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Pig Genome Newsletter #036
P I G G E N O M E U P D A T E
__________________________________________________________________
A Bimonthly Newsletter of the U.S. Pig Genome Coordination Program
************* No. 36 **************
* *
* <angenmap@db.genome.iastate.edu> *
* May 1, 1999 *
*************************************
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1. Set VIII Primers Are on Their Way
2. Pig AFLP Primers
3. The RH Panel for Swine Will Soon Be Available
4. More New Tools -- A RPCI-44 Male Porcine BAC Library
5. The Excellent Biannual Pig Breeders Roundtable met in Wye, England
6. Planning for the Future was the Purpose of FAIR
7. Plans Already Underway for PAG-VIII.
8. "Animal Gene Mapping Community Directory" Database
9. Time to Regiser for From Jay Lush to Genomics Conference
10. Upcoming Meetings (16 Items)
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Primers, primers, primers are on their way: A new set of 73 pairs of
fluorescent primers (Set VIII; April 1999) are being made and will be
available for distribution on about May 15. This brings the total number
of fluorescent primer pairs distributed by the U.S. Pig Genome Coordinator
to 377 pairs. Check our updated information on these primers at:
http://www.genome.iastate.edu/resources/fprimerintr.html or you may browse
down from our main page: http://www.genome.iastate.edu to "US Pig Gene
Mapping Coordination Program Shared Resources" section) and then to
"Fluorescent Primers". To order Set VIII fluorescent primers, please send
your request, along with your detailed postal address and your daytime
phone number (required), to mfrothsc@iastate.edu. Please continue to make
use of them and also be sure to acknowledge their source as it helps to
improve cooperation and coordination activities.
o o o o o o o o o o o
Pig AFLP primers: AFLP is a patented genome mapping technique that has
particular value for rapid assembly of a full genome map in species for
which microsatellites are not available (or are sparse) and is also of use
to find markers related to certain traits. Unfortunately, existing
commercial kits (fluorescent primers available through PE AgGen and
primers for radioactive labeling through Life Technologies, Inc.) are
designed generally for plant genomes and may not work as well with pig DNA
(or most mammalian DNA). A further problem arises because Keygene n.v.
(which holds the AFLP patent) has negotiated an exclusive agreement with
these two distributors such that buying the plant kit is the only way one
can officially be licensed to use AFLP. Extensive discussions have made
it clear that PE AgGen has no large interest in marketing a kit for animal
AFLP, and Keygene cannot do so without violating their previous agreement.
Dian Pouwels of Keygene has now indicated that those animal scientists
wishing to use AFLP should purchase the Perkin Elmer kit
(http://www2.perkin-elmer.com/ag/775601/775601.html) and then should
contact Keygene (keygene@euronet.nl) which will provide you the additional
primers needed for animal AFLP mapping for a nominal fee ($100 US). The
PE kit provides you reagents, enzyme and EcoRI primers and adapters, and
Keygene will provide the complementary TaqI primers and adapters needed
for animal genomes. You will also get MseI primers and adapters in the PE
kit which are useless to you. Alternatively, Keygene will do the whole
AFLP analysis for you on a contract basis through their Molecular Marker
Service (email to keygene@euronet.nl). Because of Keygene's concerns
about protecting their license and because some kit reagents may not be
easily stored and re-shipped by the Coordinators, we regret that we will
not be able to provide these AFLP kits directly to you as we had
previously hoped. Please also realize that the above arrangement limits
you to 64 possible primer combinations in the kits (8 EcoRI primers and 8
TaqI). While this is more than enough to test the AFLP technique out and
generate a low resolution map, one still cannot utilize the full range of
available AFLP markers (over 4,000 possible primer combinations, often
2-20 markers per primer combination) without making your own primers or
sharing with friends (kindly provided by Jerry Dodgson).
o o o o o o o o o o o
The RH panel for swine will soon be available. Developed at INRA in
Toulouse and tested extensively by the University of Minnesota the panel
is now ready for distribution. To obtain aliquots, please contact Larry
Schook at schoo009@maroon.tc.umn.edu. Considerable funding will be
provided by the US Pig Genome Coordinator to help support this
distribution activity. Another RH panel is also now available through
Research Genetics at: http://www.resgen.com .
o o o o o o o o o o o
More new tools! A RPCI-44 Male Porcine BAC Library has been constructed
by the BACPAC Resource Center in the Department of Cancer Genetics at
Roswell Park Cancer Institute in Buffalo, New York, USA. Library
construction was supported by a contract from the United States Department
of Agriculture, Agricultural Research Service, U.S. Meat Animal Research
Center, Clay Center, NE. Blood from four male pigs (breed: 37.5%
Yorkshire, 37.5% Landrace, and 25% Meishan) was pooled and genomic DNA was
isolated from the white blood cells. The DNA (partially EcoRI digested)
was size selected and cloned into the EcoRI sites of the pTARBAC2 vector.
