Brassica Genome Resource

Summary of the discussion during the PAG Brassica workshop on 16th January 2002

Ian Bancroft, February 2002

Approximately 150 scientists attended the 2002 PAG Brassica workshop. The first part of the workshop consisted of 8 presentations summarising Brassica genomics projects underway in the U.K. (Graham King), China (Jianwei Zhao), Germany (Renate Horn), Canada (Derek Lydiate) and France (Michel Renard, Boulos Chalhoub). Chris Town also summarised work being conducted at TIGR and Yong Pyo Lim talked about his project being conducted in S. Korea. There then followed a discussion on co-ordination of international Brassica genomics. There was widespread support for the integration of the various Brassica genomics projects that are underway world-wide. The discussion focused on practical mechanisms to promote this integration.

An important aspect is the integration of the many Brassica genetic maps. Derek Lydiate proposed a standardised nomenclature should be adapted for linkage groups and chromosomes and a core set of SSR markers should be defined. A set of SSR markers sponsored by the BBSRC (all of which are publicly available) have been mapped in B. napus (by Martin Trick and colleagues at JIC), and a proportion are being mapped in B. oleracea and B. rapa (by Graham King). GK, MT and IB will liaise with DL to define such a core set of markers. A proportion of the SSR markers being developed by industrial consortia (e.g. AAFC and Celera) may also be made public and could be added later. The U.K. Brassica Genome Project web site will make the details of these markers available. Further information is available via BrassicaDB. The Brassica research community should be encouraged to include these markers (amongst others) in their genetic mapping work.

An additional important element for the development of detailed and integrated maps will be the adoption of common, publicly available mapping populations. For B. oleracea, a DH mapping population is available for var. alboglabra A12DHd x var italica GHDH33 (ex. Green DukeF1) from Graham King (http://brassica.info/resources/hri/refmappops.htm). For B. rapa, a DH mapping population (to be followed later in the year by a larger RI population) is available for var pekinesis Chiifu x Kenshin from Yong Pyo Lim. Several populations are available for B. napus, including a synthetic x cultivar from Derek Lydiate, ex. Darmor dwarf x ex. Yudal from Michel Renard and (shortly) ex. Tapidor DH x ex. Ningyou 7 DH from Jianwei Zhao / Jingling Meng.

The integration of physical (BAC-based) mapping efforts was also discussed. Two aspects were agreed to be essential. Firstly, the use of common hybridization probes, especially where alignment between the Brassica and Arabidopsis genomes is an objective. The U.K. Brassica Genome Project is aiming to construct complete BAC contig maps for the A and C genomes. The details of all Arabidopsis gene specific probes used in the project (ca. 1200) are available via the Brassica Genome Project web site (./IGF). Secondly, the use of common publicly available BAC libraries was seen as valuable. Libraries are available for B. oleracea var. alboglabra A12DHd from TAMU (BoB) and Ian Bancroft (JBo), for B. rapa var pekinesis Chiifu from Yong Pyo Lim (BrH and BrB) and ssp oleifera RO18 from Ian Bancroft (JBr), for a B. napus cultivar from Derek Lydiate, for B. napus. Darmor dwarf from Boulos Chalhoub and B. napus Tapidor DH from Ian Bancroft (JBnB and JBnY). All of these libraries are being used in systematic genomics projects and are available for academic research. License fees will be required for some if they are to be used for commercial projects.

Several EST programmes are underway, however the delay in public release of large sets of data is seen as hindering academic progress. A deal was proposed such that the Canadian ESTs (Derek Lydiate) will be made publicly available immediately if the Genoplante ESTs (Michel Renard) will also be released immediately. The workshop attendees were very supportive of this offer and Michel Renard would investigate the feasibility. If agreed this would result in the public availability of ca. 100,000 ESTs in total. Together with at least 500,000 genomic sequence reads that will be generated by TIGR, these would underpin transcription analysis studies, perhaps by facilitating the commissioning of an Affymetrix Brassica array.

Further communication between Scientists involved in Brassica Genomics projects was seen as important. It was offered that the U.K. Brassica Genome Project database, which is managed by Martin Trick of JIC, would act as a reference point for information. Graham King also offered that HRI would host a site for collation of information on internationally available public-domain resources (http://brassica.info). The U.K. Brassica Genome Project database already provides A and C genome physical map data, including Arabidopsis anchor probes and clone ordering details for the JBo, JBr, JBnB and JBnY BAC libraries. Details of the proposed core SSR set, contact details for access to mapping populations and other BAC libraries could be added. There is a newsgroup for the U.K. Brassica Research Community (UK-BRC). It was requested that this newsgroup should be opened up internationally to become the main news and communication group for the world-wide Brassica genomics effort. This was agreed and interested scientists are encouraged to contact Graham King to subscribe to subscribe to an expanded newsgroup. There was support for the concept of a Multinational Brassica Genome Project, which would help co-ordinate and integrate genomics projects involving all of the Brassica genomes being studied. An expanded derivative of the UK-BRC newsgroup could act as a forum for communication and dissemination.

There will be an opportunity in March 2002 for many of the scientists working in Brassica genomics research to meet again at the Crucifer Genetics Workshop to be held at UC Davies, to continue discussions.

 
 
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