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United States Department of Agriculture

Agricultural Research Service


Location: Dale Bumpers National Rice Research Center

Title: Analysis of the RiceCAP germplasm panel for SNP diversity, population structure and seven yield-component traits of rice

item Solomon, W
item Oard, J
item Mcclung, Anna
item Mcclung, Anna
item Wright, M
item Zhao, K
item Reynolds, A
item Bustamante, C
item Kanter, D
item Mccouch, S
item Scheffler, Brian

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 1/1/2009
Publication Date: 1/10/2009
Citation: Solomon, W., Oard, J., McClung, A.M., Wright, M., Zhao, K., Reynolds, A., Bustamante, C., Kanter, D., McCouch, S., Scheffler, B.E. 2009. Analysis of the RiceCAP germplasm panel for SNP diversity, population structure and seven yield-component traits of rice. In: Proceedings of Plant and Animal Genome Conference XVII, January 10-14, 2009, San Diego, CA. P220.

Interpretive Summary:

Technical Abstract: Genotypic and phenotypic diversity was evaluated on a panel of rice germplasm consisting of 131 historic U.S. rice varieties released over the last 80 years, and 341 elite rice breeding lines from the public breeding programs in the U.S. The collection included the parents of the RiceCAP mapping populations and all lines were purified by single seed descent prior to evaluation. The collection was genotyped using an Illumina GoldenGate® platform consisting of 1,536 SNPs selected distributed across the 12 chromosomes and 1348 SNPs were validated on this material. Phenotypes were collected for: days to heading, plant height, plant maturity, productive tiller number, panicle length, seeds per panicle, seed weight per panicle, and yield-component traits in three different locations, Arkansas, Louisiana, and Mississippi, over two years. Genotypic and phenotypic diversity will be evaluated to understand how polymorphism is distributed across the genome, with-in and between different varietal groups, and to confirm pedigree information. Based on this analysis, a subset of SNPs will be selected as the basis for a mini-SNP assay to provide a more economical platform for mapping and breeding applications.

Last Modified: 09/23/2017
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