Pig Genome Update No. 15angenmap@db.genome.iastate.eduNovember 1, 1995 |
NRSP-8 and the swine gene mapping NC-210 committee had their annual meeting October 25-26. The NC-210 pig gene mapping meeting was attended by Drs. Archie Clutter, Oklahoma State University, Dan Pomp, University of Nebraska, Max Rothschild, Chris Tuggle and Lizhen Wang, Iowa State University, Bob Park, Brigham Young University, Federico Zuckermann, University of Illinois, Joan Lunney and David Grimm, USDA-ARS Beltsville, Neal Jorgensen and Dick Frahm, Administrative Advisors and Roger Gerrits, USDA-ARS. Archie Clutter presented research on identifying and mapping several genes associated with feed efficiency, appetite and fatness. Dan Pomp present his research on reproduction genes, development of a resource family for reproduction at the University of Nebraska and work on QTLs in mice. Max Rothschild and Chris Tuggle presented some integrated linkage maps for chromosomes 1 and 14, mapping of candidate genes for reproduction, growth and disease and development of a new resource family for meat quality traits. Bob Park discussed his research with RAPDs to detect QTL for several traits in pigs. Federico Zuckermann discussed his research on genes associated with growth and disease and his efforts to collect immunological data. Joan Lunney and David Grimm presented work on their development of new microsatellites from a chromosome 6 library and work on disease resistance. Roger Gerrits presented information on his efforts towards germplasm preservation.
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Further business included accepting formally the addition of the new projects from the University of Nebraska and Brigham Young University and administrative reports from Dick Frahm and Neal Jorgensen concerning progress with NC-210 and development of a new regional research project. It was agreed that the project rewrite would likely happen at a meeting in Ames in October. The swine geneome coordinator's report discussed mapping results, database developments and sharing of mapping materials. A committee of Dan Pomp, Brian Kirkpatrick and Chris Tuggle were chosen to help select the set of microsatellites to be produced with fluorescent labels. If you have suggestions for specific microsatellites they should be sent to one of these individuals.
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The second day was the joint NRSP-8 meeting. Several speakers discussed funding opportunities from NIH, NSF, BARD, OECD, and the NRI. Nearly all have homepages for grant application information. The scientific program consisted of excellent talks from Dr. Leslie Lyons, NCI who spoke on comparative genome mapping and Dr. Lothar Henninghausen, NIH, who spoke on understanding organogenesis through use of reverse genetics. The final business meeting covered improvements in the databases presented by Gail Juvik and Alan Hillyard and reports of the progess and activities from the other species. We also discussed the development of a possible new NRSP project. Joan Lunney was also thanked for her excellent help as site organizer.
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The PiGMaPII Meeting was held in Cambridge, England on September 46. There were 37 attendees from all the participating European labs, as well as the Australian and US PiGMaP participants. A representative of the MARC group also attended. All labs gave research updates, and several labs gave more than one talk. All attendees were enthusiastic and it was clear that this meeting was extremely productive regarding scientific progress and communication. Several groups reported the placement of many additional markers (primarily microsatellites) on the PiGMaP linkage map. Total number of markers has now doubled to over 500. Also a significant number of minisatellite markers (about 50) and known genes (about 4050) were added to the map. Many PiGMaP members are working on alignment of the two published maps from PiGMaP and USDA MARC and this has been completed for several chromosomes. Progress of the MARC mapping group was briefly summarized, where just over 1000 markers (over 95% microsatellites) have been placed on the MARC families.
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Informative somatic cell hybrid panels were described by two labs (Toulouse, Utrecht). These labs were very interested in sharing DNA from these hybrids with other labs interested in mapping genes. They asked only that data would be sent back to the provider of the DNA to update the information on the hybrids. Chromosome painting of pig chromosomes using human chromosomespecific probes, as well as the painting of human chromosomes using specific pig probes was reported. New mapping of genes using fluorescence in situ hybridization and cosmid and cDNA probes was reported and a new technique of FiberFISH was described. In this work, the chromosomes are treated so that long chromosome fibers are exposed to several probes for finedetail mapping. Resolution of this technique was reported to be in the range of 5200 kilobase pairs. Finemapping of the MHC was also reported, with many new genes physically mapped.
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Several QTL projects were described and plans to type a large numbers of microsatellites on these families were discussed. Automated genotyping using fluorescent primers was generally agreed to be the technology of the future, and some groups have made available lists of microsatellite markers which work well in the ABI 373/377 systems. Multiplexing of some markers has been accomplished. Other resources discussed included a 22.5 hit porcine YAC library produced in France and several groups reported significant progress in sequencing cDNAs in EST projects in small intestine, liver, granulosa cells, and brain. Genetic diversity work is also underway in some labs. (Report kindly provided by Chris Tuggle).
