Pig Genome Coordinator's Annual Update
BRIEF SUMMARY OF THE PIG GENOME COORDINATION PROGRAM FOR 2005
Max F. Rothschild
USDA/CSREES Pig Genome CoordinatorJanuary 14, 2006
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 (IMpRH7000 from INRA and the U. of Minnesota; IMNpRH12000 from INRA, U. Nevada-Reno and the U. of Minnesota).
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. Meetings have occurred at PAG and in the UK. The meetings 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. 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. USDA committed a total of 10-12 million and the Sanger Institute has also participated and will commit considerable funding. USDA held a competitive grant program for $10 million and results will be announced in January 2006. Future meetings are planned in 2006 to continue efforts associated with pig genome sequencing.
Database Activities:
As in past years the Pig Genome Database has received considerable updating. There are over 1,254 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 149,600 users making more than 3 million hits. New QTL continue to be curated into the Pig QTL Database. Up to date there are 1,263 QTLs in the database representing 236 pig traits. In addition, new functions have been added to the PigQTLdb tools to align pig RH map-human comparative maps, and pig BAC physical maps, against pig QTL. 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. Materials needed to produce a 13,000 element oligo array were produced. Pig Genome Coordinator funds were used to buy the oligos and e used to partially fund printing of these oligos on to glass slides. About 2000 slides for the community have been shared with many being free and others costing only $20/slide from the University of Minnesota facility. This year we had a committee work with vendors and Dr. Chris Elsik to design and print new arrays. It is expected that in early 2006 these will be available for printing and distribution.
International Efforts:
Communication with all international groups and individuals is excellent.
Communication:
The bimonthly Pig Genome Update has now published 75 issues and has been distributed by mail to over 110 people and electronically to nearly 1,250 people worldwide.
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