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Pig Genome Newsletter #015
Pig Genome Update No. 15
November 1, 1995
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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.
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.
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.
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.
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.
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).
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.
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.
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.
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.public.iastate.edu/~pigmap. 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.public.iastate.edu/~pigmap,
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.
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.
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.
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
Contributions to Pig Genome Update 16 including short meeting announcements are
always welcome. Please send by the 15th of December.
Max F. 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
Paid for by funds from the NRSP-8 USDA/CSREES sponsored pig genome coordination
program
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