Pig Genome Coordination Accomplishments
PROGRAM FOR 1995
January 18, 1996
Max F. Rothschild
USDA/CSREES National Pig Genome Coordinator
Coordination StructureThe 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 was hired to assist the coordinator in database and mapping activities.
Coordination Activities and Accomplishments to DateMap Development
The most important long term duty of the pig species coordinator is to help develop and manage the porcine gene map. A great deal of mapping data has been published in the past three years. This includes a physical gene map and several genetic linkage maps. Three large linkage maps have been published. These maps include the USDA-ARS linkage map with over 1100 markers (Genome Research 6:371-391), the Nordic map with 236 markers (Animal Genetics 27:255-269) and the PiGMaP map (Mammalian Genome, 6:157-175) with 280 genes and markers. The last two of these maps are being revised and combined and there are over 700 genes and markers now on them (Archibald personal communication). All combined these genetic linkage maps totaled about 1700 genes and markers. The challenge is to incorporate this information into a useable database and to develop a composite map. Several groups have now produced consensus maps from the PiGMaP, Nordic and USDA maps. All the maps are accessible through our WWW address (see database). The coordinator has been working closely with the PiGMaP and Nordic mappers in producing a consensus maps. Input from interested researchers is welcome.
Coordination of data and the species database are essential responsibilities of the coordinator. Several new developments have taken place since last year. A node was added to the National Agriculture Library. As part of the pig genome coordination efforts supported by the National Animal Genome Research Program, a World Wide Web (WWW) home page was established at Iowa State University to support the Pig Gene Mapping Effort. This year this has been greatly enlarged and improved. The URL, Universal Resource Locator, or "address" for this new information source is: http://www.genome.iastate.edu. Access via WWW allows users to obtain the following pieces of information: Coordinator Update, addresses of pig gene mappers, genome newsletters including Pig Genome Update and the NAPGR newsletter, information on Angenmap, meeting schedules, available microsatellite markers, PiGBASE access, USDA/ARS gene mapping information, international pig gene mapping information and graphics. More can be added. The database PiGBASE continues to grow in both size and use by the mapping community as the editors (A. Archibald and M. Rothschild) continue to enter new papers and review existing papers for accuracy and adherence to nomenclature guidelines for the pig.
Over the past year a great deal of effort has been made to greatly revise the database. The database design is constructed around the organizing concept of a locus and its position. Supporting evidence, both the mapping experiments themselves or the analyses performed to position the locus in the genome are fully documented and arranged in a modular fashion. This design concept will allow the rapid addition of new types of both mapping protocols and analysis to the database without a massive redesign.
Some of the mapping methods already incorporated in the design are FISH, SSCP, RAPD, SINE-PCR, PCR-RFLP, DSCP and microsatellites. Not only is the database being designed to provide the user with a complete suite of textual information, but supporting images (sequence gels, FISH, etc.) will be included as available. A rich array of supporting links to other databases, ranging from sequence databases to information about breeds will also be available. This revison is nearly complete and the new version will be eventually loaded to the National Agriculture Library. There are now over 350 citations with over 1000 genes and markers listed. The list of human homologs is also growing. With the new nodes and greater use, we have helped to make access to the database easier to use.
With the new database structure in place, new graphical tools to manipulate and examine the data are being developed as well. These range from more efficient and new map displays to more flexible query generating tools. Lastly, electronic data submission will be strongly encouraged through the use of an online form. PiGBASE will continue to offer the most flexible and powerful database environment for its users. Also a new database, named TCAGdb for The Comparative Animal Genome database, that will pull together the data from the single species databases for cross-species comparisons is nearly complete. All this work has been supported in small part by the Pig Genome Coordinator funds with the majority of effort coming from A. Archibald, Alan Hillyard, Jian Hu and Chris Mungall (BBSRC) and with funding from the UK Medical Research Council (BBSRC and the European Commission). Finally, we hope everyone in the mapping community can be involved in the evolution of the database as it develops as a central tool for genome mapping in the pig.
Several meetings involving scientists from around the world have been attended by myself or colleagues. These included PiGMaP meetings, NC-210 meetings and ISAG meetings. These meetings had representatives from all the PiGMaP labs, the Nordic labs, Australia and Japan. At these meetings information on the pig gene mapping coordination effort in the U.S. and also the various research at all labs in the U.S. has been presented. As part of the efforts to coordinate gene mapping worldwide I have imported
DNA from their reference families from Scotland, Sweden, France and the Netherlands (see section on sharing of materials). The cooperation from PiGMaP labs and map coordinators is excellent.
An important aspect of the coordinator's efforts have been to improve direct communication between members of the pig gene mapping community. We have accomplished this in several ways. This includes the following:
- Pig Genome Update is published bimonthly and distributed electronically to over 350 people
- Angenmap, the gene mapping discussion group (email@example.com), continues to grow in activity and members.•
- Several talks were given and meetings attended to discuss further coordination and cooperation.
- Several conferences have received some funding to help in support of the conference. This has included two large conferences on gene mapping and quantitative trait loci, an international genetics conference and other worthwhile meetings.
- Travel of several scientists was partially funded to attend important pig gene mapping meetings.
Coordination of shared materials and information is essential to collaborative efforts. We have made a major effort to produce probes and obtain DNA for sharing. This includes:
- A total of 294 microsatellites markers have been produced and are available for any lab doing gene mapping research (these were partially funded by NPPC and several swine breeding companies). These have been shared with over 40 labs worldwide.
- Also a total of 96 fluorescent pairs of primers have been produced.. To date more than 35 labs worldwide have requested materials. These have been shared with over 20 labs worldwide.
- New markers for different typing technology have been initiated. U.S. reference family DNA is available through each of the individual U.S. laboratories.
- PiGMaP family DNA has been imported from Edinburgh, Sweden, France, German and the Netherlands. This all can be shared once individual labs fill out a transport permit to move the DNA to their labs. This permit will be submitted by the coordinator to APHIS. Rules on sharing of materials and joint publication will need to be agreed upon if collaborative efforts are to be successful.
Individual labs will of course set their own priorities but joint efforts in pig gene mapping may help to raise additional research funds. Some open discussion is needed on ways to continue to involve industry. There has been a special effort to visit with individuals from swine breeding companies, the swine industry and other universities not already involved in the pig gene mapping efforts. In addition, several people from labs not previously represented were added to the NRSP-8 species committee. We need to have an open and useful dialog especially as it relates to activities such as looking for quantitative trait loci for production, reproduction and health traits.
A great deal can be accomplished if the pig gene mappers work together. Constructive suggestions from researchers to help this coordination program grow and succeed are appreciated.
© US Pig Genome Coordination Program