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Pig Genome Newsletter #089
From: "Rothschild, Max F [AN S]" <mfrothsc@iastate.edu>
To: angenmap@animalgenome.org
Subject: US Pig Genome Newsletter #89
Date: Thu, 21 Feb 2008 13:18:27 -0600
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. 89 **************
* *
* <angenmap@animalgenome.org> *
* March 1, 2008 *
**************************************
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1. PAG-XVI and the swine genome meetings were held in sunny San Diego
2. Planning for PAG XVII, January 10-15, 2009, is already underway
3. Dense SNP chip development continues
4. The NRSP-8 renewal application is now completed
5. USDA-NRI Grant RFA for FY 2008 is now available
6. The pig oligo arrays can be ordered
7. Upcoming meetings ( 7 items )
===========================================================================
PAG-XVI and the swine genome meetings were held in sunny San Diego January
12-16, 2008. A large crowd of over 2,200 people attended the recent PAG
meetings and the many animal workshops. The swine workshop was well
organized by Gary Rohrer and Melissa Ashwell. It included talks dealing
with evaluation of the new arrays, confirmation of a QTL/candidate gene for
meat tenderness on chromosome 2, evaluation of LD in different populations,
updates on sequencing and SNP discovery. The sequencing workshop also
addressed some of these issues and considerable discussion was directed
towards development of a 60K SNP chip. Plenary talks included some
provocative comments on the role of genomics in society, developments
in small RNA and proteomic research, ontologies for biologists, energy
genomics, epigenomics and systems approaches to understanding complex
diseases. Poster viewing was much improved in the new conference area
and workshops also had a number of updated and useful new techniques and
equipment to describe.
o o o o o o o o o o o
Planning for PAG XVII, January 10-15, 2009, is already underway. The new
chairs of the swine genome section are Melissa Ashwell and Cathy Ernst.
Ideas for speakers are gladly being taken by Max Rothschild or Hans Cheng
for plenary talks. Some reorganization of the species workshops on
Saturday and Sunday is likely to take place to avoid overlap and increase
attendance to the NRSP8 meetings. Stay tuned for developments.
o o o o o o o o o o o
Dense SNP chip development continues. Considerable discussion took
place at PAG involving development of a dense SNP chip for pigs. Based
on reports presented by a number of parties it appears possible to
develop a 60K SNP chip this year. Members of the consortium from the
USDA (ARS, CSREES), University of Illinois, Iowa State University and
the National Pork Board met with two technology providers and discussed
the technologies and the possible costs to produce chips. In addition,
a number of people and research labs continue to deposit SNPs into the
database and sequencing is producing a large number of additional SNPs.
Details for purchase of chips have yet to be determined though price is
likely to be less that $150 but more than $100 per chip. Details on
minimum orders and other issues are yet to be determined. Please write
to either Mohammad Koohmaraie (Mohammad.Koohmaraie@ARS.USDA.GOV, Larry
Schook (schook@uiuc.edu) or Max Rothschild (mfrothsc@iastate.edu) if you
consider your research program / institution would consider purchasing
and using the 60K pig SNP chip, along with likely numbers required
initially and per year so that we can include you in the mailing list
concerning chip creation and supply. Our aim is to achieve the maximum
economy of scale across the pig genomic community and in turn the lowest
unit cost per chip. Please don't hesitate to write for additional
information.
o o o o o o o o o o o
The NRSP-8 renewal application is now completed. The NRSP-8 writing
team, coordinated by Mary Delany finished recently. She and her team
are to be congratulated for their hard work. Be sure to fill out your
appendix E to state your participation and please get your director's
support for this very important project.
o o o o o o o o o o o
USDA-NRI Grant RFA for FY 2008 is now available at http://www.grants.gov
or http://www.csrees.usda.gov/. Program 43.0, Animal Genome, contains
Translational Animal Genomics, Tools and Resources, Bioinformatics, and
Functional Genomics. The deadline for these is June 5, 2008. However,
integrated proposals only for Translational Animal Genomics and all
proposals for Functional Genomics require submission of a letter of
intent by March 14, 2008. Please see the RFA for deadlines for other
animal-related programs. Letters of intent are required for some
programs/elements to insure that proposal aims meet the goals of the
program and to minimize wasted effort in the application process.
o o o o o o o o o o o
The pig oligo arrays can be ordered. Swine oligo arrays can now be
ordered at (http://www.pigoligoarray.org/ ). A validation experiment,
funded in part by the participants and the USDA Pig Genome Coordinator,
was reported on at PAG 2008.
o o o o o o o o o o o
Upcoming meetings (see:
http://www.animalgenome.org/pigs/community/meetings.html)
Midwestern Section, American Dairy Science Association, American Society
of Animal Science, Annual Meeting, Des Moines, Iowa, March 17-19, 2008.
Please see http://adsa.asas.org/midwest/2008/
Swine in Biomedical Research Conference, April 2-3, San Diego, California.
For information and registration please see
http://www.nsrrc.missouri.edu/MeetingApril2008reg.aspx.
ARK-Genomics conference 2008: 3rd International Symposium on Animal
Functional Genomics (ISAFG), April 7th - 9th, 2008. Please see
http://ebrc-launch.org/ISAFG/index.html
Swine Breeders Roundtable, UK. April 21-24. For details contact Chris
Haley at chris.haley@roslin.ed.ac.uk
ASAS 2008 Centennial meeting, July 7-11, 2008, Indianapolis, Indiana,
USA. See http://www.asas.org/100years/
XXXI conference of the International Society of Animal Genetics (ISAG)
July 20-24, 2008 Amsterdam, The Netherlands. See www.isag2008.nl
Kennedy Conference on Quantitative genetics and Animal Breeding, August
11-12, 2008 Guelph, Ontario Canada. For details please contact Larry
Schaeffer at lrs@uoguelph.ca.
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Items for Pig Genome Update 90 can be sent to me by no later than April 15
please.
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
http://www.animalgenome.org/pigs/
cc: Muquarrab Qureshi, CSREES and Caird Rexroad II, ARS
===========================================================================
U.S. PIG GENOME COORDINATION PROJECT
+-----------------------------------+
| Paid for by funds from the NRSP-8 | Web: http://www.animalgenome.org/pig
| USDA/CSREES sponsored Pig Genome | Mail: angenmap@animalgenome.org
| Coordination Program |
+-----------------------------------+--------------------------------------
