Pig Genome Coordinator's Annual Update
BRIEF SUMMARY OF THE PIG GENOME COORDINATION PROGRAM FOR 2001
January 2002
Max F. Rothschild
USDA/CSREES Pig Genome Coordinator
Coordination Structure
A number of faculty members and support staff are participating in the national pig genome coordination effort as part of Iowa State University's contribution to the project. Dr. Y. Zhang has been active in the database effort as assistant to the Coordinator.
Map Development Update
New anonymous markers and genes continue to be placed on the linkage maps but at a slower pace. There are a number of maps that have been published and some integration has taken place as QTL maps are expanded. However, no new large-scale maps have been published recently. In total there are over 653 genes and 1,480 markers in the database. There is a developing AFLP map with about 2,000 AFLPs that is likely to be added to the PiGMaP linkage map some time in the future. The physical map is also growing quickly and there are now nearly 1,500 genes and anonymous markers thanks to a very useful somatic cell hybrid panel and a radiation hybrid panel (RHP) from France. The RHP is available now and being shared.
QTLs and Candidate Genes
QTL have been reported on nearly all chromosomes for growth, carcass and meat quality traits and several chromosomes for reproduction. Some extensive QTL papers have just been published including new ones for meat quality. Candidate gene analyses have proved successful with gene tests for stress susceptibility, fat, feed intake, growth, meat quality, litter size and coat color.
Database Activities
Database Activities: This year 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 960 citations in the database on about 2,133 loci, over 584 clone entries and 95 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 34,000 users making 900,000 hits. In addition, a new EST database (http://pigest.genome.iastate.edu/data.html) has been developed should be a useful resource. It is now in use and contains over 98,000 pig EST entries and further development will continue.
Shared Materials
Primers for three types of microsatellite typing systems have been provided. A total of 559 fluorescent primer pairs (184 new primers from three sets this year) covering the entire porcine genome, have now been produced for fluorescent typing and have been shared in over 40 labs world wide. Some question of sharing these primers and possible patent infringement has been resolved this year. Funding for primers for 120 microsatellites have also been made for another typing system. For gene expression, 30 dd-PCR primers have been made. The U.S. reference family DNA is available from Iowa State University and USDA-MARC. PiGMaP family DNA can be shared also. Shared use of YAC and BAC libraries is continuing. We continue to help other labs wishing to get these needed resources and to develop new ones. We are working to develop new EST resources for the gene mapping community.
International Efforts
Communication with all international groups and individuals is excellent.
Communication
The Pig Genome Update has now published 52 issues bimonthly and has been distributed by mail to over 110 people and electronically to nearly 860 people worldwide. Angenmap, the gene mapping discussion group continues to grow in activity and members. The current list of subscribers has over 860 users in 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
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