ARS | Publication request: “Rice Diversity Panel”: A Genetic Resource for Exploring Phenotype-Genotype Associations in O. sativa.

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: November 8, 2010
Publication Date: December 13, 2010
Citation: Ali, M., Goodall, D., Jia, M.H., Tung, C., Wright, M.H., Zaho, K., Bustamante, C.D., Mcclung, A.M., Mccouch, S.R., Eizenga, G.C. 2010. “Rice Diversity Panel”: A Genetic Resource for Exploring Phenotype-Genotype Associations in O. sativa.. Plant and Animal Genome Conference. http://www.intl-pag.org/19/abstracts/P05b_PAGXIX_255.html.

Technical Abstract: A “Rice Diversity Panel” comprised of 409 purified rice (Oryza sativa L.) accessions originating from 79 countries was fingerprinted with 36 SSR markers, 1,536 SNP markers and more recently with a 44,100 SNP array. These accessions grouped into five ancestral subpopulations, indica, aus, tropical japonica, temperate japonica and aromatic/GroupV. Accessions were characterized phenotypically for heading date, six plant morphology-related traits, seven yield-related traits, nine grain morphology-related traits, three cooking, eating and nutritional quality-related traits, and the biotic/abiotic stress traits: rice leaf blast and straighthead. There was a wide range of variation for all these traits across all the accessions and within individual subpopulations. A web-based Seed Photo Library (http://www.ricediversity.org/photolibrary/) was developed to display high resolution digital images of the seed, with and without the hull, and panicles of each accession. Genome-wide association scans (GWAS) have been completed using 44,100 SNP array and more detailed GWAS will be conducted once genotyping is completed with the newly developed 1,000,000 SNP array. This diversity panel provides a resource for exploring genotype-phenotype associations, developing mapping populations for in-depth genetic studies, selecting parents to improve traits of interest, and as the basis for selecting subsets of SNPs to construct 384-SNP arrays denoted as “Breeder’s Chips”. Breeder’s chips are used for variety identification, quality control of seed lots, trait selection in a breeding program, and mapping of genes and QTLs of interest. Information about phenotypes and genotypes of each accession will soon be available at our project web site (www.ricediversity.org) and at the Genetic Stocks-Oryza center (http://www.ars.usda.gov/Main/docs.htm?docid=8318).