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United States Department of Agriculture

Agricultural Research Service

Research Project: RESPONSE OF DIVERSE RICE GERMPLASM TO BIOTIC AND ABIOTIC STRESSES

Location: Dale Bumpers National Rice Research Center

Title: A “Rice Diversity Panel” evaluated for genetic and agro-morphological variation between subpopulations

Authors
item Ali, M. Liakat -
item Hancock, Teresa -
item Jia, Melissa
item Mccouch, Susan -
item Zhao, Keyan -
item Tung, Chih-Wei -
item Wright, Mark -
item Reynolds, Andy -
item Bustamante, Carlos -
item McClung, Anna
item McClung, Anna
item Eizenga, Georgia

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: January 15, 2010
Publication Date: February 22, 2010
Citation: Ali, M., Hancock, T.A., Jia, M.H., McCouch, S.R., Zhao, K., Tung, C., Wright, M., Reynolds, A., Bustamante, C.D., McClung, A.M., Eizenga, G.C. 2010. A “Rice Diversity Panel” evaluated for genetic and agro-morphological variation between subpopulations. In: Proceedings 33rdRice Technical Working Group Meetings, February 22-25, 2010, Biloxi, MS. CDROM

Technical Abstract: Since ancient times, Indica and Japonica have been recognized as the two major subspecies of Asian rice (Oryza sativa L.). First with isozymes and subsequently with DNA markers, five subpopulations indica, aus, temperate japonica, tropical japonica and aromatic/GroupV were identified. A “Rice Diversity Panel” composed of 409 purified accessions originating from 79 countries was established to explore the genetic and phenotypic diversity within and between these subpopulations. Currently, this diversity panel is being genotyped with an Affymetrix 44K SNP chip with the ultimate aim of conducting an association mapping study for the agronomic, morphological and grain quality traits included in this study. Phenotypic data were collected from three representative plants of each accession in two replications in the field for characterization during two different years. The accessions were fingerprinted with 36 SSR markers to determine the molecular variation, gene diversity, clustering, and population structure of the diversity panel using the Arlequin, PowerMarker, and Structure software. The Diversity Panel was evaluated for over 40 agro-morphological traits and the grain quality traits, amylose content, protein content, and alkali spreading value (ASV) which is a measure of gelatinization temperature. In addition to the 36 SSRs, the panel also was screened with DNA markers associated with amylose content (RM190 and Intron1) and ASV (Alk). Differences between the accessions and subpopulations were assessed based on 18 agro-morphological traits using canonical discriminant analysis (CDA) in the CANDISC procedure (SAS software) and between the pairs of subpopulation group means for the individual traits by t-tests and LSD values using the procedure ANOVA (SAS software). A total of 330 alleles were detected with an average of 9.17 alleles per locus across all accessions, an average PIC value of 0.63 and gene diversity of 0.68. The accessions clustered into five ancestral groups (subpopulations), indica (90 accessions), aus (59), aromatic/Group V (15), tropical japonica (104) and temperate japonica (108) based on genetic distance-based clustering and model-based Structure analyses. Thirty-three accessions with <60% ancestry from any single group were identified as ‘admixtures’. The genetic diversity was higher in the indica and aus subpopulations than in aromatic, temperate japonica or tropical japonica. CDA identified the agronomic traits plant height, panicle number/plant, flag leaf width and panicle length, panicle branch number, and grain traits (length, width, weight, and volume) as the main discriminatory characteristics. Both SSR allele- and phenotypic trait-based analyses indicated a close relationship between aus and indica, and similarly between temperate and tropical japonica. Both methods agreed that indica and aus are only distantly related to temperate and tropical japonica types, supporting the existence of two deeply divided major clades, Indica and Japonica. The aromatic/GroupV rice represents a distinct small group that is more closely related to tropical japonica based on SSR alleles but to aus and indica based on phenotype. Aus had the highest amylose content whereas temperate japonica had the lowest. Aus had alleles for Intron1 associated with high/intermediate amylose content while 75% of temperate japonica had the allele associated with low amylose. Similarly, for RM190, 96% of aus had alleles associated with high amylose while 95% of temperate japonica had alleles associated with low amylose. Temperate japonica and indica were classified as having low gelatinization temperatures whereas aus and tropical japonica had intermediate gelatinization temperatures. Sixty percent of temperate japonica had alleles associated with low gelatinization temperature whereas all the aus and 88% of tropical japonica had alleles for intermediate/high gelatinization temperature. Results from the association mapping will be presented which should further delineate the population sub-structure, lead to a better understanding of the domestication process and have applications in rice breeding, especially related to hybrid rice. Panicle and seed images, and seed stocks will be available through the USDA-ARS Genetic Stocks-Oryza collection upon completion of this project.

Last Modified: 9/22/2014
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