ARS | Publication request: Genetic Diversity, Population Structure and Linkage Disequilibrium in U.S. Elite Winter Wheat (Triticum Aestivum L.)

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 29, 2010
Publication Date: September 15, 2010
Citation: Zhang, D., Bai, G., Zhu, C., Yu, J., Carver, B. 2010. Genetic Diversity, Population Structure and Linkage Disequilibrium in U.S. Elite Winter Wheat (Triticum Aestivum L.). The Plant Genome. 3:117-127.

Interpretive Summary: Knowledge of genetic diversity and population structure of elite wheat breeding lines facilitates effective use of limited resources. We analyzed 205 wheat-breeding lines from major winter wheat breeding programs in the U.S.A. using 245 molecular markers across the wheat genome. We found that US winter wheat breeding lines had a high level of genetic diversity. Breeding activities did not reduce the genetic diversity of modern breeding materials due to extensive exchange of materials among breeding programs and introduction of new genes from different sources. All 205 lines can be statistically divided into two major groups, soft verse hard wheat. Hard wheat can be further divided into three subgroups. Hard wheat appeared to be more diverse than soft wheat in this study. The extent of linkage disequilibrium (LD) was highly variable throughout the genomes, but was mainly distributed around centromere regions. Our results on genetic diversity and LD distribution of breeding materials facilitate the effective use of genetic resources for wheat breeding and the choice of markers in gene mapping and marker-assisted breeding.

Technical Abstract: Information on genetic diversity and population structure of elite wheat breeding lines promotes effective use of genetic resources. We analyzed 205 elite wheat breeding lines from major winter wheat breeding programs in the U.S.A. using 245 markers across the wheat genomes. This collection showed a high level of genetic diversity as reflected by allele number per locus (7.2) and polymorphism information content (0.54). However, the diversity of U.S. modern wheat appeared to be lower than previously reported diversity levels in worldwide germplasm collections. As expected, this collection was highly structured according to geographic origin and market class with soft and hard wheat clearly separated between each other. Hard wheat accessions were further divided into three subpopulations. Linkage disequilibrium (LD) was primarily distributed around centromere regions. The mean genome-wide LD decay estimate was 10 cM (r2>0.1), although the extent of LD was highly variable throughout the genome. Our results on genetic diversity of different gene pools and the distribution of LD facilitates the effective use of genetic resources for wheat breeding and the choice of marker density in gene mapping and marker-assisted breeding.