Pig Genome Coordinator's Annual Update
PROGRAM FOR 1998
January 18, 1999
Max F. Rothschild
USDA/CSREES National Pig Genome Coordinator
The role of the USDA/CSREES National Pig Genome Coordinator is to help facilitate development of pig genome mapping and the search for important quantitative trait loci (QTL). 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 individuals and their percent of time contributed include Max Rothschild (30%) as national coordinator and he is assisted by his colleagues Drs. Philip Spike (5%), Chris Tuggle (5%) and Lauren Christian (5%). Dr. Phil Spike helps with computing and database development, Dr. Chris Tuggle assists in development of molecular biology tools and Dr. Lauren Christian assisted with industry matters until his recent unfortunate death. Dr. Jack Dekkers and Dr. Rohan Fernando will be assisting with some new programs. Dr. Zhiliang Hu has been assisting in database and mapping activities.
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 450 anonymous markers and 225 genes. The data from the Nordic map has been included and represents the largest number of possible meiosis of all the linkage maps. The total of the three linkage maps is now about 1800 genes and markers. In addition, the biggest development is that of an AFLP map. About 2000 AFLPs are being developed and added to the PiGMaP linkage map.
The physical map is also growing quickly and there are now nearly 700 gene and anonymous markers, thanks to a very useful somatic cell hybrid panel from France. Considerable progress is also being made using a radiation hybrid panels (RHP) from France. This has been used extensively by the University of Minnesota and by other researchers. The number of genes and markers mapped now exceeds 1,000 on this RH map. Access to the RHP is likely to be available very soon.
A chromosome 13 workshop was held at the Int. Soc. Animal Genetics (ISAG) meeting in New Zealand. The workshop committee was chaired by Chris Tuggle and sponsored in part by the U.S. Pig Genome Coordinator. Organizing Committee members included individuals from pig genome mapping community in the US and abroad. The workshop was a real success and a total of 47 genes were placed on the chromosome 13 map.
QTLs and Candidate Genes
Several laboratories world wide are conducting exciting QTL experiments and some QTL have been reported on several chromosome including 1, 2, 3, 4, 6, 7, 13 and X for growth and carcass traits and chromosomes 1, 6 and 8 for reproduction. Some results are now published for disease resistance and immune response parameters. Much of these results were presented at the 6th World Congress on Quantitative Genetics Applied to Livestock, which was held in early January in Armidale, Australia and at the Pig Gene Mapping workshop at ISAG. For more details see the published proceedings from both meetings.
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. Results of these are also likely to be presented in Australia and New Zealand in 1998.
The Pig Genome Database has received considerable updating and a great deal of new information on the maps and mapping tools has been added. There are now over 670 citations in the database on over 1800 loci, 458 clone entries and 88 library entries. The database is coedited by Alan Archibald and Max Rothschild. The group in Edinbugh is to be thanked for their efforts in revising the database. In addition, a new computer at ISU is now acting as the node for both the chicken and the pig databases. This will speed information requests. Entry to the database can be made through the U.S. Pig Genome Coordination home page at http://www.genome.iastate.edu . Dr. Zhiliang Hu is supervising these activities at ISU.
Primers for three types of microsatellite typing systems have been provided. With this year's addition of over 150 pairs of new fluorescent primer pairs, a total of 304 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 90 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. Production of AFLP primers is now under consideration.
U.S. reference family DNA is available from Iowa State University and USDA-MARC. PiGMaP family DNA has been imported and can be shared also.
Shared use of YAC and BAC libraries is now possible. We continue to help other labs wishing to get these needed resources.
Communication with all international groups and individuals continues to be excellent. Several US labs are now participating in the international PiGMaP efforts. Some travel support to meetings including ISAG for US pig gene mappers was provided by the US Pig Genome Coordinator.
The Pig Genome Update has now published 34 issues bimonthly and has been distributed by mail to over 100 people and electronically to over 600 people worldwide. Items of interest to be included in the newsletters are always encouraged. Please submit them.
Angenmap, the gene mapping discussion group continues to grow in activity and members. The current list of subscribers has over 600 users. The old address: firstname.lastname@example.org has been replaced by email@example.com. New functions exist to facilitate rapid communication. All past mail can be searched for specific subjects and retrieved by using the US Pig Genome Coordination web site.
US pig gene mappers have contributed to many recent international meetings including ones in Europe, Asia and New Zealand. Participants, including the coordinator, are acting to develop a US/EU task force to address new issues related to genomics. International cooperation has been encouraged.
Travel and Meeting Support
Several conferences have received some funding from the coordinator. Travel of several scientists was partially funded to attend important pig gene mapping meetings. A travel award - Jorgensen Award was given this year to a graduate student with an outstanding abstract. This support has come under fire from some administrative advisors and will be reviewed and is likely to be reduced.
The role of the USDA/CSREES National Pig Genome Coordinator is to help facilitate development of pig genome mapping and the search for important quantitative trait loci. Advanced development of a node for PiGBASE is continuing. Constructive suggestions from researchers to help this coordination and facilitation program grow and succeed are appreciated.
Max Rothschild U.S. Pig Genome Coordinator 225 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