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

Published: 29 December 2010

Additional files

Additional file 1:

Complete list of wheat cultivars used in the study. The file contains the list of spring and winter wheat cultivars selected from 17 breeding programs in US and CIMMYT. Pedigree (when available/known) of each cultivar is also provided.

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Additional file 2:

SNPs and their flanking sequences used for the design of wheat OPA. The file contains the list of SNPs and their flanking sequences used for the design of wheat Illumina OPA. The Illumina® Assay Design Tool was used to generate designability rank scores for each SNP.

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Additional file 3:

List of 219 SNPs used for population structure analysis. The file contains the list of 219 SNPs and their genetic map locations. The analysis of population structure was performed using all SNPs and SNPs separated into genome-specific sets (91 A-genome specific SNPs, 89 B-genome specific SNPs, and 39 D-genome specific SNPs).

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Additional file 4:

Relationship between the log probability of data and the number of clusters K. The log probability of data (Ln Pr(X|K)) was plotted as a function of the number of clusters K for different SNP datasets and structure models assuming correlated (top three graphs) and independent (bottom three graphs) alleles frequencies. Means (black bars) and 95% confidence intervals (grey bars) of log probability of data Ln Pr(X|K) for each value of K were calculated from 10 independent runs of Structure with 100,000 burn-in steps and 106 simulation steps.

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Additional file 5:

Membership coefficients of 17 pre-defined wheat populations in 2 clusters (K = 2). Clustering was estimated using SNPs mapped to the A-, B- and D-genomes. Membership coefficients were calculated from 10 independent runs of Structure with 100,000 burn-in steps and 106 simulation steps.

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Additional file 6:

Membership coefficients of 17 pre-defined wheat populations in 9 clusters (K = 9). Membership coefficients (Q) were estimated for 17 wheat populations assuming 9 clusters in data (K = 9). Clustering was estimated using combined set of 219 SNPs from 10 independent runs of Structure with 100,000 burn-in steps and 106 simulation steps.

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Additional file 7:

Distribution of FST estimates for individual SNP loci and windows of 5 SNPs. A) The distribution of single-locus FST values between spring and winter wheat populations. B) The distribution of FST values in a sliding window of 5 consecutively located SNP loci.

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Additional file 8:

Summary of significant LD in the spring, winter and combined populations. The file contains mean and median estimates of statistically significant LD in the A- B- and D-genomes of spring, winter and combined populations. The pair-wise LD was measured using the squared allele-frequency correlations r2 according to Weir [50]. The statistical significance of individual r2 estimates was calculated by the exact test following the procedure described by Weir [50]. The false discovery rate (FDR) was established at 0.01 using the Benjamini & Hochberg method [52].

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Additional file 9:

Summary of LD estimates. The file contains the exact test for LD, genetic distances between pairs of SNP markers and minor allele frequencies (MAF) of alleles used for LD calculation. The pair-wise LD was measured using the squared allele-frequency correlations r2 according to Weir [50]. The statistical significance of individual r2 estimates was calculated by the exact test following the procedure described by Weir [50]. The false discovery rate (FDR) was established at 0.01 using the Benjamini & Hochberg method [52].

Format: XLSX Size: 3.4MB Download file

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