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Pig Genome Newsletter #087
From: "Rothschild, