Open Access Highly Accessed Research article

Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.)

Shiaoman Chao1, Jorge Dubcovsky2, Jan Dvorak2, Ming-Cheng Luo2, Stephen P Baenziger3, Rustam Matnyazov184, Dale R Clark5, Luther E Talbert6, James A Anderson7, Susanne Dreisigacker8, Karl Glover9, Jianli Chen10, Kim Campbell11, Phil L Bruckner12, Jackie C Rudd13, Scott Haley14, Brett F Carver15, Sid Perry16, Mark E Sorrells17 and Eduard D Akhunov4*

Author affiliations

1 USDA ARS Genotyping Laboratory, Biosciences Research Laboratory, Fargo, ND, USA

2 Department of Plant Sciences, University of California, Davis, CA, USA

3 Plant Science Building, University of Nebraska, Lincoln, NE, USA

4 Department of Plant Pathology, Kansas State University, Manhattan, KS, USA

5 WestBred, LLC, Bozeman, MT, USA

6 Department of Plant Sciences, Montana State University, Bozeman, MT, USA

7 Dept. of Agronomy & Plant Genetics, University of Minnesota, St. Paul, MN, USA

8 Genetic Resources and Enhancement Unit, CIMMYT, Mexico, D.F., Mexico

9 Plant Science Department, South Dakota State University, Brookings, SD, USA

10 University of Idaho Aberdeen Research & Extension Center, Aberdeen ID, USA

11 USDA-ARS Wheat Genetics, Quality, Physiology & Disease Research Unit, Washington State University, Pullman WA, USA

12 Plant Sciences and Plant Pathology, Bozeman, MT, USA

13 Texas AgriLife Research and Extension Center, Amarillo, TX, USA

14 Soil and Crop Sciences Department, Colorado State University, Fort Collins, CO, USA

15 Oklahoma State University, Department of Plant and Soil Sciences, Stillwater, OK, USA

16 WestBred, LLC, Haven, KS, USA

17 Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA

18 Institute of Biochemistry and Genetics, RAS, Ufa Russia

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Citation and License

BMC Genomics 2010, 11:727  doi:10.1186/1471-2164-11-727

Published: 29 December 2010



Single nucleotide polymorphisms (SNPs) are ideally suited for the construction of high-resolution genetic maps, studying population evolutionary history and performing genome-wide association mapping experiments. Here, we used a genome-wide set of 1536 SNPs to study linkage disequilibrium (LD) and population structure in a panel of 478 spring and winter wheat cultivars (Triticum aestivum) from 17 populations across the United States and Mexico.


Most of the wheat oligo pool assay (OPA) SNPs that were polymorphic within the complete set of 478 cultivars were also polymorphic in all subpopulations. Higher levels of genetic differentiation were observed among wheat lines within populations than among populations. A total of nine genetically distinct clusters were identified, suggesting that some of the pre-defined populations shared significant proportion of genetic ancestry. Estimates of population structure (FST) at individual loci showed a high level of heterogeneity across the genome. In addition, seven genomic regions with elevated FST were detected between the spring and winter wheat populations. Some of these regions overlapped with previously mapped flowering time QTL. Across all populations, the highest extent of significant LD was observed in the wheat D-genome, followed by lower LD in the A- and B-genomes. The differences in the extent of LD among populations and genomes were mostly driven by differences in long-range LD ( > 10 cM).


Genome- and population-specific patterns of genetic differentiation and LD were discovered in the populations of wheat cultivars from different geographic regions. Our study demonstrated that the estimates of population structure between spring and winter wheat lines can identify genomic regions harboring candidate genes involved in the regulation of growth habit. Variation in LD suggests that breeding and selection had a different impact on each wheat genome both within and among populations. The higher extent of LD in the wheat D-genome versus the A- and B-genomes likely reflects the episodes of recent introgression and population bottleneck accompanying the origin of hexaploid wheat. The assessment of LD and population structure in this assembled panel of diverse lines provides critical information for the development of genetic resources for genome-wide association mapping of agronomically important traits in wheat.