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Published on November 14, 2008; 10.1104/pp.108.129734

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Received September 10, 2008
Accepted November 12, 2008

Analysis of intraspecies diversity in wheat and barley genomes identifies breakpoints of ancient haplotypes and provides insight in the structure of diploid and hexaploid Triticeae gene pools

Thomas Wicker , Simon Krattinger , Evans S. Lagudah , Takao Komatsuda , Mohammad Pourkheirandish , Takashi Matsumoto , Sylvie Cloutier , Laurenz Reiser , Hiroyuki Kanamori , Kazuhiro Sato , Dragan Perovic , Nils Stein , and Beat Keller *

Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland; CSIRO Plant Industry, GPO Box 1600, Canberra, ACT, 2601, Australia; National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan; Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Road, Winnipeg, MB, Canada R3T 2M9; Institute of Society for Techno-Innovation of Agriculture, Forestry and Fisheries (STAFF), Tsukuba 305-0854, Japan; Research Institute for Bioresources, Okayama University, Japan; Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany; Present address: Julius-Kuehn-Institute (JKI), Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, D-06484 Quedlinburg, Germany

* Corresponding author; email: bkeller{at}botinst.uzh.ch.

A large number of wheat and barley 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, 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 which 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 (InDels) showed that large events caused by transposable element insertions, illegitimate recombination or unequal crossing-over were relatively rare. Most InDels were small and caused by template slippage in short homopolymers of only a few bp in size. Such frequent polymorphisms could be exploited for future molecular marker development.




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