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United States Department of Agriculture

Agricultural Research Service

Research Project: RESPONSE OF DIVERSE RICE GERMPLASM TO BIOTIC AND ABIOTIC STRESSES Title: A rice diversity panel evaluated for genetic and agro-morphological diversity between subpopulations and its geographic distribution

Authors
item Ali, M. Liakat -
item Eizenga, Georgia
item Jia, Melissa
item Kimball, Jennifer -
item Mccouch, Susan -
item McClung, Anna
item McClung, Anna

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 18, 2011
Publication Date: June 21, 2011
Citation: Liakat Ali, M., McClung, A.M., Jia, M.H., Kimball, J.A., McCouch, S.R., Eizenga, G.C. 2011. A rice diversity panel evaluated for genetic and agro-morphological diversity between subpopulations and its geographic distribution. Crop Science. 51(5):2021-2035.

Interpretive Summary: A diverse collection of 410 genetically pure rice accessions (cultivars) was developed for molecular studies. This study was conducted to further characterize the accessions in this collection for geographical distribution, subpopulation group based genotype, and 18 agronomic and grain traits. The accessions in this collection were from all rice growing regions of the world including East, Southeast, South, West and Central Asia, Africa, Oceania, Europe, North, Central and South America, and the Caribbean. Analysis of the molecular data revealed these accessions clustered into the five ancestral rice groups (or subpopulations), indica (91 accessions), aus (59), aromatic (15), tropical japonica (104) and temperate japonica (108), with the remaining accessions having a background in two or more ancestral groups. Analysis of the agronomic and grain traits revealed the five ancestral groups also were characterized by a defining set of agronomic and grain traits with days to heading, plant height, number of panicles per plant, flag leaf width, panicle length, and the grain traits (length, width, weight and volume) being the most discriminatory traits. This suggests that during rice domestication in different regions of the world, man selected for different types of rice in the various rice growing regions, as reflected in the plant and seed traits that characterize the phenotype and genotype of each rice accession (cultivar). This collection of rice accessions will be used to determine where the genes controlling these important agronomic traits are located on the rice chromosomes. Ultimately this information will be used by rice breeders to develop improved rice cultivars, especially in creating hybrid rice.

Technical Abstract: A diverse collection of 410 purified rice accessions originating from 77 countries was developed by identifying a representative plant from each accession. These accessions were fingerprinted with 36 SSR markers distributed throughout the genome and evaluated for 18 agro-morphological traits. A total of 330 alleles were detected with an average of 9.11 alleles per locus across all accessions, an average polymorphism information content (PIC) value of 0.63 and gene diversity of 0.68. The accessions clustered into five ancestral groups (subpopulations), indica (91 accessions), aus (59), aromatic or 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. Canonical discriminant analysis identified agronomic traits such as days to heading, plant height, panicle number per plant, flag leaf width and panicle length, and grain traits (length, width, weight and volume) as the main discriminatory characters. Both SSR allele- and phenotypic trait-based analyses indicated a close relationship between aus and indica, and similarly between temperate japonica and tropical japonica. In addition, 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 or varietal groups, Indica and Japonica. The aromatic (Group V) rice represents a distinct small group that is more closely related to tropical japonica based on SSR alleles but to to indica and aus based on phenotype. This diversity germplasm panel with accompanying genetic and phenotypic information will be of immense value for future association mapping studies, better understanding the domestication process, and applications in rice breeding, especially related to hybrid rice.

Last Modified: 11/25/2014
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