Brassica Genome Gateway
 

Summary of the discussion during the 13th Crucifer Genetics Workshop 24th - 25th March 2002

Graham King, April 2002

Detailed tables of resources also available here

This discussion was well attended and followed on from the previous workshop held at Plant Animal Genome X in January 2002 (see summary). The discussion took place in two sessions - i) general and ii) specifically relating to plant resources.

There was acceptance of the requirement for bringing together various national projects under the banner of "Multinational Brassica Genome Project" (MBGP). It was agreed than general information and lists / links to resources for the MBGP would be collated and placed on an information web site: www.brassica.info/ managed by Graham King and genome data and information would be made available through the Brassica Genome Gateway site: http://brassica.bbsrc.ac.uk managed by Martin Trick and Paul Beckett.

  1. Initial discussion focused on of the principle of 'public domain' resources and limitations which may arise from use of Materials Transfer Agreements (MTAs). It was generally accepted that:
    • the Brassica research community should aim to restrict scope of MTAs to 'limitation of liability' and option of non-exclusive licence to provider in order to adhere to and benefit from 'public domain' resources.
    • the onus should be on the resource provider to pursue any issue relating to an MTA following use of a resource
  2. The following issues were discussed as requirements in terms of providing a sound basis for future integration of information, and to stimulate use and adoption of resources to benefit the multinational effort:
    • The is a continuing need for agreement and convergence on common nomenclature for linkage groups etc
      • e.g. recent alignment of the Brassica oleracea karyotype with linkage map (Howell et al. Genetics, in press) has assigned linkage group numbers (originating from Derek Lydiate's team) to chromosomes. (in this system B. oleracea = O1-O9, B. rapa = R1-R10, B. napus = N1-N19, where N1-N10 are equivalent to R1-R10 and N11-N19 equivalent to O1-O9).
      • Alignment of linkage maps requires use of common, public-domain sequence-tagged markers. It is therefore important to ensure that, where possible, the product of markers from the population in question is sequenced (either sequence RFLP probe, or PCR product if is a PCR/SSR marker). RFLP markers are not ideal, as ambiguity can arise due to presence of monomorphic bands or nulls.
    • Archiving
      • Plant populations (see detailed notes below)
      • BAC libraries, etc - should be present in two locations (for security) if are to represent a long-term resource.
    • Database structures - requires additional discussion. Guidelines for naming conventions would be of benefit.

    Resources currently or imminently available were reviewed through short presentation/announcements. A summary is presented below. More detailed information is being collated at www.brassica.info. To facilitate this process, please provide any relevant information to Graham King, and check the website for regular updates. Information and discussion about resources can be disseminated via the associated mailing list (log on to web site to register as a member of this list). Where ever possible, details of sequence-tagged markers, map populations and scoring strings should be lodged in a public domain database - BrassicaDB currently stores such data - contact Martin Trick.

    At the meeting, the resources were presented by country - however, for ease of reading, they are presented here in tabular form by resource type.

  3. A discussion on Brassica plant genetic stocks available for deposit in the Ohio Arabidopsis Biological Resource Center.
    • Randy Scholl, who is the Director, was present and gave an outline of willingness to hold stocks for distribution. More information on this will be posted here soon. There are limitations posed by the costs of regenerating some Brassica stocks, due to self-incompatibility, size, etc.
    • In addition, HRI hosts an ex situ genetic resource unit (HRI GRU) primarily for accessions of vegetable crops and their wild relatives.
      • Although HRI is unlikely to be able to set up a distribution for the Brassica stocks, the GRU would be able to hold back-up or security stocks in a 'black-box' system, which could supplement any distribution system set up by ABRC or elsewhere. The standard conditions are low humidity and -20 C. Stocks would only be opened with written permission of donor.
    • Other sites around the world also hold ex situ resource centres which include Brassica accessions - information on these will be collated at www.brassica.info.

Data collated by Graham King and Tom Osborn - for tables of resources download Word97 document or view here.

 
 
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