The average insert size is 165 kb and there is 10X coverage. The library
has been arrayed into 384-well microtiter dishes and also gridded onto
22x22cm high-density nylon hybridization filters for screening by probe
hybridization. Each hybridization membrane represents over 18,000
distinct porcine BAC clones, stamped in duplicate. As part of the Pig
Genome Coordination effort, up to $650 will be supplied to US laboratories
interested in obtaining the filter sets. This will pay for approximately
50% of the filters. Prior to taking advantage of this offer, please
contact me at mfrothsc@iastate.edu to confirm availability of funds.
o o o o o o o o o o o
The excellent biannual Pig Breeders Roundtable met in Wye, England in
March. Nearly 120 researchers, students and industry people met to
discuss new developments in the genetics of pigs. Topics included
genetics of performance, reproduction, health and behavior. In terms of
molecular genetics there were talks on Leptin in mice, QTLs and new
candidate genes in pigs for health, growth, backfat and reproduction. As
is traditional, the meeting tries to foster open exchanges among industry
members and challenging discussion. We extend a special thanks to Dr.
John King for organizing and hosting this interesting meeting.
o o o o o o o o o o o
Planning for the future was the purpose of FAIR (Food Animal Integrated
Research) 2002 meeting sponsored by many animal groups. This meeting was
held in mid April in Baltimore and brought 200 people from very diverse
backgrounds to follow up on the previous FAIR 95. The FAIR 95 discussions
had included enhancing responsiveness to consumer and societal concerns,
increasing efficiency and competitiveness, developing integrated food
animal management systems, enhancing environmental quality, improving food
safety and quality and enhancing animal well being. Fair 2002 "Animal
Products for the Next Millenium" followed up on these and had
presentations and discussion sections on the world situation, enhanced
public and animal health and well being, economic and environmental
sustainability, and animal agricultural in society and a global
marketplace. The extremely diverse group of participants included
individuals from farms and ranches, the production and food industries,
animal health, universities, government agencies and animal welfare
groups. Discussions were extremely useful and recommendations have been
put forth. Hopefully this meeting and the information coming from it will
provide some direction to obtain more research funds and to move our
industry along in the future. This will be reported in a document to be
developed in the near future.
o o o o o o o o o o o
Plans already underway for PAG-VIII. Under the leadership of Steve
Heller, planning for PAG-VIII was underway even before we left San Diego.
A draft schedule of the meeting workshops, plenary sessions, and computer
demos is nearly complete (http://www.intl-pag.org/pag/pag8work.html).
Please note that we're starting about a week earlier next year. Plant
genomics and animal genomics sessions will run concurrently after an
initial plenary talk to open the day on both Tuesday and Wednesday. In
addition, next year's meeting will provide more time for dinner in between
the afternoon and evening workshops, and all of Tuesday night will be free
to heed the call of San Diego's (or Tijuana's) evening attractions.
Finally, PAG-VIII will end with the banquet on Wednesday evening and there
will be no Thursday morning sessions. However, for those interested,
PAG-VIII will be followed directly by the first Ag Microbial Genome
meeting. Speakers for morning talks at PAG-VIII are being chosen and
contacted. Thanks to all who have already provided suggestions and
comments (kindly provided by Jerry Dodgson).
o o o o o o o o o o o
We have developed an "Animal Gene Mapping Community Directory" database.
