P i g G e n o m e C o o r d i n a t o r 's U p d a t e
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U.S. Pig Genome Coordination Program Annual Work Review for 2000
************ January 18, 2001 ***********
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* Max F. Rothschild *
USDA/CSREES National Pig Genome Coordinator
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* 1. Coordination Structure *
* 2. Map Development Update *
* 3. QTLs and Candidate Genes *
* 4. Database Activities *
* 5. Web Page Activities *
* 6. Shared Materials *
* 7. International Efforts *
* 8. Communication *
* 9. Travel and Meeting Support *
* 10. Future Activities *
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NRSP-8 NATIONAL ANIMAL GENOME RESEARCH PROGRAM
BRIEF SUMMARY OF PIG GENOME COORINATION ACCOMPLISHMENTS FOR 2000
1. Coordination Structure
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 include Drs. Max Rothschild, Phil Spike, Chris Tuggle and
Jack Dekkers. Dr. Yuandan Zhang has joined the database effort as the
assistant to the Coordinator in March of this year.
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2. Map Development Update
New anonymous markers and genes continue to be placed on the linkage maps
but at a slower pace. In addition to these individual genes and marker
reports being published, the PiGMaP second linkage map will be submitted
for publication sometime soon according to A. Archibald. This map will
contain over 500 anonymous markers and 230 genes. The total number of loci
on the three linkage maps is now about 2,000 genes and markers. There is a
developing AFLP map with about 2,000 AFLPs that is likely to be added to
the PiGMaP linkage map. The physical map is also growing quickly and there
are now nearly 1,300 genes and anonymous markers in large part due to a
very useful somatic cell hybrid panel and a radiation hybrid panel (RHP)
from France. The RHP is available now and being shared.
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3. QTLs and Candidate Genes
QTL have been reported on most chromosomes for growth, carcass and meat
quality traits and several chromosomes for reproduction. Some extensive
QTL papers have just been published or are in the submittal stage.
Candidate gene analyses have proved successful with gene tests for stress
susceptibility, fat level, meat quality, litter size and most coat colors
in the pig. Commercial DNA tests and their use in the industry have
increased greatly.
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4. Database Activities
Once again this year the Pig Genome Database has undergone considerable
updating and a great deal of new information on the maps and mapping tools
has been added. There are over 900 citations in the database on about
2,000 loci, over 425 clone entries and 90 library entries. Access to the
database can be made at http://www.genome.iastate.edu through the US Pig
Genome Coordination home page. This last year the US Pig Genome database
had 4,000 monthly users making 80,000 hits monthly and a total of over
650,000 hits in 1999. This database activity is supported primarily
through the efforts of Alan Archibald and his colleagues at Roslin.
Yuandan Zhang and Zhiliang Hu are assisting from the U.S. side. Alan
Archibald and Max Rothschild serve as co-editors of the pig genome
database called PIGBase.
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5. Web Page Activities
The web page for the pig genome activities continues to be updated and
revised. This can be found at: http://www.genome.iastate.edu.
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6. Shared Materials
Primers for three types of microsatellite typing systems have been
provided. Kits including 464 fluorescent primer pairs (91 primers sets
this year) covering the entire porcine genome, have now been produced for
fluorescent typing and have been shared in over 40 labs world wide. Some
question of sharing these primers and possible patent infringement has
held up additional production of kits this year. Primer pairs for a total
of 294 microsatellite markers for non-fluorescent genotyping systems have
been produced and shared with over 40 labs worldwide. Funding for primers
for 120 microsatellites have also been made for another new typing system.
For gene expression, 33 differential display PCR primers have been made
and continue to be widely distributed. U.S. reference family DNA is
available from Iowa State University and USDA-MARC. PiGMaP family DNA can
be shared also. Shared use of YAC and BAC libraries is continuing. We
continue to help other labs wishing to get these needed resources and to
develop new ones. We are working to develop new EST resources for the gene
mapping community. Funds are also provided to help in the sharing of the
RH panel.
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7. International Efforts
Communication with all international groups and individuals continues to
be excellent. As coordinator I have traveled and met with several groups
during the year and worked on helping projects begin in several countries.
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8. Communication
The Pig Genome Update has now published 46 issues bimonthly and has been
distributed by mail to over 100 people and electronically to nearly 800
people worldwide. Angenmap, the gene mapping discussion group continues to
grow in activity and members. The current list of subscribers has over 750
users in 41 countries. The address is angenmap@db.genome.iastate.edu.
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9. Travel and Meeting Support
Several conferences have received some funding from the coordinator
including the upcoming ISAG. Travel of several scientists was partially
funded to attend important pig gene mapping meetings in the US.
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10. Future Activities
Constructive suggestions from researchers to help this coordination and
facilitation program grow and succeed are appreciated.
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 Caird Rexroad II, ARS
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U.S. PIG GENOME COORDINATION PROJECT
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| Paid for by funds from the NRSP-8 | Web: http://www.genome.iastate.edu
| USDA/CSREES sponsored Pig Genome |
| Coordination Program | Mail: angenmap@db.genome.iastate.edu
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