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Pig Genome Newsletter #049
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. 49 **************
* *
* <angenmap@db.genome.iastate.edu> *
* July 1, 2001 *
**************************************
+==========================================================================+
1. NC210 and NC220 regional research projects met and a merger is underway
2. Web-based user-friendly QTL mapping software
3. Efforts to increase genome funding are underway
4. New URL for ARKdb
5. New primers and more aliquots of old ones are now available
6. Ideas for support materials are needed
7. The Sixth International Conference on Pig Reproduction was held
8. Planning is already well underway for PAG-X next year
9. Upcoming meetings
+==========================================================================+
NC210 and NC220 regional research projects met and a merger is underway.
Just two weeks ago a group of 30 individuals representing the existing
pig genomics and pig genetics regional projects met to write a brand new
integrated project for regional research. This effort was led by Jack
Dekkers, who chaired the writing committee, that consists of Ron Bates
and Cathy Ernst (Michigan State University), Daniel Pomp (University of
Nebraska), Max Rothschild (Iowa State University), Rodger Johnson
(University of Nebraska) and Jon Beaver (University of Illinois). The
meeting was hosted by Rodger Johnson and Daniel Pomp and was extremely
productive in sorting out the objectives and the basis for future work.
The following project title and objectives have been proposed:
Quantitative Genetic and Genomic approaches to improve pig production
and health and pork quality. Objectives: Through the integration of
quantitative and molecular genetics we will: 1) Determine genetics
factors to improve pre-harvest production efficiency, environmental
sustainability, animal health, and welfare and 2) Discover genetic
mechanisms controlling post-harvest quality of pork. The committee is
still looking for expressions of interest of potential participants in
this new project. Specifically, we are looking for the following input.
These should include: 1) Names of faculty that would be interested to
participate in this project and 2) Specifics on what your station could
contribute to this project (e.g. genetic/animal resources, molecular
genetic resources, knowledge, specific research areas) and on how
research opportunities at your station would be enhanced by
collaboration from other stations. Please email Jack Dekkers
(jdekkers@iastate.edu) as soon as possible.
o o o o o o o o o o o
Web-based user-friendly QTL mapping software is now available!!! The
development team of Chris Haley, Mike Kearsey, Sara Knott, George Seaton
and Peter Visscher are pleased to announce the release of QTL Express, a
simple-to-use web-based package for QTL analysis using regression
interval mapping techniques. QTL Express currently supports analyses of
F2 data from crosses between inbred or outbred lines, and data from
outbred half-sibpopulations. Modules allowing analysis of other
data-structures and further enhancements will be added in due course.
Special features of the program include: error checking, help files,
example data files, marker segregation distortion test, inclusion of
fixed effects and covariates, permutation tests to set significance
thresholds, bootstrapping to determine confidence intervals and single
and linked QTL models. QTL Express is appropriate for the analysis of
experimental data and ideal for teaching purposes. It can be reached
directly (http://qtl.cap.ed.ac.uk) or by going to the pig genome web
page (http://www.genome.iastate.edu) and looking under the section
marked QTLs. For more information or for comments on the package,
emails to george.seaton@ed.ac.uk.
o o o o o o o o o o o
Efforts to increase genome funding are underway. An Alliance for Animal
Genome Research, a non-profit organization, comprised of major companies
in the animal industry, agricultural groups, and research universities
has been formed to increase awareness of the importance of animal genome
research and the urgent need for increased federal research funding.
The objective of the initiative is to acquire increased funding for
mapping and BAC libraries, low coverage sequencing, bioinformatics and
long term competitive grant funding for functional genomics. Increased
resources will come from greater access to existing genomics funding and
increased appropriations. The focus will be on cattle, swine, poultry,
and companion animals and through comparative genomics positioning the
initiative as an integral component of the overall public genomics
effort, including human and model species. For more information please
contact the Alliance at 415 591 5416 or 301 951 3345 (kindly provided by
Dr. Roger Wyse).
o o o o o o o o o o o
Have you adjusted your URL for ARKdb - it has moved !! The Roslin
Institute Bioinformatics (http://bioinformatics.roslin.ac.uk) Group is
pleased to announce that the ARKdb database system has moved to a new,
easy-to-remember domain. The main site can now be found at
http://www.thearkdb.org. The Roslin site is also accessible as
http://roslin.thearkdb.org, while the mirror sites at Texas A&M and Iowa
State can be accessed as http://texas.thearkdb.org and
http://iowa.thearkdb.org. The full set of ArkDB genome databases
covering pigs, chickens, sheep, cattle, horses, deer, cats, tilapia,
salmonids and turkey can be found on the Roslin site. The Iowa mirror
site carries chicken and pig databases and the Texas mirror site houses
cattle, horses and sheep. If you need to cite data held within the
ARKdb databases, please cite ARKdb-<species name> genome database, with
URL http://www.thearkdb.org and refer to the published paper Hu et al.,
(2001). Nucleic Acids Research 29(1), 106-110 also noting the date on
which the data were retrieved or accessed (kindly provided by Andy Law).
