Rice Genetics IV - IRRI books - International Rice Research Institute

provide a bridge for moving rapidly and efficiently from phenotype to sequence informationand vice versa, and providing a foundation for understanding the evolutionaryconsequences of sequence variation.The International Rice Microsatellite Initiative (IRMI) is a consortium of publicand private research groups that are working together to generate a high-resolutionset of microsatellite markers for rice. With the recent release of more than 7,000uncharacterized SSR sequences (http://www.riceresearch.org) and with new genomicsequences emerging all the time from both public and private rice sequencing efforts,opportunities for developing, characterizing, and using SSR markers in high-resolutionstudies in rice have opened up dramatically. IRMI aims to make the primer sequences,PCR conditions, polymorphism information, and map positions of thesemarkers publicly available over the Internet (www.gramene.org). To facilitate the useof SSRs in automated analyses, all primer pairs are being tested using a standard PCRprotocol and panel of rice genotypes. Results of IRMI’s decentralized effort are coordinatedin a central database in which each contributor’s input is recognized.It is of great interest not only to harness SSRs as genetic markers but also tounderstand the role they play in the biology and evolution of organisms and as contributorsto the rapidly evolving repetitive fraction of the rice genome. The power ofSSR markers resides in their abundance, co-dominance, hypervariability, and easeand economy of use in both manual and automated systems. Groups interested in therice genome can use them for evolutionary studies, to examine patterns of variation inspecific regions of the genome, compare recombination frequencies across populations,fingerprint varieties, analyze pedigree relationships, construct high-resolutiongenetic and physical maps, discover and isolate genes and QTLs, screen mutant populations,and in molecular breeding programs. By establishing a core set of publiclyavailable semiautomated SSR markers that can be readily used by independent groupsworldwide, a large amount of data bridging sequence, genotype, and phenotype canbe accumulated and readily integrated into a single database that integrates informationacross studies. Within the next few years, all SSRs in rice will likely be identifiedand their genomic locations known. This will provide the rice community with a richsource of material for addressing a wide array of scientific questions of both basicand applied interest.ReferencesAkagi H, Yokozeki Y, Inagaki A, Fujimura T. 1996. Microsatellite DNA markers for rice chromosomes.Theor. Appl. Genet. 94:61-67.Ayres NM, McClung AM, Larkin PD, Bligh HFJ, Jones CA, Park WD. 1997. Microsatellitesand a single nucleotide polymorphism differentiate apparent amylose classes in an extendedpedigree of US rice germplasm. Theor. Appl. Genet. 94:773-781.Bao, JS, Zheng XW, Xia YW, He P, Shu QY, Lu X, Chen Y, Zhu LH. 2000. QTL mapping forthe paste viscosity characteristics in rice (Oryza sativa L.). Theor. Appl. Genet. 100:280-284.Blair MW, McCouch SR. 1997. Microsatellite and sequenced-tagged site markers diagnosticfor the rice bacterial leaf blight resistance gene xa-5. Theor. Appl. Genet. 95:174-184.Microsatellite markers in rice: . . . 131