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First published online March 4, 2005; 10.1105/tpc.104.029181

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The Plant Cell 17:1033-1045 (2005)
© 2005 American Society of Plant Biologists

Molecular Basis of Evolutionary Events That Shaped the Hardness Locus in Diploid and Polyploid Wheat Species (Triticum and Aegilops){boxw}

Nathalie Chantreta,1, Jérôme Salseb,1, François Sabotc, Sadequr Rahmand, Arnaud Bellecb, Bastien Laubinc, Ivan Duboise, Carole Dossate, Pierre Sourdillec, Philippe Joudrierf, Marie-Françoise Gautierf, Laurence Cattolicoe, Michel Beckertc, Sébastien Aubourgb, Jean Weissenbachg, Michel Cabocheb, Michel Bernardc, Philippe Leroyc and Boulos Chalhoubb,2

a Institut National de la Recherche Agronomique-Centre de Cooperation Internationale en Recherche Agronomique pour le Développement, Biotrop, F-34398 Montpellier Cedex 5, France
b Laboratory of Genome Organization, Unité de Recherches en Génomique Végétale-Institut National de la Recherche Agronomique, F-91057 Évry Cedex, France
c Unité Mixte de Recherche 1095-Institut National de la Recherche Agronomique Amélioration et Santé des Plantes, Domaine de Crouël, F-63039 Clermont-Ferrand Cedex 2, France
d Commonwealth Scientific and Industrial Research Organization Plant Industry, ACT 2601, Camberra, Australia
e GENOSCOPE, Consortium National de Recherche en Génomique, F-91057 Evry Cedex, France
f Institut National de la Recherche Agronomique-Unité Mixte de Recherche, Polymorphismes d'Intérêt Agronomique, 34060 Montpellier Cedex 01, France
g GENOSCOPE, Consortium National de Recherche en Génomique, Centre Nationale de Recherche Scientifique, Unité Mixte de Recherche 8030, F-91057 Evry Cedex, France

2 To whom correspondence should be addressed. E-mail chalhoub{at}evry.inra.fr; fax 33-160874549.

The Hardness (Ha) locus controls grain hardness in hexaploid wheat (Triticum aestivum) and its relatives (Triticum and Aegilops species) and represents a classical example of a trait whose variation arose from gene loss after polyploidization. In this study, we investigated the molecular basis of the evolutionary events observed at this locus by comparing corresponding sequences of diploid, tertraploid, and hexaploid wheat species (Triticum and Aegilops). Genomic rearrangements, such as transposable element insertions, genomic deletions, duplications, and inversions, were shown to constitute the major differences when the same genomes (i.e., the A, B, or D genomes) were compared between species of different ploidy levels. The comparative analysis allowed us to determine the extent and sequences of the rearranged regions as well as rearrangement breakpoints and sequence motifs at their boundaries, which suggest rearrangement by illegitimate recombination. Among these genomic rearrangements, the previously reported Pina and Pinb genes loss from the Ha locus of polyploid wheat species was caused by a large genomic deletion that probably occurred independently in the A and B genomes. Moreover, the Ha locus in the D genome of hexaploid wheat (T. aestivum) is 29 kb smaller than in the D genome of its diploid progenitor Ae. tauschii, principally because of transposable element insertions and two large deletions caused by illegitimate recombination. Our data suggest that illegitimate DNA recombination, leading to various genomic rearrangements, constitutes one of the major evolutionary mechanisms in wheat species.




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