Pig Genome Coordination Accomplishments
PROGRAM FOR 1993
January 18, 1994
Max F. Rothschild
USDA/CSREES National Pig Genome Coordinator
Map DevelopmentThe 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 year. This includes a physical gene map and genetic linkage maps. Three linkage maps have been published or are in press at the time of this report. These maps include the USDA-ARS linkage map with about 380 markers (Genetics 136:231-245), the Nordic map with 128 genes and markers (Genetics 137:1089- 1100) and the PiGMaP map (Mammalian Genome, in press) with 240 genes and markers. All combined these genetic linkage maps should have about 650-700 genes and markers. In addition approximately 130 genes and gene markers have been physically mapped to chromosomes. The challenge is to incorporate this information into a useable database and to develop a consensus map. The USDA-ARS map has been accessible through our WWW address (see database) and both the USDA and PiGMaP linkage maps will be accessible through PIGBASE by the time of this meeting or shortly after the meeting. The Nordic map will be added to the database this year. Efforts to combine existing maps are underway. The coordinator has been working closely with the PiGMaP and Nordic mappers to help in producing a consensus map for all chromosomes. Input from interested researchers is welcome.
Database ActivitiesCoordination of the pig genome database is an essential responsibility of the coordinator. Last year at this time we presented information on a database for pig gene mapping that had been developed here in the U.S. in collaboration with the European PiGMaP project. The database has been constructed at the Jackson Laboratory. It is called PIGBASE. Several new developments have taken place since last year.
As part of the pig genome coordination efforts supported by the National Animal Genome Research Program, a World Wide Web (WWW) server has been established at Iowa State University to support the Pig Gene Mapping Effort. The WWW server makes hypertext files including graphic images available for easy access by anyone with internet access. You can get information or browse through the various resources with a simple point and click interface with the mouse on your computer. The URL, Universal Resource Locator, or "address" for this new information source is: http://www.genome.iastate.edu. Not only will this address provide a convenient gateway to PIGBASE, it will also allow the presentation of graphics and documents germane to pig gene mapping, e-mail addresses of colleagues, upcoming meeting announcements, and pointers to other genome related databases. The WWW is comparable to both WAIS and Gopher, in that it is a client server information system running over the internet. The WWW system has an open addressing scheme allowing links to be made to any objects on WWW, WAIS, Gopher, FTP, NFS, or Network News servers.
Access via WWW will allow 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, comparative MHC map, international pig gene mapping information and finally a whole set of interesting graphics. More will be added.
The database PIGBASE continues to grow in both size and use by the mapping community as the editors continue to enter new papers and review existing papers for accuracy and adherence to nomenclature guidelines for the pig. The past year has seen not only the establishment of the database but also its alliance with its European counterpart and the establishment of a node in New Zealand for workers in the Australpacific region. The announcement of the availability of the database in Human Genome News has led to increased visibility among the human mapping community as well. With the new nodes and greater use, we have continually strived to make access to the database and its use easier and this has led to the establishment of a World Wide Web (WWW) home page for the NAGRP with links to both to the available database nodes as well as to other items of interest to the pig mapping community.
The prospect of future development is also exciting; the next release of the pig database will feature WWW forms access and hyperlinked text and graphics. This will form the core of new database development, will provide identical access regardless of the hardware platform chosen, and will provide a point and click environment for those using a windowing environment. The choice of WWW will also make linking information to other resources such as Entrez, GDB (the human database), and sequence analysis tools such as FASTA and BLAST possible without leaving the WWW environment. Hyperlinked text and graphics will make it possible to explore a particular gene or region of the genome providing a global view of the information or an extremely detailed view as needed. The database itself is also undergoing successive transformations as it will strive to bring more complete mapping data including such details as PCR primers and conditions. The parallel development of the databases for the other target species will facilitate the exchange of mapping information. Lastly, we hope to make an annotation facility available so that 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.
This past year I have attended the PiGMaP meetings in Europe and the ISAG meeting in Prague. These meetings had representatives from all the PiGMaP labs, the Nordic labs, Australia and Japan. I also travelled to St. Petersburg, Russia. At these meetings I have presented information on the pig gene mapping coordination effort in the U.S. and also the various research at all labs in the U.S. 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 between the coordinators from PiGMaP and the U.S. 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:
- Pig Genome News is published bimonthly and mailed to 150 people and distributed electronically to over 500 people.
- Angenmap, the gene mapping discussion group (firstname.lastname@example.org ), continues to grow in activity and members.
- Human Genome News printed an update on U.S. pig gene mapping efforts.
- The NPPC LEADER LETTER published an update on U.S. pig gene mapping efforts.
- The USDA-CSRS Experiment Station newsletter published an update on the database activities.
- Several talks were given, including at the National Swine Improvement Federation meeting, National Canadian Workshop on Genome Mapping, the Future Genetics Conference, the ISAG Pig Gene Mapping workshop and many other locations to discuss U.S. gene mapping.
- Several conferences have received some funding to help in support of the conference. This has included a symposium sponsored by the American Society of Animal Science, the Future Genetics Conference and some travel support for individuals for the Chromosome 6 symposium.
Shared MaterialsCoordination 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 170 microsatellites markers have been produced and are available for any lab doing gene mapping research. To date more than 10 labs world wide have requested materials. Additional ones will be selected by a committee of J. Lunney, D. Troyer, B. Kirkpatrick, C. Tuggle and the coordinator.
- U.S. reference family is available through each of the individual U.S. laboratories.
- PiGMaP family DNA has been imported from Edinburgh, Sweden, France 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 for a successful collaboration.
Research PrioritiesIndividual labs will of course set their own priorities but joint efforts in pig gene mapping may help to raise additional research funds. I have made 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. Some open discussion is needed on new ideas and ways to continue to involve the industry.
Future ActivitiesA great deal can be accomplished if the pig gene mappers work together. A lack of professionalism and cooperation is counter productive. Constructive suggestions from researchers to help this coordination program grow and succeed are appreciated.
© US Pig Genome Coordination Program