Notes from discussion meeting held at the Crucifer Genetics Workshop, 24^th & 25^th March 2002

Graham King

Tom Osborn

This discussion was well attended and followed on from previous workshop held at Plant Animal Genome X in January 2002 (see here). 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: http://www.brassica.info/ managed by Graham King and genome data and information would be made available through the Brassica Genome Gateway: http://brassica.nbi.ac.uk/ managed by Martin Trick.

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:

1. 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.
2. 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:

1. The is a continuing need for agreement and convergence on common nomenclature for linkage groups etc

1. 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).
2. 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.

2. Archiving

1. Plant populations (see detailed notes below)
2. BAC libraries, etc – should be present in two locations (for security) if are to represent a long-term resource.

3. 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 http://www.brassica.info/ . To facilitate this process, please provide any relevant information to graham.king@bbsrc.ac.uk, 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@bbsrc.ac.uk

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.

(http://www.biosci.ohio-state.edu/~plantbio/Facilities/abrc/abrchome.htm).

1. 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.

2. In addition, WHRI hosts an ex situ genetic resource unit (HRI GRU) primarily for accessions of vegetable crops and their wild relatives.

1. 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.

3. 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.

Resource

Species

Country

Institution

Contact

Comments

RFLP markers

Various

USA

Wisconsin

Tom Osborn

• Sequenced set due to be submitted to GenBank

Various

UK/Canada

Derek Lydiate

• probes sequenced but currently owned by two breeding companies. However, relative position in A.thaliana can be specified (Parkin et al., in press)

SSR markers

Various

UK

IACR/JIC

Martin Trick

• public domain set generated in BBSRC funded project (Martin Trick, Keith Edwards)
• Sequence of clones and primers in BrassicaDB
• Map data for 70 in B. napus in BrassicaDB
• SSRs currently being evaluated and mapped in B.oleracea and B. rapa at HRI

Various

Canada

AAFC

Andy Sharpe

• SSRs from AAFC consortium – Consortium due to be polled first half 2002 whether able to release a subset into public domain

Various

Celera

• Celera consortium SSRs – unknown status

BAC libraries

B. napus

France

INRA (Genoplante)

Boulos Chaloub

• from Genoplante consortium (separate unit for BAC libraries)
• 2x BAC libraries available (link)

B. oleracea

UK/USA

HRI/TAMU

Graham King

• B. oleracea ‘BoB’ – publicly available from TAMU
• Being contiged as part of UK physical map programme

B. oleracea

UK

PBL/JIC

Ian Bancroft

• B. oleracea ‘JBo’ - MTA
• Being contiged as part of UK physical map programme

B. oleracea

USA

UC Davis

Carlos Quiros

• 18,000 clones (3x) (Carlos Quiros)
• var. italica ‘Early Big’

B. oleracea

USA

U Georgia

Andy Paterson

• to be generated
• T01434 rapid cycling line 73,000 (10x) -
• T01434 is a self of T01000 which is a S5 from SC rapid cycling
• TIGR B. oleracea genomic sequencing was carried out on a DH from T01000

B. oleracea

USA

U Georgia

Andy Paterson

• to be generated
• Badger Inbred 16 18,000 (3x)

BAC libraries

B. rapa

UK

PBL/JIC

Ian Bancroft

• B. rapa ‘JBr’ - MTA
• Being contiged as part of UK physical map programme

B. rapa

S. Korea

Taejon

Yong Pyo Lim

• From ‘Chifu’ type

B. napus

UK

JIC

Ian Bancroft

• B. napus Tapidor large insert "JBnB"
• Partially contiged as part of EC – China collaboration
• B. napus Tapidor binary library "JBnY"
• Tapidor is a parent in "TN" population

B. napus

Canada

AAFC

Isobel Parkin

• publicly available
• From DH parent of DH mapping population

B. napus

China

• 80,000 clones 70kb inserts
• not public until about 2003

BAC filter hybridisation

USA

U Georgia

Andy Paterson

• overgo probe sets being used for filter hybridisation

ESTs

B. napus

France

INRA (Genoplante)

Michel Rennard

• (+ GSTs)
• from Geniplante consortium
• target of 30,000
• will be available at least one year after obtained. Thus these will not be available until after April/May 2003.
• (Arabidopsis ESTs were available 6 months after made)

B. napus

Canada

AAFC +

Andy Sharpe

(Isobel Parkin)

• website being set up which is searchable and will allow distribution on request subject to MTA
• Likely to be available in public domain in about 1 year (April 2003?)

B. napus

Germany

GABI

Friedt

• cDNAs but industrial consortium, not in public domain

BAC end sequences

B. rapa

S. Korea

Yong Pyo Lim

• From ‘Chifu’ library - BAC end sequences and cDNAs (to be put on arrays)

Genomic sequences

B. oleracea

USA

TIGR

Chris Town

• 300,000 in Genbank
• aiming for ...

Provisional list of Brassica genetic stocks available for deposit in Ohio Arabidopsis Stock Center (ARBC) c/o Randy Scholl, subject to further discussion and agreement with ABRC

Rapid cycling base populations

USA

Williams

Rapid cycling stocks (CrGC)

• One population for each of seven species
• must be maintained by cross pollination

Mutant stocks

USA

Williams

CrGC RCB mutants

• 50 mutant or cytoplasm stocks, mostly B. rapa (Williams)

USA

Tom Osborn/

Rick Amasino

EMS mutants

• 50-200 B. oleracea EMS mutants, all SC (Osborn, Amasino)

Mapping populations

B. oleracea

UK

Graham King

"AG"

• A12DHd x GDDH33
• 120 DH lines, SC or semi-SI, (alboglabora x broc.)
• mapped DH lines available

UK

Mike Kearsey

"AG" substitution lines

• A12DHd x GDDH33
• mapped substitution lines available

UK

Graham King

• parent lines of other mapping populations

B. oleracea

USA

Tom Osborn

"TB" population

• 200 DH lines, SC, RC
• T01000 DH self-compatible rapid cycling x broccoli

B. rapa

S. Korea

Yong Pyo Lim

"CK" population

• 86 DH lines, SI (Chifu x ‘Kenshin’) (Lim)
• SI but being bulked - appears weak SI and able to be pollinated by flies
• 250 RI lines (i6-i7) to be released when ready
• Being anchored with public domain SSRs at HRI

B. rapa

USA

Osborn

"IR" population

• 200 RI lines, SC
• (RC x Sarson R500)

Mapping populations

(cont.)

B. rapa

• Parents of other pops

B. napus

USA

Osborn

"MS" pop.

• 100 DH lines
• SC
• ‘Major’ x ‘Stellar’
• (winter x spring)

B. napus

Canada

Lydiate

"SG" pop

• 300 DH lines
• (spring x resyn.)

B. napus

France

Rennard

"DY" pop

• 120 DH
• winter x spring

B. napus

China

Meng

"TN" pop

• 200 DH lines
• (winter x semi winter)
• oilseed double low x high

B. napus

• Parents of other pops