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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #277812

Title: Using a rice diversity panel for association mapping and it's validation

item Eizenga, Georgia
item McClung, Anna
item ALI, M - University Of Arkansas
item TUNG, CHIH-WEI - Cornell University
item WRIGHT, MARK - Cornell University
item MEZEY, JASON - Cornell University
item MCCOUCH, SUSAN - Cornell University

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 2/27/2012
Publication Date: 10/21/2012
Citation: Eizenga, G.C., Mcclung, A.M., Ali, M.L., Tung, C., Wright, M.H., Mezey, J.G., Mccouch, S.R. 2012. Using a rice diversity panel for association mapping and it's validation. Rice Technical Working Group Meeting Proceedings. 34th Rice Technical Working Group. Hot Spring, AR Feb. 27-Mar. 1, 2012. pg. 51-52.

Interpretive Summary:

Technical Abstract: Cultivated Asian rice (Oryza sativa L.) has tremendous phenotypic and genotypic diversity that traces back to ancient times. A "Rice Diversity Panel" composed of 413 diverse rice accessions from 82 countries was assembled to explore this genotypic and phenotypic variation. The objectives of this study were to purify the accessions in the panel, collect phenotypic data from the panel accessions in a replicated study, genotype the panel with 44,100 SNP (single nucleotide polymorphism) markers, and conduct a genome-wide association study (GWAS). The accessions in the panel were purified by single seed decent and grown as space plants in a RCBD with two replications for two years. Phenotypic data was collected at Stuttgart, Arkansas for 32 traits related to plant development, plant morphology, grain size, grain quality and stress tolerance. Analysis of the population structure using principle component analysis (PCA) identified the five rice subpopulations plus those that were admixtures of two or more subpopulation groups. The accessions were placed into subpopulation groups as follows: indica (87 accessions), aus (57 accessions), aromatic (14 accessions), tropical japonica (97 accessions), temperate japonica (96 accessions) and admixture of two or more subpopulation groups (62 accessions). The first four components accounted for almost half of the genotypic variation in the panel with the first component partitioning the subspecies Indica and Japonica; the second partitioning Indica into the indica and aus subpopulations; the third partitioning Japonica into temperate and tropical japonica and the fourth separated the aromatic subpopulation from the other O. sativa subpopulations and admixtures. The results of GWAS revealed the most significant marker-trait associations with the traits days to heading, plant height, panicle length, panicle branching, seeds per panicle, grain shape (length, width, length:width ratio, volume), pericarp color, amylose, alkali spreading value and rice blast disease. A survey of the literature revealed many of the associations identified in this study could be traced to previously reported genes or QTLs affecting the trait. To validate the results of the GWAS, four bi-parental mapping populations within Japonica are presently under development. The parents in these populations represent the extremes of the phenotypic variation observed for days to heading, plant height, panicle length, number of panicles per plant, primary branch number per panicle, filled grain number per panicle, spikelets per panicle, grain length, grain width, grain length:width ratio, and seed weight. A new Affymetrix SNP array with one million (1M) SNPs has been developed and our diversity panel is being genotyped with this new array. Once the genotyping and allele calling is completed, another GWAS will be undertaken using the 1M SNPs and the phenotypic data to determine if improved resolution or additional marker-trait associations can be identified.