This "Directory" will contain a name list of scientists/ researchers in
the research areas including but not limited to animal gene mapping,
molecular biology, genome analysis and related fields. The "Directory"
will serve the community as a people/ address finder, and as a guide to
the current studies in the community. Please go to
http://www.genome.iastate.edu/community/join.html to add your own
information. The database information is accessible to the ANGENMAP
subscribers only.
o o o o o o o o o o o
It is not too late to register for a special conference: From Jay Lush to
Genomics: Visions for Animal Breeding and Genetics which will be held May
16-18, 1999 at Iowa State University Ames, Iowa. This not-to-be-missed
conference will bring together quantitative and molecular geneticists from
industry, government, and academe to discuss the future of animal breeding
and genetics in light of changes in the fields of molecular genetics and
bioinformatics. The program will feature eleven plenary lectures by
renowned international scientists and a poster session of current research
by participants. The schedule is arranged to encourage participant
interaction and discussion. Information on the program and speakers can be
found at http://www.public.iastate.edu/~ans/graduate/visions.html .
o o o o o o o o o o o
Upcoming meetings:
From Jay Lush to Genomics: Visions for Animal Breeding and Genetics:
May 16-18, 1999 at Iowa State University Ames, IA. Information at:
http://www.public.iastate.edu/~ans/graduate/visions.html.
Genome Sequencing and Biology, May 19-23, 1999, Cold Spring Harbor
Laboratory, Cold Spring Harbor, NY. Contact:
http://www.cshl.org/meetings.
1999 Summer Institute in Statistical Genetics, May 26-June 11, 1999, North
Carolina State U., Raleigh, NC. Contact http://www.stat.ncsu.edu.
Symposium on Genome Diversity and Evolution in conjunction with the Annual
Meeting of the American Genetic Association, June 12-13, 1999, Penn State
U., University Park, PA. Contact: Dr. Masatoshi Nei, Telephone:
814-863-7334, Fax: 814-863-7336
11th North American Colloquium on Domestic Animal Cytogenetics and Gene
Mapping, June 14-18, 1999, U. of Minnesota Twin Cities Campus,
Minneapolis/St. Paul, MN. See
http://www.extension.umn.edu/Courses/cytogene.htm.
Molecular Biology Techniques Workshop, June 14-24, 1999, U. of Minnesota,
St. Paul, MN. Sponsored by the Food Animal Biotechnology Ctr. See:
http://fabctr.umn.edu/mbtw/1999.htm.
Agricultural Genomics: New Technologies, Functions, and Advances, June
23-25, 1999, Sheraton San Diego Hotel and Marina, San Diego, CA. See:
http://www.iir-ny.com.
Techniques in Bioinformatics and Comparative Genomics, June 27-July 2,
1999, Madison Wisconsin. Five day computer laboratory course offered by
the Biopharmaceutical Technology Center Institute. See:
http://www.btci.org/courses/TBCG99.htm.
American Society of Animal Science Annual meeting, July 21-24, 1999,
Indianapolis, IN. See: http://www.asas.uiuc.edu/99meet.
Transgenic Animal Research Conference, August 14-19, 1999, Granlibakken
Conference Center, Tahoe City, CA. Sponsored by the U.C. Davis
Biotechnology Program. Contact info.: mmmcgloughlin@ucdavis.edu.
50th Annual Meeting of the European Association for Animal Production
(EAAP): August 22 - 26, 1999
in Zurich (Switzerland). Information at: http://eaap-1999-zurich.ethz.ch.
Candidate Genes for Animal Health (sponsored by the Research Institute for
the Biology of Farm Animals), August 25-27, 1999, Rostock, Germany.
Contact: http://www.fbn-dummerstorf.de/fb3/Symp99.htm.
The Microarray Meeting, Sept. 22-25, 1999, Phoenix, Arizona. Hosted by
Nature Genetics. More information to follow or see
http://genetics.nature.com.
Cold Spring Harbor Fall Courses: Genome Informatics; Positional Cloning:
Contig to Candidate Gene; Computational Genomics, application deadline,
July 15, 1999. Contact: http://www.cshl.org/meetings.
Plant and Animal Genome VIII, joint with the NAGRP annual meetings, Jan.
8-13, 2000, Town & Country Convention Center, San Diego, CA. See:
http://www.intl-pag.org. Followed immediately by Ag Microbial Genome I,
Jan. 13-14, same location. See http://www.ag-microbial.org/agm.
International Society of Animal Genetics: Minneapolis, MN, USA will be
held July 24-27, 2000. Contact Brian Kirkpatrick at
bwkirkpat@facstaff.wisc.edu.
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Contributions to Pig Genome Update 37 including short meeting announcements
are always welcome. Please send by June 10.
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
+-----------------------------------+
| Paid for by funds from the NRSP-8 | Web: http://www.genome.iastate.edu
| USDA/CSREES sponsored Pig Genome | Mailing list:
| Coordination Program | angenmap@db.genome.iastate.edu
+-----------------------------------+
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