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Open Access Research

A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat

Romain Philippe1, Etienne Paux1, Isabelle Bertin1, Pierre Sourdille1, Fréderic Choulet1, Christel Laugier1, Hana Šimková2, Jan Šafář2, Arnaud Bellec3, Sonia Vautrin3, Zeev Frenkel4, Federica Cattonaro5, Federica Magni5, Simone Scalabrin5, Mihaela M Martis6, Klaus FX Mayer6, Abraham Korol4, Hélène Bergès3, Jaroslav Doležel2 and Catherine Feuillet1*

Author Affiliations

1 INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France

2 Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovska 6, CZ-77200 Olomouc, Czech Republic

3 Centre National des Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge - Auzeville 31326 Castalnet Tolosan, France

4 University of Haifa, Institute of Evolution and Department of Evolutionary and Environmental Biology, Haifa 31905, Israel

5 Instituto di Genomica Applicata, Via J. Linussio 51, Udine, 33100, Italy

6 MIPS/IBIS; Helmholtz-Zentrum München, 85764 Neuherberg, Germany

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Genome Biology 2013, 14:R64  doi:10.1186/gb-2013-14-6-r64

Published: 25 June 2013

Abstract

Background

As for other major crops, achieving a complete wheat genome sequence is essential for the application of genomics to breeding new and improved varieties. To overcome the complexities of the large, highly repetitive and hexaploid wheat genome, the International Wheat Genome Sequencing Consortium established a chromosome-based strategy that was validated by the construction of the physical map of chromosome 3B. Here, we present improved strategies for the construction of highly integrated and ordered wheat physical maps, using chromosome 1BL as a template, and illustrate their potential for evolutionary studies and map-based cloning.

Results

Using a combination of novel high throughput marker assays and an assembly program, we developed a high quality physical map representing 93% of wheat chromosome 1BL, anchored and ordered with 5,489 markers including 1,161 genes. Analysis of the gene space organization and evolution revealed that gene distribution and conservation along the chromosome results from the superimposition of the ancestral grass and recent wheat evolutionary patterns, leading to a peak of synteny in the central part of the chromosome arm and an increased density of non-collinear genes towards the telomere. With a density of about 11 markers per Mb, the 1BL physical map provides 916 markers, including 193 genes, for fine mapping the 40 QTLs mapped on this chromosome.

Conclusions

Here, we demonstrate that high marker density physical maps can be developed in complex genomes such as wheat to accelerate map-based cloning, gain new insights into genome evolution, and provide a foundation for reference sequencing.

Keywords:
chromosome 1BL; evolution; gene space; grasses; hexaploid wheat; map-based cloning; physical mapping; sequencing; synteny