Population Structure and Linkage Disequilibrium in U.S. Barley Germplasm: Implications for Association Mapping

Previous studies have shown that there is considerable population structure in cultivated barley (Hordeum vulgare L.), with the strongest structure corresponding to differences in row number and growth habit. U.S. barley breeding programs include six-row and two-row types and winter and spring types in all combinations. To facilitate mapping of complex traits in breeding germplasm, 1816 barley lines from 10 U.S. breeding programs were scored with 1536 single nucleotide polymorphism (SNP) genotyping assays. The number of SNPs segregating within breeding programs varied from 854 to 1398. Model-based analysis of population structure showed the expected clustering by row type and growth habit; however, there was additional structure, some of which corresponded to the breeding programs. The model that fi t the data best had seven populations: three two-row spring, two six-row spring, and two six-row winter. Average linkage disequilibrium (LD) within populations decayed over a distance of 20 to 30 cM, but some populations showed long-range LD suggestive of admixture. Genetic distance (allele-sharing) between populations varied from 0.11 (six-row spring vs. six-row spring) to 0.45 (two-row spring vs. six-row spring). Analyses of pairwise LD revealed that the phase of allelic associations was not well correlated between populations, particularly when their allele-sharing distance was >0.2. These results suggest that pooling divergent barley populations for purposes of association mapping may be inadvisable. M.T. Hamblin, Inst. for Genomic Diversity, 156 Biotechnology Bldg., Cornell Univ., Ithaca, NY 14853; T.J. Close, Dep. of Botany & Plant Sciences, Univ. of California, Riverside, CA, 92521; P.R. Bhat, Monsanto Research Centre, Bangalore, 560092, India; S. Chao, USDAARS, Biosciences Research Lab., 1605 Albrecht Blvd., Fargo, ND 58105-5674; J.G. Kling and P.M. Hayes, Dep. of Crop and Soil Science, 109 Crop Science Bldg., Oregon State Univ., Corvallis, OR 97331-3002; K.J. Abraham, Dep. of Epidemiology and Biostatistics, Case Western Reserve Univ., Cleveland, OH 44106; T. Blake, Dep. of Plant Sciences and Plant Pathology, 109 Ag Biosciences Bldg., Montana State Univ., Bozeman, MT 59717; W.S. Brooks, Crop & Soil Environmental Sciences Dep., Virginia Tech, Blacksburg, VA 24061; B. Cooper, Busch Agricultural Resources Inc., 3515 E. Richards Lake Rd., Fort Collins, CO 80524; C.A. Griff ey, Crop & Soil Environmental Sciences Dep., 334-A Smyth Hall, Virginia Tech, Blacksburg, VA 24061; D.J. Hole, Small Grains Research, 4820 Old Main Hill, Utah State Univ., Logan, UT 84322; R.D. Horsley, Dep. of Plant Sciences, Loftsgard Hall 370H, North Dakota State Univ., Fargo, ND 58108; D.E. Obert, Small Grains and Potato Research Facility, 1691 South 2700 West, Aberdeen, ID 83210; K.P. Smith and G.J. Muehlbauer, Dep. of Agronomy and Plant Genetics, 1991 Upper Buford Cir., Univ. of Minnesota, Saint Paul, MN 55108; S.E. Ullrich, Dep. of Crop and Soil Sciences, Washington State Univ., Pullman, WA 99164; J.-L. Jannink, USDA-ARS, R.W. Holley Center for Agriculture and Health, Cornell Univ., Ithaca, NY 14853. This work was supported by USDACSREES-NRI Grant no. 2006-55606-16722, “Barley Coordinated Agricultural Project: Leveraging Genomics, Genetics, and Breeding for Gene Discovery and Barley Improvement.” KJA was supported by Grant no. RR03655 from the National Center for Research Resources. Received 14 Apr. 2009. *Corresponding author ( [email protected]). Abbreviations: BA, Busch Agric. Resources, Inc.; BOPA, barley oligonucleotide pool assay; CAP, coordinated agricultural project; CP, coeffi cient of parentage; DArT, diversity arrays technology; GWAS, genome-wide association studies; LD, linkage disequilbrium; MAF, minor allele frequency; MN, Univ. of Minnesota; N2, North Dakota State Univ., two-row; N6, North Dakota State Univ., six-row; OR, Oregon State Univ.; PCA, principal components analysis; QTL, quantitative trait loci; SNP, single nucleotide polymorphism; sp, spring; UT, Utah State Univ.; VT, Virginia Tech; WA, Washington State Univ.; wi, winter. Published in Crop Sci. 50:556–566 (2010). doi: 10.2135/cropsci2009.04.0198 Published online 6 Jan. 2010. © Crop Science Society of America | 677 S. Segoe Rd., Madison, WI 53711 USA All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher.