Brassica : Harvesting the Genome, Diversity and Products
Setting Priorities: MBGP goals and objectives
Prioritisation of objectives
History of meetings of the MBGP
Jan 2002 Initial discussion at PAGX
Mar 2002 Discussion and tabulated list of MBGP resources from Crucifer Genetics Workshop
Jan 2003 1st Steering Group Meeting, San Diego
Jan 2004 2nd Steering Group Meeting, San Diego
Oct 2004 3rd Steering Group Meeting, Daejon, S. Korea
Jan 2005 4th Steering Group Meeting, San Diego
Navigating between trait and genome
Integration of genetic and physical maps
Determining the genome sequence
B. rapa Genome sequence A Concept note for the Brassica genome sequencing project was prepared 11th June, 2003 by Ian Bancroft (firstname.lastname@example.org) and Yong Pyo Lim (email@example.com) on behalf of the Steering Group for the Multinational Brassica Genome Project.
Deliverables: The project aims initially to produce, from BAC clones, "Phase 2" sequence (i.e. fully oriented and ordered sequence but some small sequence gaps and low quality sequences) for the ca. 500 Mb genome of Brassica rapa subspecies pekinensis. The genome sequence is to be anchored to a reference genetic map by ca. 1000 molecular markers. Note that sequencing to Phase 2 halves the cost of the systematic project compared to the production of fully finished sequence. Scientists requiring finished sequence from a specific region can finish it themselves, accessing trace files that will be archived in an agreed format at TIGR, MIPS and NIAB (National Institute of Agricultural Biotechnology, Suweon, S. Korea). The systematic annotation of the genome sequence, although not to fully finished standard, will be feasible due to the availability of the annotated genome sequence of the related species Arabidopsis thaliana.
Work plan: An international consortium, working to agreed standards and using common resources, will conduct the sequencing of the Brassica genome. TIGR, MIPS and NIAB will conduct integration, annotation and public serving of the data. The work plan comprises three partially overlapping stages:
Stage 1: Preliminary work
Establish a general Brassica information site (http://www.brassica.info/) and gateway site for the Multinational Brassica Genome Project (http://brassica.bbsrc.ac.uk/ & http://www.niab.go.kr). Establish communal databases for genetic mapping data (http://ukcrop.net/perl/ace/search/BrassicaDB and http://www.niab.go.kr) and physical mapping data (http://brassica.bbsrc.ac.uk/IGF/index.htm and ).
Define reference BAC libraries for genome sequencing: B. rapa pekinensis (Chinese cabbage) variety Chiifu-401 libraries KBrH and KBrB. Each library consists of 144 x 384-well plates, made using HindIII (KBrH) or BamHI (KBrB) digested genomic DNA. A total of 110,592 clones, providing 20-fold redundant representation of the genome are available. The libraries were constructed at Chungnam National University (CNU), Daejeon, S. Korea.
Establish international distribution centres for KBrH and KBrB BAC libraries: at NIAB (for eastern hemisphere) and JIC (John Innes Centre, U.K.) (for western hemisphere).
Define communal reference populations for genetic mapping in Chiifu: CKDH and CKRI. CKDH consists of 86 DH lines available now; use for low-resolution mapping. CKRI will consist of at least 200 RI lines when complete (2004); use for high-resolution mapping. Construct high quality genetic maps for each population using communal markers and make publicly available. Includes input from CNU, AAFC Agriculture and Agri-Food Canada), WHRI (Warwick HRI, U.K.).
Draft White Paper for Multinational Brassica Genome Project (MBGP); 12/01/2006