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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #277810

Title: Rich phenotypic and genotypic variation found in a "Rice Diversity Panel"

item ALI, M - University Of Arkansas
item HANCOCK, TERESA - University Of Arkansas
item DECLERCK, GENEVIEVE - Cornell University
item McClung, Anna
item MCCOUCH, SUSAN - Cornell University
item Eizenga, Georgia

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 10/4/2012
Publication Date: 2/20/2012
Citation: Ali, M.L., Hancock, T.A., Declerck, G.A., Mcclung, A.M., Mccouch, S.R., Eizenga, G.C. 2012. Rich phenotypic and genotypic variation found in a "Rice Diversity Panel". Rice Technical Working Group Meeting Proceedings. 34th Rice Technical Working Group. Hot Springs, AR Feb. 27-Mar. 1, 2012. pg. 66-67.

Interpretive Summary:

Technical Abstract: A "Rice Diversity Panel" composed of 413 purified accessions originating from 82 countries was fingerprinted with 36 SSR (simple sequence repeat) and 44,100 SNP (single nucleotide polymorphism) markers. Based on both SSR and SNP markers, the accessions were grouped into five distinct subpopulations, indica, aus, temperate japonica, tropical japonica, aromatic (Group V), or admixture, which has two or more subpopulation groups represented. Both marker types grouped the accessions into nearly the same subpopulation groups. Phenotypic data were collected from three representative plants of each accession in two replications grown in the field for two different years. This panel was systematically phenotyped for 34 agro-morphological traits including three quality traits, amylose content, protein content, and alkali spreading value (ASV) which is a measure of gelatinization temperature. Differences between the accessions and subpopulations were assessed based on eight agro-morphological traits (plant height, panicle number per plant, panicle length, flag leaf width, grain length, grain width, grain length:width ratio and grain volume) using canonical discriminant analysis (CDA) and between the pairs of subpopulation group means for the individual traits by t-tests and LSD values. These traits were the main discriminatory traits based on our initial CDA analysis. The five subpopulations exhibited very significant differences for these eight traits based on t-tests and LSD values. Analysis of the phenotypic data indicated a close relationship between the aus and indica subpopulations, and between the tropical and temperate japonica subpopulation groups. Phenotypically, the small aromatic group was more closely related to both aus and indica than to the tropical or temperate japonica. Data on the three grain quality traits, amylose content, ASV and protein content analyzed by both CDA and t-tests revealed significant differences between all the subpopulations except aus and indica. Digital images of the panicles and seeds were taken as a reference for the individual accessions and archived. The images of the panicles are available at the Genetic Stocks – Oryza (GSOR) website. Images of the seed are part of the Seed Photo Library ( Seeds for all the accessions in this panel are now available for public distribution through GSOR, Stuttgart, Arkansas and the International Rice Research Institute in the Philippines.