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The European Association of Animal Production (EAAP) met in Prague on September 3-8. Several talks focused on new genes mapped and candidate gene work dealing with ESR, RN- and other swine genes. Next year's meeting will be in Norway and will highlight QTL results.
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A new set of 25 primer pairs has been produced and is available. This brings the total to 294 pairs of primers that have been shipped to gene mappers and QTL researchers in over 26 labs in 10 countries.
Ideas from pig gene mappers are always appreciated. We are now compiling a list of microsatellite primers that could be used in automated genotyping projects. Once a list is complete, we will consider making fluorescent markers for some or all of these primers. Other ideas of services that can be provided as part of the coordination effort are under consideration. Your thoughts on these matters would be appreciated.
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Pig Genome Home Page grows. We continue to update the home page for pig gene mapping. It serves as a gateway for other databases, information on gene mapping, newsletters, meeting updates and much much more. This is your home page so please give us your ideas to include.
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Confused by all databases and how to use them? As a way to help new users a PIGBASE update is included here. PIGBASE developed originally by PiGMaP and USPIGBASE, developed as a part of the USDA/CSRS sponsored effort to coordinate pig genome mapping, have officially merged and PIGBASE has been retained as the name. It is presently administered jointly by Iowa State University, the National Agricultural Library and the Roslin Institute in the UK. This database is available either through telnet or WWW (World Wide Web) and three nodes exist. Enrollment is required to connect through telnet and may be done at no cost by contacting the Pig Genome Coordinator. Entry through WWW requires no previous enrollment. Obtaining information through WWW is very convenient. The URL for the U.S. node of PIGBASE on WWW is http://www.genome.iastate.edu. The database contains genetic maps including all relevant citations and data, a list of all loci typed in the pig genome, human homology information and a list of all references. The WWW access to PIGBASE is through four managers (LOCUS, MAP, REFERENCE and SQL) and two lists (LOCUS LIST and REFERENCE LIST). Of particular note is the ability for dynamic map generation directly from the database and the opportunity for users with unique questions to query the database using the industry standard SQL. The database currently includes about 300 citations, 2067 data lines and nearly 865 mapped loci and is growing to keep pace with the expanding pig genome literature. The database will be modified to incorporate clone/probe information and other new features as they become needed or available. This work has been funded by some funds from the US Pig Genome Coordinator and considerable help from Alan Archibald, Jian Hu and Chris Mungall (BBSRC), Alan Hillyard and funding from UK Medical Research Council (BBSRC and the European Commisison). Enclosed is a brief list of steps to use the database.
Through WWW:
1. Open URL with
http://www.genome.iastate.edu,
2. Click the pig gene mapping activities to go to the next screen,
3. Click pigbase managers to get a menu of the managers (Locus, map,
reference and SQL) and lists (Locus and Reference), and
4. Use these managers and lists to pursue your search.
5. If you want to know the update of the summary report on the
database, click the Statistics.
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Through telnet:
1. Telnet aretha.jax.org,
2. Enter pigbase for both login id and password,
3. Key in your specific user id and password (note they are in lower
case),
4. Use Esc key to get to the command line at the bottom of the
screen,
5. Select the command, enter, to get into the database main menu,
6. Select the letter on the right hand sides of screen to go on, and
7. Follow the selfexplained commands on each screen to continue (note:
whenever needed, use Esc key to get to the command line).
If you have any questions and problems, just let us know.
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We expect several new database developments. We will be developing in conjunction with Alan Hillyard and PiGMaP a new database containing more detailed experimental information. In addition, a new database, named TCAGdb for The Comparative Animal Genome database, is planned that will pull together the data from the single species databases for crossspecies comparisons.
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Upcoming meetings: ISAG Pig Genetics meeting, Ghent, Belguim, November 16-17, 1995, contact mfrothsc@iastate.edu for details
Plant Genome IV, San Diego, CA January 14-18 1996
Midwest ASAS/ADSA meetings March 18-20, 1996, Des Moines, IA
XXV International Conference on Animal Genetics, International Society of Animal Genetics. Vinci Congress Centre, Tours, France, July 22-26, 1996, contact sjlamont@iastate.edu for details.
Allerton II, Genetic Analysis of Economically Important Traits in Livestock, Allerton Park, Illinois, November 1996, contact blood@vmd.cso.uiuc.edu for details
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Contributions to Pig Genome Update 16 including short meeting announcements are always welcome. Please send by the 15th of December.
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
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