Pig Genome Coordinator's Annual Update
PROGRAM FOR 1997

January 18, 1998

Max F. Rothschild

USDA/CSREES National Pig Genome Coordinator

Coordination Structure

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. 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 (15%), 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 assists with industry matters. Dr. Lizhen Wang has been assisting in database and mapping activities. On December 1 she left to take another job and has been replaced by Dr. Zhiliang Hu.

Map Development Update

New anonymous markers and genes continue to be placed on the linkage maps at a steady pace. In addition to these individual genes and marker reports being published the PiGMaP second linkage map will be submitted for publication. This map will contain over 400 anonymous markers and 200 genes. The data from the Nordic map has been included and represents the largest number of possible meiosis of all the linkage maps.

The physical map is also growing quickly and there are now over 600 gene and anonymous markers on it thanks to a very useful somatic cell hybrid panel from France. The most recent cytogenetics map has been published (Yerle et al., Mammalian Genome 8:592-607). Considerable progress is also being made using the somatic cell hybrid and the radiation hybrid panels from France.

A chromosome 13 workshop is planned for the ISAG meeting in New Zealand. The workshop committee will be chaired by Chris Tuggle and sponsored in part by the U.S. Pig Genome Coordinator. Organizing Committee members include individuals from pig genome mapping community in the US and abroad.

QTLs and Candidate Genes

Several laboratories world wide are conducting exciting QTL experiments and QTL have been reported on several chromosome including 2, 3, 4, 6, 7 and 13 for growth and carcass traits and chromosome 1 and 8 for reproduction. 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. For more details see the published proceedings.

Candidate gene analysis has proved successful with gene tests for stress susceptibility, meat quality, litter size and some coat colors in the pig. Results of these are also likely to be presented in Australia. Two talks on candidate gene analyses and markers will also be presented at the PAGVI meeting in San Diego in January 1988.

NC-210 has been revised and approved

The revised project entitled "Positional and functional identification of economically important genes in the pig" has been formerly approved and the officers for this year are Archie Clutter and Sara Sunden. The first meeting will be in January 1998.

Database Activities

The Pig Genome Database has received a face lift and a great deal of new information on the maps and mapping tools have been added. There are now over 500 citations in the database on over 1600 loci, 350 clone entries and 82 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. Entry to the database can be made through the U.S. Pig Genome Coordination home page at http://www.genome.iastate.edu. Plans for a new node at Iowa State University are underway.

Shared Materials

Primers for three types of microsatellite typing systems have been provided. With the addition of over 50 pairs of new fluorescent primer pairs, a total of 154 primer pairs has 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 microsatellites 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.

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 also now possible.

International Efforts

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 is being provided by the US Pig Genome Coordinator.

Communication

The Pig Genome Update has now published 30 issues bimonthly and has been distributed by mail to over 100 people and electronically to over 400 people worldwide. Items of interest are always encouraged. Please submit them. Angenmap, the gene mapping discussion group (angenmap@iastate.edu), continues to grow in activity and members with over 400 users.

US pig gene mappers have contributed to many recent international meetings including ones in Holland, Britian, China and Australia. 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 outs tanding abstract.

Future Activities

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. Several ISU faculty are helping in the is endeavor. Constructive suggestions from researchers to help this coordination and facilitation program grow and succeed are appreciated.

© US Pig Genome Coordination Program