Pig Genome Coordinator's Annual Update
BRIEF SUMMARY OF THE PIG GENOME COORDINATION PROGRAM FOR 2003
January 2004
Max F. Rothschild
USDA/CSREES Pig Genome Coordinator
Coordination Structure
Iowa State University faculty and staff help support the national pig genome coordination effort as part of Iowa State University's contribution. Dr. Zhiliang Hu continued his outstanding efforts as assistant to the Coordinator.
Map Development Update:
New gene markers continue to be identified and mapped and some integration of the maps continues to have taken place as QTL maps are expanded. However, no new large-scale maps have been published recently. In total there are over 1,381 genes and 2,262 markers in the database. The physical map is also growing quickly and there are now nearly 1,315 genes and anonymous markers thanks to a very useful somatic cell hybrid panel and two radiation hybrid panels from France.
QTLs and Candidate Genes:
QTL have continued to be reported on all chromosomes for many traits. QTL studies continue to find imprinted QTL. Candidate gene analyses have proved successful with several gene tests being used in the industry for many traits including, fat, feed intake, growth, meat quality, litter size and coat color.
Sequencing Efforts:
The Swine Genome Sequencing Consortium (SGSC) met for the first time in Jouy-en-Josas, France on September 23 to 26, 2003. The meeting included individuals from a number of countries including the US, France, Britain, Denmark, China, Korea, and Japan. Representatives from the USDA, the Alliance for Animal Genome Research and several of the authors of the "Pig Genome Sequencing White paper" participated. Each participant provided updates relating to the state of the art of pig genome research and funding possibilities for the pig genome sequencing project. It was estimated that 50 million dollars would be required but we already have some commitments including a 1X coverage, estimated to be worth 6 million dollars, that was donated by the SinoDanish sequencing project. Korea also agreed in principle to make a donation of 2 million dollars. Strong support was also given by the USDA representatives. A draft mission statement was discussed and will be circulated for comment. The Principles of Cooperation were discussed by the group. The principles of the SNP Consortium and the Human Genome Initiative were reviewed. It was the group consensus that all information would be public and that sequence information would be made public following accepted guidelines used in the Human Genome Initiative. Future meetings are planned early in 2004 to continue to make efforts to acquire the necessary funding for pig genome sequencing project.
Database Activities:
As in past years the Pig Genome Database has received considerable updating and a great deal of new information on the maps and mapping tools have been added. There are over 1,180 citations in the database on about 3,643 loci, over 602 clone entries and 96 library entries. Entry to the database can be made at http://www.genome.iastate.edu through the US Pig Genome Coordination home page. This last year the US Pig Genome database had over 113,500 users making 1.8 million hits. In addition, a new EST database (http://pigest.genome.iastate.edu) has been developed and should be a useful resource. It is now in use and contains over 98,988 pig EST entries and further development will continue. Database activities were transferred to the Bioinformatics Coordinator.
Shared Materials:
The last of the microsatellite primers have now been distributed and no new production is planned. We are trying to get unused sets returned. For gene expression, 30 dd-PCR primers have been made and a few are left. Materials needed to produce a 13,000 element oligo array have been produced. Pig Genome Coordinator funds were used to buy the oligos and will be used to partially fund printing of these oligos on to glass slides. Initial printing of about 400 slides for the community will take place. To insure that the arrays are not wasted, individual researchers can request 20 free arrays and later up to 50 additional ones but they will be responsible for the printing costs of the additional ones. Printing costs will be $20 dollars a slide and will be billed directly to the researcher from the University of Minnesota facility where they will be printed. Two steps are required to order the arrays. Please go to the following web site: http://www.genome.iastate.edu/resources/array_request.html and place an order. Please note, to get the information on the gene list you must sign the Qiagen non-disclosure agreement (NDA). This likely requires visiting with your purchasing and or intellectual property office on your campus. Shipping will occur after you specify by email when you want the arrays.
International Efforts:
Communication with all international groups and individuals is excellent.
Communication:
The Pig Genome Update has now published 64 issues bimonthly and has been distributed by mail to over 100 people and electronically to nearly 1,000 people worldwide. Angenmap, the gene mapping discussion group continues to grow in activity and members. The current list of subscribers has over 990 users from over 40 countries. The address is angenmap@db.genome.iastate.edu.
Travel and Meeting Support:
Some conferences have received support funding from the Coordinator. Travel of several scientists was partially funded to attend important pig gene mapping meetings.
Future Activities:
Constructive suggestions from researchers to help this coordination and facilitation program grow and succeed are appreciated.
Max Rothschild U.S. Pig Genome Coordinator 2255 Kildee Hall, Department of Animal Science Iowa State University Ames, Iowa 50011 Phone: 515-294-6202, Fax: 515-294-2401 mfrothsc@iastate.edu
This report is also available in PDF format
© US Pig Genome Coordination Program