Summary of the Brassica Genomics Workshop held on September 27th 2001 at the BBSRC GARNet/Brassica IGF Annual Meeting in York
Ian Bancroft – 5th October 2001
Approximately 40 scientists attended the workshop, held in the evening. Although primarily members of the UK Brassica Research Community, we were appreciative of the attendance of, and active participation by, scientists involved in the Canadian, French and German national genomics programmes involving Brassica species. International cooperation is an important feature of the development of Brassica genomics. Scientists from two companies also attended the workshop and participated in the discussion.
A wide range of potential underpinning resources were discussed. Although potentially very useful, T-DNA/transposon knockout lines were not viewed as high priority for generation at present. Mis-expression, using RNAi or similar technology, might be more appropriate. But the feeling was that natural variation was the most important source of genetic variation in Brassica species.
To exploit natural variation in Brassica species genetic maps (primarily QTL maps) incorporating molecular markers, are vital. However, the populations and traits involved are very specific to particular biological analyses, so the generation of new maps and molecular markers per se were not regarded as high priorities for community resources.
The BAC-based physical maps of the Brassica A and C genomes that are being constructed as part of the Brassica IGF project will be a key resource. It was felt that their utility for the exploitation of natural variation in Brassica species would be greatly enhanced by unambiguous integration with the many existing Brassica genetics maps. This could be achieved by anchoring SSLP markers to the BAC libraries, the generation of SNP markers using BAC-derived sequences and mapping in the diploid Brassica species and also in oilseed rape, and by cytogenetic anchoring (in Brassica oleracea) using in situ hybridisation. It was considered by the workshop participants to be essential that the unambiguous genetic/cytogenetic anchoring of all BAC contigs should be conducted as soon as possible. This is required in order to maximise the utility to be made of the physical maps.
The need for Brassica sequence data was discussed. Although there was widespread interest in the generation of Brassica EST sequence date for the design and production of microarrays for the analysis of gene expression, it was felt that an EST project would be premature. Large-scale EST projects were under way in oilseed rape in Canada and France and the data from these may become available eventually. It is not yet known how the sequences of the transcriptomes of the diploid Brassica species might differ from each other and from that of oilseed rape, but it was clear that a variety of tissues/developmental stages must be included to provide resources of community-wide interest. It was felt that a preliminary experiment should be conducted to assess the sequence level differences of a range of orthologous genes represented in a variety of Brassica genomes and varieties. A programme is under way at TIGR to sequence six regions (ca. 3 megabases) of the genome of B. oleracea using BAC clones mapped at JIC. Collaborators in Korea will be sequencing B. rapa BACs representing the homoeologues of some of these regions, but there is no project aiming to sequence homoeologous regions from oilseed rape. An important (and complementary) investigation would be to sequence a number of selected gene families across a wide range of Brassica species and varieties. It was considered by the Workshop participants to be essential that genome sequence data for homoeologous segments of the genomes of B. oleracea, B. rapa and oilseed rape be determined, and some gene families sequenced across a greater range of varieties. This would permit rational evaluation of the community requirements for Brassica EST and genome sequence data. It would also give rise to important insights into plant genome structure and evolution. Suitable BAC contigs for the analysis of the homoeologous regions of B. rapa and B. napus are presently being constructed as part of the CSG-funded programme at JIC, and can be made available for sequencing. Appropriate gene families for wider analysis could be suggested by the UK-BRC.
The Workshop participants agreed that international links, although already good, should be further strengthened. Also, that ways should be found to accomplish the two highest priority tasks identified, i.e. the genetic and/or cytogenetic mapping of all BAC contigs generated by the IGF project and comparative Brassica sequence analysis from defined genomic regions and gene families.
Please post further comments and suggestions to these newsgroups UK-BRC and ArabUk or directly to me (Ian Bancroft).