Structural and Temporal Variation in Genetic Diversity of European Spring Two-Row Barley Cultivars and Association Mapping of Quantitative Traits

Two hundred sixteen barley (Hordeum vulgare L.) cultivars were selected to represent the diversity and history of European spring two-row barley breeding and to search for alleles controlling agronomic traits by association genetics. The germplasm was genotyped with 7864 gene-based single nucleotide polymorphism markers and corresponding field trial trait data relating to growth and straw strength were obtained at multiple European sites. Analysis of the marker data by statistical population genetics approaches revealed two important trends in the genetic diversity of European two-row spring barley, namely, i) directional selection for approximately 14% of total genetic variation of the population in the last approximately 50 yr and ii) highly uneven genomic distribution of genetic diversity. Association analysis of the phenotypic and genotypic data identified multiple loci affecting the traits investigated, some of which co-map with selected regions. Collectively, these data show that the genetic makeup of European two-row spring barley is evolving under breeder selection, with signs of extinction of diversity in some genomic regions, suggesting that “breeding the best with the best” is leading towards fixation of some breeder targets. Nevertheless, modern germplasm also retains many regions of high diversity, suggesting that site-specific genetic approaches for allele identification and crop improvement such as association genetics are likely to be successful. Cultivated crop germplasm is a subset of the total genetic diversity originally available in the wild progenitor species. For the Triticeae cereal crops cultivated in Europe (wheat [Triticum aestivum L.], barley [Hordeum vulgare L.], and rye [Secale cereale L.]), the structure of modern cultivar germplasm developed in three phases. First, domestication of the wild plant progenitors occurred around 8,000 to 12,000 yr ago in the Fertile Crescent. Second, locally adapted landraces emerged across Eurasia. Third, modern crop breeding commenced around 1900 (Cleveland and Soleri, 2002). Modern breeding has been reported to have had different effects on the pattern of genetic diversity of Triticeae cereals, varying from substantial reduction in diversity to no significant effect Published in The Plant Genome 6 doi: 10.3835/plantgenome2013.03.0007 © 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. A. Tondelli and L. Cattivelli, Consiglio per la Ricerca e la sperimentazione in AgricolturaGenomics Res. Centre, Via S. Protaso, 302., I–29017 Fiorenzuola d’Arda PC, Italy; X. Xu, M. Moragues, and A.J. Flavell, Div. of Plant Sci., Univ. of Dundee at JHI, Invergowrie, Dundee, DD2 5DA, UK; R. Sharma and B. Kilian, Leibniz Inst. of Plant Genet. and Crop Plant Res. (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany; F. Schnaithmann and K. Pillen, Martin-LutherUniversität Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle/ Saale, Germany; C. Ingvardsen and S.K. Rasmussen, Dep. of Plant and Env. Sci., Faculty of Life Sci., Univ. of Copenhagen, 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Denmark; O. Manninen and A.H. Schulman, Plant Genomics, Dep. of Biotech. and Food Res., MTT Agrifood Res. Finland, FIN-31600 Jokioinen, Finland; J. Comadran, J. Russell, R. Waugh, and W.T.B. Thomas, The James Hutton Inst., Invergowrie, Dundee, DD2 5DA, UK. Received 20 Mar. 2013. *Corresponding author ([email protected]). Abbreviations: AMOVA, analysis of molecular variance; BLUE, best linear unbiased estimate; CRA, Genomics Research Centre, Fiorenzuola d’Arda, Italy; FST, Wright’s FST statistic; GWAS, genomewide association scan/scanning; HVCC, Hordeum vulgare spring two-row cultivar collection; IPK, Leibniz Institute, Gatersleben, Germany; JHI, James Hutton Institute, Dundee, UK; LD, linkage disequilibrium; MAF, minor allele frequency; PC, principal coordinate; PCO, principal coordinate analysis; PIC, polymorphism information content; QTL, quantitative trait loci; SNP, single nucleotide polymorphism; SSR, simple sequence repeat; UHA, Halle University, Germany.