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A 3,000-Loci transcription map of chromosome 3B unravels the structural and functional features of gene islands in hexaploid wheat

C. Rustenholz, F. Choulet, C. Laugier, Jan Safar, Hana Simkova, Jaroslav Dolezel, Federica Magni, Simone Scalabrin, Federica Cattonaro, Sonia Vautrin, Arnaud Bellec, Hélène Bergès, Catherine Feuillet and Etienne
Institut National de la Recherche Agronomique-Université Blaise Pascal, Unité Mixte de Recherche 1095, Génétique Diversité et Ecophysiologie des Céréales, F–63100 Clermont-Ferrand, France (C.R., F.C., C.L., C.F., E.P.); Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, CZ–77200 Olomouc, Czech Republic (J.S., H.S., J.D.); Istituto di Genomica Applicata, Parco Scientifico e Tecnologico di Udine “Luigi Danieli,” I–33100 Udine, Italy (F.M., S.S., F.C.); and Institut National de la Recherche Agronomique-Centre National de Ressources Génomiques Végétales, F–31326 Castanet Tolosan, France (S.V., A.B., H.B.)  

Abstract

To improve our understanding of the organization and regulation of the wheat (Triticum aestivum) gene space, we established a transcription map of a wheat chromosome (3B) by hybridizing a newly developed wheat expression microarray with bacterial artificial chromosome pools from a new version of the 3B physical map as well as with cDNA probes derived from 15 RNA samples. Mapping data for almost 3,000 genes showed that the gene space spans the whole chromosome 3B with a 2fold increase of gene density toward the telomeres due to an increase in the number of genes in islands. Comparative analyses with rice (Oryza sativa) and Brachypodium distachyon revealed that these gene islands are composed mainly of genes likely originating from interchromosomal gene duplications. Gene Ontology and expression profile analyses for the 3,000 genes located along the chromosome revealed that the gene islands are enriched significantly in genes sharing the same function or expression profile, thereby suggesting that genes in islands acquired shared regulation during evolution. Only a small fraction of these clusters of cofunctional and coexpressed genes was conserved with rice and B. distachyon, indicating a recent origin. Finally, genes with the same expression profiles in remote islands (coregulation islands) were identified suggesting long-distance regulation of gene expression along the chromosomes in wheat.

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