MBE Advance Access published online on April 18, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm077
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Research Article |
Grinding up Wheat: a Massive Loss of Nucleotide Diversity Since Domestication
1 UMR Diversité et Adaptation des Plantes Cultivées, Montpellier SupAgro – INRA –IRD – UMII, 2, Place Pierre Viala, 34060 Montpellier Cedex 1, France
2 UMR Amélioration et santé des plantes, INRA Site de Crouëlle, 234, avenue du Brézet, 63039 Clermont-Ferrand cedex 2, France
3 INRA, Centre National de Génotypage, 2, rue Gaston Crémieux, CP5708, 91057 Evry cedex, France
4 Institut des Sciences de l'Evolution, Université Montpellier 2, place Eugène Bataillon, Montpellier, France
5 BiRC - Bioinformatics Research Center, Department of Genetics and Ecology, University of Aarhus, Hoegh-Guldbergs Gade 10, Building 1090, DK-8000 Aarhus C, Denmark
Corresponding Author: Annabelle Haudry1, telephone number: (+33)4 67 29 06 40, fax number: (+33)4 67 29 39 90, e-mail: haudry{at}ensam.inra.fr
Received for publication February 8, 2007. Accepted for publication March 27, 2007.
Several demographic and selective events occurred during the domestication of wheat from the allotetraploid wild emmer (Triticum turgidum ssp. dicoccoides). Cultivated wheat has since been affected by other historical events. We analysed nucleotide diversity at 21 loci in a sample of 101 individuals representing four taxa corresponding to representative steps in the recent evolution of wheat (wild, domesticated, cultivated durum and bread wheats), to unravel the evolutionary history of cultivated wheats and to quantify its impact on genetic diversity. Sequence relationships are consistent with a single domestication event and identify two genetically different groups of bread wheat. The wild group is not highly polymorphic, with only 212 polymorphic sites among the 21,720 bp sequenced, and, during domestication, diversity was further reduced in cultivated forms — by 69% in bread wheat and 84% in durum wheat — with considerable differences between loci, some retaining no polymorphism at all. Coalescent simulations were performed and compared with our data, to estimate the intensity of the bottlenecks associated with domestication and subsequent selection. Based on our 21-locus analysis, the average intensity of domestication bottleneck was estimated at about 3 — giving a population size for the domesticated form about one third that of wild dicoccoides. The most severe bottleneck, with an intensity of about 6, occurred in the evolution of durum wheat. We investigated whether some of the genes departed from the empirical distribution of most loci, suggesting that they might have been selected during domestication or breeding. We detected a departure from the null model of demographic bottleneck for the hypothetical gene HgA. However, the atypical pattern of polymorphism at this locus might reveal selection on the linked locus Gsp1A, which may affect grain softness — an important trait for end-use quality in wheat.
Key Words: wheat • domestication • nucleotide diversity • bottleneck • coalescence
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