Genetic Diversity, Population Structure, and Linkage Disequilibrium in U.S. Elite Winter Wheat

Information on genetic diversity and population structure of elite wheat (Triticum aestivum L.) breeding lines promotes effective use of genetic resources. We analyzed 205 elite wheat breeding lines from major winter wheat breeding programs in the USA using 245 markers across the wheat genomes. This collection showed a high level of genetic diversity as refl ected 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 from 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 markerassisted breeding. W rice (Oryza sativa L.), and maize (Zea mays L.) are the three staple food crops in the world. As the human population increases and more maize is dedicated to a growing biofuel industry, the demand for high yields of good quality wheat grain will increase. In the past century, wheat breeders worldwide have made remarkable progress in improving disease resistance, grain yield, and end-use quality of wheat. However, continuous breeding activities may result in erosion of genetic diversity as a result of intense selection pressure, recurrent use of a few adapted elite germplasm lines as parents, and adoption of breeding schemes that do not perpetuate genetic recombination (Hoisington et al., 1999). Th e degree of genetic diversity in contemporary germplasm from breeding programs may indirectly refl ect the level of genetic progress achievable in future cultivars. Th erefore, evaluation of the genetic diversity resident in current breeding programs at the molecular level and integration of this information into cultivar development programs are essential to using genetic resources eff ectively in breeding programs (Chao et al., 2007). Genetic diversity, population structure, and LD of a population provide strategic information for association mapping and marker-assisted breeding. Th e resolution of association mapping and eff ectiveness of marker-assisted Published in The Plant Genome 3:117–127. Published 15 Sept. 2010. doi: 10.3835/plantgenome2010.03.0004 © Crop Science Society of America 5585 Guilford Rd., Madison, WI 53711 USA An open-access publication 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. Dadong Zhang, Chengsong Zhu, and Jianming Yu, Dep. of Agronomy, Kansas State Univ., 2004 Throckmorton Hall, Manhattan, KS 66506; Guihua Bai, USDA-ARS Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506; Brett Carver, Dep. of Plant and Soil Sciences, Oklahoma State Univ., 368 Agricultural Hall, Stillwater, OK 74078. Received 21 Dec. 2009. *Corresponding author ([email protected]). Abbreviations: AMOVA, an analysis of molecular variance; LD, linkage disequilibrium; PCoA, principal coordinate analysis; PIC, polymorphism information content; QTL, quantitative trait locus(i); SNP, single-nucleotide polymorphism; STS, sequence-tagged site; SSR, simple sequence repeat; UPGMA, unweighted pair group method with arithmetic mean.