o o o o o o o o o o o
New primers and more aliquots of old ones are now available. A new set
of primers for 41 microsatellite markers are now available. These were
produced by Research Genetics and are in 5000 pmoles amounts. In
addition Set III has been reproduced in limited number to meet
additional demand. A total of 509 microsatellite markers have been
included in our ten sets. More information on all sets of primers can
be found at the web site:
http://www.genome.iastate.edu/resources/fprimerintr.html. A Java graphic
view of the microsatellite markers has been created. This graphic viewer
of primer sets draws markers on each chromosome according to their
relative location:
http://www.genome.iastate.edu/resources/PrimerOnChr.html. The new
primers are available and are free of charge. If you would like to
request a new set, please fill the web primer request form:
http://www.genome.iastate.edu/resources/primer_request.html. We will
respond to you as soon as possible. In addition, there are a limited
number of bags of the previous set of primers (set IX)
available. For additional questions please contact me
(mfrothsc@iastate.edu) or Dr. Yuandan Zhang (ydzhang@iastate.edu).
o o o o o o o o o o o
Ideas for support materials are needed. The Pig Genome Coordinator is
looking for more suggestions of items that can be made available to
swine committee members and pig genome researchers. Please send your
ideas to Max Rothschild (email to:mfrothsc@iastate.edu).
o o o o o o o o o o o
The Sixth International Conference on Pig Reproduction was held June
3-6, 2001 at the University of Missouri-Columbia. The meeting was
extremely well attended and featured talks on all aspects of pig
reproduction, transgenics and cloning. A number of papers touched on
genetics and one paper by Daniel Pomp discussed functional approaches to
study reproduction. The seventh ICPR will be held four years from now
and will be in the Netherlands. Dr. Billy Day was honored and roasted
by his former students and colleagues at the social event of the
meeting. A special thanks go to the hosts and organizing committee for
a very cutting edge meeting.
o o o o o o o o o o o
Planning is already well underway for PAG-X next year. Please see
http://www.intl-pag.org/pag for more information. Dr. Francis Collins,
"Czar" of the Human Genome Program at NIH, has agreed to give one of the
plenary talks. Several changes are on tap for next year. PAG-X will
again be at the Town & Country Convention Center in San Diego, CA, next
year running from Sat., Jan. 12, through Wed., Jan. 16. Next year PAG-X
will include plant, animal and agricultural microbe genomics all in one
meeting. Also it is planned that a weekend-only registration rate
($175) will be made available in addition to the usual student ($225),
non-profit ($425 early/$525), and industry ($550 early/$650) full week
registrations. Registration badges will be required to participate in
any workshop. As is the usual case the swine committee will be meeting
during the first few days. Jon Beaver, chair, is planning the swine
sessions and is happy to accept suggestions for speakers. Please note
that some support will be available from the Pig Genome Coordinator for
member and student participation, including the Neal Jorgensen Travel
Award for Swine. Contact Max Rothschild (email to:mfrothsc@iastate.edu)
for details.
o o o o o o o o o o o
Upcoming meetings (for more details see:
http://www.genome.iastate.edu/community/meetings.html)
The Sixth International Veterinary Immunology Symposium, July 15-20,
2001 at Uppsala, Sweden. For information please contact: ivis@slu.se.
12th North American Colloquium on Animal Cytogenetics and Gene Mapping,
July 15-19, 2001 at the University of California, Davis CA. For
information please contact: animalcyto@vgl.ucdavis.edu or
http://www.vgl.ucdavis.edu/research/cytoconf/.
International Animal Agriculture and Food Science Conference July 24-28,
2001, Indianapolis, Indiana. This is the Joint Annual Meeting of the
American Dairy Science Association, American Society of Animal Science,
Poultry Science Association, Reciprocal Meat Conference of the American
Meat Science. For information please contact Federation of Animal
Science Societies at fass01@assochq.org.
The 14th Conference of the Association for the Advancement of Animal
Breeding and Genetics, July 30 - August 2, 2001, Queenstown, New
Zealand. For information please contact Dr.Ken Dodds at
doddsk@agresearch.cri.nz.
4th International Meeting on SNPs and Complex Gene Analysis, Stockholm,
Sweden October 10-13, 2001. For more information see:
http://snp2001.cgr.ki.se/
Plant and Animal Genome X Januay 12-16, 2002 at the Town and Country
Convention Center, San Diego, CA. For information please contact D.
Sherago, Sherago International at darrins@scherago.com.
International Society of Animal Genetics, Göttingen, Germany, August
11-15, 2002. See http://www.gwdg.de/~bbrenig/ISAG2002.html for further
information.
7th World Congress of Genetics Applied to Livestock Production, August
19-23, 2002, Montpellier, France. See http://www.wcgalp.org for more
information.
Additional items can be found at:
http://www.agbiotechnet.com/calendar/index.asp.
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Contributions to Pig Genome Update 50 including short meeting
announcements are always welcome. Please send by August 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
+==========================================================================+
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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