Sequencing and exploitation of the Brassica A genome

Lead Research Organisation: John Innes Centre
Department Name: Crop Genetics

Abstract

Brassica crops are major contributors to healthy human diet and agricultural economies worldwide. They include oil crops such as oilseed rape (B. napus) and vegetables such as cabbage, cauliflower, broccoli (B. oleracea) and Chinese cabbage and turnip (B. rapa). The UK provides 5% of worldwide production of rapeseed, the oil from which has important nutritional properties and has potential as a biofuel or a renewable resource for industrial applications. Brassica vegetables are rich sources of vitamins, minerals and compounds that help protect against cancer. Despite the importance of Brassica crops in the UK, efforts to develop their potential further are hampered by the complexity of their genetic composition. This is the result of hybrid formation in their ancestry, resulting in amplification of their genomes. For B. oleracea and B. rapa, this results in there typically being 2 copies of each unique gene in closely related species, such as the widely studied Arabidopsis thaliana. In B. napus, the situation is worse still as this species is the result of a very recent hybridization between B. oleracea and B. rapa, resulting in an additional doubling of gene numbers. Fortunately, all of the cultivated Brassica species are closely related and genome structure is very highly conserved between them. This means that detailed knowledge of genome structure and composition in any one species can be readily exploited in the others, providing the necessary data interpretation and information-sharing resources are put in place. A worldwide consortium has initiated the Brassica rapa Genome Sequencing Project, with ongoing activity in Korea, Australia, Germany, Canada, USA and elsewhere. All 10 chromosomes of the homozygous genotype to be sequenced, (Chiifu-401, a Chinese cabbage) have been adopted for sequencing by members of the consortium. The sequencing of two of them is underway in Korea and proposals are being developed to sequence the remainder. In all cases, the methods and standards to be adopted have been agreed. We have established an alliance with scientists in China and the USA, exploiting the complementary expertise available from the partners, to sequence two chromosomes. In addition, we will develop 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, obtaining sequences from oilseed rape to enable the identification of corresponding regions of its genome, and a database system with displays tailored to enhance the ability of the various user communities to exploit the sequence data for research and the improvement of the Brassica crops of importance in the UK.

Technical Summary

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 BAC 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. (Joint with BB/E017797/1 and BB/E017479/1)

Publications

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Li F (2014) Genome-wide association study dissects the genetic architecture of seed weight and seed quality in rapeseed (Brassica napus L.). in DNA research : an international journal for rapid publication of reports on genes and genomes

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Lu G (2014) Associative transcriptomics study dissects the genetic architecture of seed glucosinolate content in Brassica napus. in DNA research : an international journal for rapid publication of reports on genes and genomes

 
Description Detailed understanding has been gained of genome organisation in Brassica species
Exploitation Route Platform for marker development by breeders
Sectors Agriculture, Food and Drink

 
Description The genome sequences that this project helped to produce are being used throughout the global rapeseed breeding industry for the development of molecular markers to support marker-assisted selection and improve the efficiency of breeding new varieties.
First Year Of Impact 2011
Sector Agriculture, Food and Drink
Impact Types Economic

 
Title Associative Transcriptomics 
Description Form of association genetics using functional genotypes derived from mRNA-seq data, allowing association of trait variation with both gene sequence variation and gene expression variation. 
Type Of Material Data analysis technique 
Year Produced 2012 
Provided To Others? Yes  
Impact Molecular markers identified for a broad range of traits in oilseed rape and wheat.