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Analysis of Intraspecies Diversity in Wheat and Barley Genomes Identifies Breakpoints of Ancient Haplotypes and Provides Insight into the Structure of Diploid and Hexaploid Triticeae Gene Pools^1,[OA]

Institute of Plant Biology, University of Zurich, 8008 Zurich, Switzerland (T.W., S.G.K., L.R., B.K.); Commonwealth Scientific and Industrial Research Organization Plant Industry, Canberra, Australian Capital Territory 2601, Australia (E.S.L.); National Institute of Agrobiological Sciences, Tsukuba 305–8602, Japan (T.K., M.P., T.M.); Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, Manitoba, Canada R3T 2M9 (S.C.); Institute of Society for Techno-Innovation of Agriculture, Forestry, and Fisheries, Tsukuba 305–0854, Japan (H.K.); Research Institute for Bioresources, Okayama University, Okayama 710–0046, Japan (K.S.); and Leibniz Institute of Plant Genetics and Crop Plant Research, D–06466 Gatersleben, Germany (D.P., N.S.)

A large number of wheat (Triticum aestivum) and barley (Hordeum vulgare) varieties have evolved in agricultural ecosystems since domestication. Because of the large, repetitive genomes of these Triticeae crops, sequence information is limited and molecular differences between modern varieties are poorly understood. To study intraspecies genomic diversity, we compared large genomic sequences at the Lr34 locus of the wheat varieties Chinese Spring, Renan, and Glenlea, and diploid wheat Aegilops tauschii. Additionally, we compared the barley loci Vrs1 and Rym4 of the varieties Morex, Cebada Capa, and Haruna Nijo. Molecular dating showed that the wheat D genome haplotypes diverged only a few thousand years ago, while some barley and Ae. tauschii haplotypes diverged more than 500,000 years ago. This suggests gene flow from wild barley relatives after domestication, whereas this was rare or absent in the D genome of hexaploid wheat. In some segments, the compared haplotypes were very similar to each other, but for two varieties each at the Rym4 and Lr34 loci, sequence conservation showed a breakpoint that separates a highly conserved from a less conserved segment. We interpret this as recombination breakpoints of two ancient haplotypes, indicating that the Triticeae genomes are a heterogeneous and variable mosaic of haplotype fragments. Analysis of insertions and deletions showed that large events caused by transposable element insertions, illegitimate recombination, or unequal crossing over were relatively rare. Most insertions and deletions were small and caused by template slippage in short homopolymers of only a few base pairs in size. Such frequent polymorphisms could be exploited for future molecular marker development.

² These authors contributed equally to the article.

³ Present address: Julius-Kuehn-Institute, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Strasse 27, D–06484 Quedlinburg, Germany.

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Beat Keller (bkeller{at}botinst.uzh.ch).

^[OA] Open Access articles can be viewed online without a subscription.

www.plantphysiol.org/cgi/doi/10.1104/pp.108.129734

^* Corresponding author; e-mail bkeller{at}botinst.uzh.ch.

Received September 10, 2008; accepted November 12, 2008; published November 14, 2008.

This article has been cited by other articles:

				E. A. Kellogg and C. R. Buell Splendor in the Grasses Plant Physiology, January 1, 2009; 149(1): 1 - 3. [Full Text] [PDF]