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United States Department of Agriculture

Agricultural Research Service

Title: Evaluation of genetic diversity and genome-wide linkage disequilibrium among US wheat (Triticum aestivum L.) germplasm representing different market classes

Authors
item Chao, Shiaoman
item Zhang, Wenjun - UNIV OF CALIFORNIA DAVIS
item Dubcovsky, Jorge - UNIV OF CALIFORNIA DAVIS
item Sorrells, Mark - CORNELL UNIV

Submitted to: Plant and Animal Genome VX Conference Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: November 3, 2006
Publication Date: January 13, 2007
Citation: Chao, S., Zhang, W., Dubcovsky, J., Sorrells, M. 2007. Evaluation of genetic diversity and genome-wide linkage disequilibrium among US wheat (Triticum aestivum L.) germplasm representing different market classes. Plant and Animal Genome VX Conference Abstracts. p. 168.

Technical Abstract: Genetic diversity and genome-wide linkage disequilibrium (LD) were investigated among forty-three U.S. wheat (Triticum aestivum L.) elite cultivars and breeding lines representing seven U.S. wheat market classes using 242 wheat genomic simple sequence repeat (SSR) markers distributed throughout the wheat genome. These lines were selected from 18 wheat breeding programs across the U.S. as part of a collaborative Wheat Coordinated Agricultural Project funded by USDA CSREES (http://maswheat.ucdavis.edu/). Genetic diversity among these lines was examined using genetic distance-based and model-based clustering methods, and analysis of molecular variance. Four populations were identified from the model-based analysis, which partitioned each of the spring and winter populations into two subpopulations, corresponding largely to major geographic regions of wheat production in the US. This suggests that the genetic diversity existing among these US wheat germplasm was influenced more by regional adaptation than by market class, and that the individuals clustered in the same model-based population shared related ancestral lines in their breeding history. For this germplasm collection, genome-wide LD estimates were generally less than 1cM for genetically linked loci pairs. This may result from the population stratification and small sample size that reduced statistical power. Most of the LD regions observed were between loci less than 10cM apart. However, the distribution of LD was not uniform based on linkage distance and was independent of marker density. Consequently, LD is likely to vary widely among wheat populations and caution must be used in designing association studies in wheat.

Last Modified: 11/22/2014
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