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Open Access Research article

Specific patterns of gene space organisation revealed in wheat by using the combination of barley and wheat genomic resources

Camille Rustenholz1, Pete E Hedley2, Jenny Morris2, Frédéric Choulet1, Catherine Feuillet1, Robbie Waugh2 and Etienne Paux1*

Author Affiliations

1 INRA UMR 1095, Génétique Diversité et Ecophysiologie des Céréales, 63100 Clermont-Ferrand, France

2 Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK

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BMC Genomics 2010, 11:714  doi:10.1186/1471-2164-11-714

Published: 19 December 2010

Abstract

Background

Because of its size, allohexaploid nature and high repeat content, the wheat genome has always been perceived as too complex for efficient molecular studies. We recently constructed the first physical map of a wheat chromosome (3B). However gene mapping is still laborious in wheat because of high redundancy between the three homoeologous genomes. In contrast, in the closely related diploid species, barley, numerous gene-based markers have been developed. This study aims at combining the unique genomic resources developed in wheat and barley to decipher the organisation of gene space on wheat chromosome 3B.

Results

Three dimensional pools of the minimal tiling path of wheat chromosome 3B physical map were hybridised to a barley Agilent 15K expression microarray. This led to the fine mapping of 738 barley orthologous genes on wheat chromosome 3B. In addition, comparative analyses revealed that 68% of the genes identified were syntenic between the wheat chromosome 3B and barley chromosome 3 H and 59% between wheat chromosome 3B and rice chromosome 1, together with some wheat-specific rearrangements. Finally, it indicated an increasing gradient of gene density from the centromere to the telomeres positively correlated with the number of genes clustered in islands on wheat chromosome 3B.

Conclusion

Our study shows that novel structural genomics resources now available in wheat and barley can be combined efficiently to overcome specific problems of genetic anchoring of physical contigs in wheat and to perform high-resolution comparative analyses with rice for deciphering the organisation of the wheat gene space.