Brassica : Harvesting the Genome, Diversity and Products
Status and aims of Brassica genome research
The latest release of EMBL/Genbank includes 404Mb of Brassica oleracea DNA sequence, with additional large datasets of B. napus and other ESTs.
A number of EST programmes have been initiated in different countries. A B. napus EST programme funded by Genoplante in France released sequences into the public databases in summer 2003. B. rapa ESTs are being sequenced as part of the S. Korean B. rapa sequencing effort. A UK-Canadian B. oleracea EST programme is releasing data during 2005.
Genetic maps have been generated for all Brassica species. Most effort has been fociused on B. napus, B. oleracea and B. rapa. Until recently there has been relatively little widespread integration of maps with public-domain sequence-tagged common markers. There is an ongoing effort to generate such integrated information and to standardise nomenclature and orientation of linkage groups. A number of maps exist that have been constructed with EST or other sequence tags from Arabidopsis.
Physical maps and BAC libraries
BAC libraries are available for many Brassica species in the public domain. The UK genome effort has initially focused on developing fingerprinted contigs of the A and C genomes, anchored to the Arabidopsis genome through hybridisation with 1200+ gene-specific probes. An overgo-hybridisation programme with additional Arabidopsis probes is underway in the USA.
Reference BAC libraries have been generated in Korea for the B. rapa sequencing programme, and distributed to laboratories around the world.
For B. oleracea chromosome FiSH analysis has allowed orientaiton and assignment of all chromosomes to the linkage groups. For B. rapa a similar exercise has been carried out in Korea.
Mutant lines of Brassica have been compiled and characterised in the past. Sets of rapid cycling lines were generated from the Wisconsin Crucifer Genetics Co-operative, and are used as a successful teaching tool worldwide. The first plant to complete its life cycle in space was a rapid cycling line of B. rapa (Astro-plant) on the MIR space station. The Astro-plant lines have been used in subsequent zero-gravity experiments.
The Targeted Induced Local Lesions In Genomes (TILLING) platform provides a means to screen (usually EMS) mutagenised populations for mutations in specific candidate gene families. The presence of duplicated chromosomal segments and several paralogous copies of each gene suggest that Brassica species should be able to carry a relatively high mutational load (due to gene redudancy). Initial exploratory TILLING populations have been established for B. napus and B. oleracea, and are underway for B. rapa. The labour-intensive tasks of maintaining tens of thousands of mutagenised lines indicates that future development of comprehensive Brassica TILLING resources should be managed within an international network.
Other experimental resources
A range of functional genomic resources are required to fully utilise genomic information arising from Brassica and Arabidopsis. Genotypes of some species of Brassica are relatively easy to transform, and thus study up and down regulation of individual genes or gene families.
Information, knowledge and bioinformatics
A considerable amount of information is available world-wide relating to Brassica traits, genetics and genomics. There is a requirement for the international community to develop methodologies for establishing conventions for nomenclature and information exchange, in order to harness the full benefits from genome-based resources. Some progress has been made in this area, with specific examples of comparative genomic data that enable navigation between the Arabidopsis and Brassica genomes.
Draft White Paper for Multinational Brassica Genome Project (MBGP); 12/01/2006