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 1999
************ January 18, 2000 ***********
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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. Shared Materials *
* 6. International Efforts *
* 7. Communication *
* 8. Travel and Meeting Support *
* 9. Future Activities *
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NRSP-8 NATIONAL ANIMAL GENOME RESEARCH PROGRAM
BRIEF SUMMARY OF PIG GENOME COORINATION ACCOMPLISHMENTS FOR 1999
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. Zhiliang Hu served as assistant to the coordinator
until September 1. That position is now open and a search is being
conducted to fill it.
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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. This map will contain over 500 anonymous
markers and 225 genes. The total of the three linkage maps is now about
1,800 genes and markers. In addition, the biggest development is that of
an AFLP map. About 2,000 AFLPs are being developed and added to the
PiGMaP linkage map. The physical map is also growing quickly and there
are now nearly 1,200 gene and anonymous markers, thanks to a very useful
somatic cell hybrid panel (SCHP) and a radiation hybrid panel (RHP) from
France. The RHP has been tested primarily by the University of Minnesota.
The RHP is available now for distribution.
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3. QTLs and Candidate Genes
QTL have been reported on several chromosomes including 1, 2, 3, 4, 5, 6,
7, 13 and X for growth and carcass traits and chromosomes 1 and 8 for
reproduction. Candidate gene analysis has proved successful with gene
tests for stress susceptibility, fat level, meat quality, litter size and
some coat colors in the pig. The numbers of tests coming to the industry
have increased greatly.
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4. Database Activities
The Pig Genome Database has received considerable updating and a great
deal of new information on the maps and mapping tools have been added.
There are over 783 citations in the database on over 1800 loci, 55 clone
entries and 90 library entries. Entry to the database can be made
through the US Pig Genome Coordination home page at
http://www.genome.iastate.edu.
This activity is supported primarily through the efforts of Alan Archibald
and his colleagues at Roslin. 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. A total of 468 fluorescent primer pairs covering the entire
porcine genome, have now been produced for fluorescent typing and have
been shared in over 30 labs world wide. In addition, primer pairs for a
total of 294 microsatellite markers for non-fluorescent genotyping
systems have been produced and these have been shared with over 40 labs
worldwide. In order to meet all needs, funding for primers for 120
microsatellites have also been made for another new typing system. To
improve our understanding of gene expression, 30 dd-PCR primers have been
made with the help of Daniel Pomp and have been widely distributed.
Additional aliquots are available. US reference family DNA is available
from Iowa State University and USDA-MARC. PiGMaP family DNA has been
exported and can be shared also. Shared use of YAC and BAC libraries and
filters is now possible. We continue to help other labs wishing to get
these needed resources. 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 40 issues bimonthly and has been
distributed by mail to over 100 people and electronically to over 600
people worldwide. We regularly ask for news items. Angenmap, the gene
mapping discussion group continues to grow in activity and members. The
current list of subscribers has over 600 users. More details on the list
activity can be found at
http://www.genome.iastate.edu/community/discuss.html. The address to
post messages 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.
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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