Pig Genome Coordinator's Annual Update

NRSP-8 NATIONAL ANIMAL GENOME RESEARCH PROGRAM
BRIEF SUMMARY OF PIG GENOME COORINATION ACCOMPLISHMENTS FOR 2000

January 2001

Max F. Rothschild

USDA/CSREES National Pig Genome Coordinator

Coordination Structure

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. Yuandan Zhang has joined the database effort as the assistant to the Coordinator in March of this year.

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 according to A. Archibald. This map will contain over 500 anonymous markers and 230 genes. The total number of loci on the three linkage maps is now about 2,000 genes and markers. There is a developing AFLP map with about 2,000 AFLPs that is likely to be added to the PiGMaP linkage map. The physical map is also growing quickly and there are now nearly 1,300 genes and anonymous markers in large part due 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 most chromosomes for growth, carcass and meat quality traits and several chromosomes for reproduction. Some extensive QTL papers have just been published or are in the submittal stage. Candidate gene analyses have proved successful with gene tests for stress susceptibility, fat level, meat quality, litter size and most coat colors in the pig. Commercial DNA tests and their use in the industry have increased greatly.

Database Activities

Once again this year the Pig Genome Database has undergone considerable updating and a great deal of new information on the maps and mapping tools has been added. There are over 900 citations in the database on about 2,000 loci, over 425 clone entries and 90 library entries. Access 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 4,000 monthly users making 80,000 hits monthly and a total of over 650,000 hits in 1999. This database activity is supported primarily through the efforts of Alan Archibald and his colleagues at Roslin. Yuandan Zhang and Zhiliang Hu are assisting from the U.S. side. 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.

Shared Materials

Primers for three types of microsatellite typing systems have been provided. Kits including 464 fluorescent primer pairs (91 primers 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 held up additional production of kits this year. Primer pairs for a total of 294 microsatellite markers for non-fluorescent genotyping systems have been produced and shared with over 40 labs worldwide. Funding for primers for 120 microsatellites have also been made for another new typing system. For gene expression, 33 differential display PCR primers have been made and continue to be widely distributed. 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. Funds are also provided to help in the sharing of the RH panel.

International Efforts

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.

Communication

The Pig Genome Update has now published 46 issues bimonthly and has been distributed by mail to over 100 people and electronically to nearly 800 people worldwide. Angenmap, the gene mapping discussion group continues to grow in activity and members. The current list of subscribers has over 750 users in 41 countries. The address is angenmap@db.genome.iastate.edu.

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.

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

cc: Dick Frahm, CSREES and Roger Gerrits, ARS

© US Pig Genome Coordination Program