Sequencing and exploitation of the Brassica A genome

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Brassica crops are a major contributor to healthy human diet and agricultural economies worldwide, but efforts to further develop their potential are hampered by the complexity of their genomes. This is the result of polyploidy in their ancestry. For B. oleracea and B. rapa, an ancestral genome triplication, which has undergone extensive diploidization, results in there typically being two copies retained of each unique gene in Arabidopsis. B. napus is an allotetraploid (although functionally diploid) resulting from hybridization between B. oleracea and B. rapa within the last 10,000 years. Its gene content has therefore doubled again. Genome structure of the cultivated Brassica species has been studied both at the level of comparative linkage maps and in terms of gene-by-gene order, and is highly conserved. Consequently, sequence-level knowledge of genome structure in any one species has the potential to be exploited in the others.

A worldwide consortium has initiated the Brassica rapa Genome Sequencing Project. All 10 chromosomes of B. rapa, have been adopted for sequencing by members of the consortium. Common methods and standards have been agreed, i.e. a defined genotype (Chinese cabbage Chiifu-401), a BAC-by-BAC approach with extension from genetically mapped seed BACs via AC end sequences, and with Phase 2 completion required. We have established an alliance with scientists in China (who will provide low-cost sequencing) and the USA (who will adapt and make available to us proven bioinformatics tools). An important part of the project is the development of bioinformatics resources to facilitate the exploitation of the entire B. rapa genome sequence, which we expect to be available at the end of 2009. These include systematic annotation of the genome sequence and a database system with displays tailored to enhance the ability of the various user communities to conduct comparative analyses and exploit the sequence data.

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