Pig Genome Coordinator's Annual Update
BRIEF SUMMARY OF THE PIG GENOME COORDINATION PROGRAM FOR 2004
Max F. Rothschild
USDA/CSREES Pig Genome CoordinatorJanuary 15, 2005
Coordination Structure
Iowa State University faculty and staff help support the national pig genome coordination effort as part of Iowa State University’s contribution. 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 1,588 genes and 2,493 markers in the database. The physical map is also growing quickly and there are now nearly 6,000 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) continued its efforts this past year and considerable advances have been made. Several meeting have occurred at PAG, ISAG and in the UK. 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. It was estimated that now 30-35 million dollars would be required to produce a 6X coverage. Funds have been committed by the National Pork Board, Iowa Pork producers Association, University of Illinois and Iowa State University, with other groups likely to follow. A total of 12-15 million is needed from USDA and Sanger Institute may commit a match of nearly 15 million dollars. Future meetings are planned for early in 2005 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 1,236 citations in the database on about 4081 loci, over 602 clone entries and 96 library entries. This last year the US Pig Genome database had over 141,500 users making 2.3 million hits. In addition, a new QTL database is being developed and should be a useful resource. It can be seen at http://www.animalgenome.org/QTLdb/ . 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 1,400 slides for the community have been shared with many being free and others costing only $20/slide from the University of Minnesota facility. Two steps are required to order additional 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). Shipping will occur after you specify by email when you want the arrays. This year we plan to design and print new arrays if there is interest.
International Efforts:
Communication with all international groups and individuals is excellent.
Communication:
The Pig Genome Update has now published 70 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 and has 1,000 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
© US Pig Genome Coordination Program