Pig Genome Coordinator's Annual Update
NRSP-8 NATIONAL ANIMAL GENOME RESEARCH PROGRAM BRIEF SUMMARY OF PIG GENOME COORINATION ACCOMPLISHMENTS FOR 1999
January 18, 2000
Max F. Rothschild
USDA/CSREES National Pig Genome Coordinator
A number of individuals are participating in the national pig genome coordination effort as part of Iowa State University's contribution to the project. These include Drs. Max Rothschild, Phil Spike, Chris Tuggle and Jack Dekkers. Dr. Zhiliang Hu served as assistant to the coordinator until September 1. That position is now open and a search is being conducted to fill it.
Map Development Update
New anonymous markers and genes continue to be placed on the linkage maps but at a slower pace. In addition to these individual genes and marker reports being published, the PiGMaP second linkage map will be submitted for publication sometime soon. This map will contain over 500 anonymous markers and 225 genes. The total of the three linkage maps is now about 1,800 genes and markers. In addition, the biggest development is that of an AFLP map. About 2,000 AFLPs are being developed and added to the PiGMaP linkage map. The physical map is also growing quickly and there are now nearly 1,200 gene and anonymous markers, thanks to a very useful somatic cell hybrid panel (SCHP) and a radiation hybrid panel (RHP) from France. The RHP has been tested primarily by the University of Minnesota. The RHP is available now for distribution.
QTLs and Candidate Genes
QTL have been reported on several chromosomes including 1, 2, 3, 4, 5, 6, 7, 13 and X for growth and carcass traits and chromosomes 1 and 8 for reproduction. Candidate gene analysis has proved successful with gene tests for stress susceptibility, fat level, meat quality, litter size and some coat colors in the pig. The numbers of tests coming to the industry have increased greatly.
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 783 citations in the database on over 1800 loci, 55 clone entries and 90 library entries. Entry to the database can be made through the US Pig Genome Coordination home page at http://www.genome.iastate.edu. This activity is supported primarily through the efforts of Alan Archibald and his colleagues at Roslin. Alan Archibald and Max Rothschild serve as co-editors of the pig genome database called PIGBASE.
Web Page Activities
The web page for the pig genome activities continues to be updated and revised. This can be found at: http://www.genome.iastate.edu.
Primers for three types of microsatellite typing systems have been provided. A total of 468 fluorescent primer pairs covering the entire porcine genome, have now been produced for fluorescent typing and have been shared in over 30 labs world wide. In addition, primer pairs for a total of 294 microsatellite markers for non-fluorescent genotyping systems have been produced and these have been shared with over 40 labs worldwide. In order to meet all needs, funding for primers for 120 microsatellites have also been made for another new typing system. To improve our understanding of gene expression, 30 dd-PCR primers have been made with the help of Daniel Pomp and have been widely distributed. Additional aliquots are available. US reference family DNA is available from Iowa State University and USDA-MARC. PiGMaP family DNA has been exported and can be shared also. Shared use of YAC and BAC libraries and filters is now possible. We continue to help other labs wishing to get these needed resources. Funds are also provided to help in the sharing of the RH panel.
Communication with all international groups and individuals continues to be excellent. As coordinator I have traveled and met with several groups during the year and worked on helping projects begin in several countries.
The Pig Genome Update has now published 40 issues bimonthly and has been distributed by mail to over 100 people and electronically to over 600 people worldwide. We regularly ask for news items. Angenmap, the gene mapping discussion group continues to grow in activity and members. The current list of subscribers has over 600 users. More details on the list activity can be found at http://www.genome.iastate.edu/community/discuss. The address to post messages is email@example.com.
Travel and Meeting Support
Several conferences have received some funding from the coordinator including the upcoming ISAG. Travel of several scientists was partially funded to attend important pig gene mapping meetings in the US.
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 firstname.lastname@example.org
cc: Dick Frahm, CSREES and Roger Gerrits, ARS
© US Pig Genome Coordination Program