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

Romain Philippe, Etienne Paux, Isabelle Bertin, Pierre Sourdille, Fréderic Choulet, Christel Laugier, Hana Šimková, Jan Šafář, Arnaud Bellec, Sonia Vautrin, Zeev Frenkel, Federica Cattonaro, Federica Magni, Simone Scalabrin, Mihaela M. Martis, Klaus F.X. Mayer, Abraham Korol, Hélène Bergès, Jaroslav Doležel, Catherine Feuillet

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Article numberR64
JournalGenome Biology
Volume14
Issue number6
DOIs
StatePublished - 25 Jun 2013

Bibliographical note

Funding Information:
The authors want to thank Rudi and Diane Appels for their support in identifying the number of QTL mapped on chromosome 1BL in the wheat gene catalogue. We also want to thank the International Wheat Genome Sequencing Consortium for generating the wheat chromosome survey sequences and making them available for analysis in advance of publication. We are grateful to Kellye Eversole for critical editing of the manuscript. Hybridization experiments were performed at Institut National de la Recherche Agronomique Clermont-Ferrand on the GENTYANE genotyping platform [105]. This work was supported by the European Community’s Seventh Framework Programme TriticeaeGenome (grant agreement n°FP7-212019).

Keywords

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

ASJC Scopus subject areas

  • Genetics
  • Ecology, Evolution, Behavior and Systematics
  • Cell Biology

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