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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT AND CHARACTERIZATION OF GENETIC RESOURCES FOR AGRONOMIC AND QUALITY TRAITS USING GENOMIC TOOLS Title: Using High-Throughput Genotyping to Narrow a Global Germplasm Collection of Rice

item Yan, Wengui
item McClung, Anna
item McClung, Anna
item Mccouch, Susan -

Submitted to: ASA-CSSA-SSSA Proceedings
Publication Type: Proceedings
Publication Acceptance Date: August 15, 2012
Publication Date: October 21, 2012
Citation: Yan, W., Mcclung, A.M., Mccouch, S. 2012. Using High-Throughput Genotyping to Narrow a Global Germplasm Collection of Rice. ASA-CSSA-SSSA Proceedings. Oct. 21-24, 2012. Cincinnatti, OH. pg. 375-2.

Technical Abstract: TThe USDA rice core collection represents about 10% of the whole collection of some 18,000 accessions and has been demonstrated to be an effective representation of the whole collection with 88% certainty. Genotyping the 1,794 accessions in the core with 75 SSR markers demonstrated that a great majority of genetic variance was due to within instead of among geographic regions, and within instead of among countries. Germplasm accessions obtained from the Southern Asia, Southeast Asia and Africa were highly diversified, while those from North America, and Western and Eastern Europe had the lowest diversity. Ancestry analysis proportioned the core collection to 35% indica, 27% temperate japonica, 24% tropical japonica, 10% aus and 4% aromatic. A mini-core including 217 entries was formed using PowerCore software based on 26 phenotypic traits and 70 SSRs. The mini-core has been evaluated for 26 traits and captures all 962 alleles identified by 70 of the markers genotyped in the core collection. In addition, 159 accessions in the core have been included as part of Rice Diversity Pancel and have been extensively phenotyped and genotyped using a custom-designed Affymetrix array consisting of 44,100 SNPs. The mini-core has been phenotyped for 40 traits in both Arkansas and Texas, and is under resequencing for genome-wide association study. All of the core and mini-core accessions are publicly available to the global research community.

Last Modified: 10/6/2015
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