecular markers of SSR, STS, and indel. The total alleles detected were 115 with an average per locus of genetic diversity value of 0.71. There were five markers with PIC values &gt;0.75, i.e. RM167, RM223, R8M33, R10M10, and GBSS1. The accessions were divided into two main groups based on their pericarp color. It is necessary to analyze the physicochemical content of the local rice accessions to complement the existing diversity information and identify potential pigmented rice accessions with high palatability.

Tillering ability is an important agronomic trait that determines the yield of rice. Tiller type in rice is categorized as primary, secondary and tertiary tiller which produces panicle at generative phase. Tillering ability as well as the tiller type varies between varieties, especially among germplasms. Our study aimed to identify the tiller profile diversity of upland rice germplasm in ICABIOGRAD Genebank. A total of 100 accessions of local upland rice varieties were planted in a randomized completely block design with two replications under greenhouse condition. The number of tiller from each type was observed weekly from 35 to 63 days after sowing (DAS). The result of the study showed that the number of primary tiller increased slowly from 35 DAS until 63 DAS. After 49 DAS there was no significant addition in secondary tiller number. Generally, the average mean number of tertiary tiller accross the accessions was far below compared to the number of primary and secondary tiller. The highest number of primary tiller, i.e. 8, was expressed by Pae Daye Indolobye (North Sulawesi), Padi Pulut Pute Iteung (East Kalimantan) and K. Puyuk (Central Kalimantan). Up to 22 secondary tillers were formed by Gadabung, a local upland rice variety from Central Kalimantan. Information on tillering ability of local upland variety will benefit rice breeder for selecting appropriate accessions as a gene source for breeding.

The present study was carried out to characterize 103 Indonesian local rice germplasm on the basis of 20 agro-morphological traits. The local rice germplasm originated from Riau and Jambi province in Sumatera island. Principal Component Analysis (PCA) was used to analyzed 11 quantitative data. PCA explained the genetic diversity of the rice germplasm accession. Most of the morphological characters showed variation in different accession. PC1 and PC2 explained about 32.5% and 22.1% of the variability, respectively. PCI and PC2 mostly related with traits such as productive tiller number (PTN), vegetative tiller number (VTN), plant height (PH), and culm length (CL). PCA-Biplot showed accession from Jambi and Riau manage to be separated, even though the PCA percent is only 54.6%. Accession originated from Riau marked by number of tillers (PTN, VTN), and grain weight (GW) traits. Based on cluster analysis, rice germplasm grouped in to 4 main clusters. Most of the accession from Jambi and Riau grouped in the same cluster, which is cluster I. Whereas eight local accessions from Riau grouped in the same cluster separately (cluster II). Two accession which are Padi Jarum (Acc 2711) and Ketan Hitam (Acc 9300) are individually, separated from others.