Comparative Genomics Approaches to the Analysis of Temperate Grasses

Lead Research Organisation: John Innes Centre
Department Name: Contracts Office

Abstract

We aim to establish a comparative genomics approach to the members of the Pooideae subfamily of grasses that includes wheat and barley, the most important crop species in the UK and Europe. Brachypodium is a member of this family but it has a compact genome of about 300 Mb, a little smaller than that of rice, compared to the 16,000 Mb hexaploid genome of wheat. There is a much greater conservation of gene sequence and a general conservation of gene order between wheat and Brachypodium than between wheat and rice. Comparison of gene order and sequence in wheat, barley, rice and Brachypodium has been used to assemble and interpret a large region of wheat chromosome 5B containing the Ph1 locus controlling chromosome pairing and to characterise the Hardness loci in bread wheat and its progenitors. Probes isolated from Brachypodium genes invariably give unambiguous hybridisation signals when used on wheat BAC filters and southern blots and permitted large physical maps of wheat to be made rapidly. The close similarity of gene sequences permitted their exon-intron structures to be defined. A physical map of the Brachypodium distachyon genome will be assembled from end-sequenced BAC clones for use in whole-genome comparative genomic studies in wheat and barley. The physical map of BACs can be made very efficiently by initial alignment of BAC end sequence to the rice genome to generate shorter-scale assemblies that will be verified by correlation to the Brachypodium genetic map. The physical map provides a very high density of sequences that can be used to identify wheat ESTs for aligning wheat BAC contigs and for designing sets of very high density markers. It therefore provides a very cost-effective resource for gene identification in bread wheat and its progenitors, barley and forage grasses.

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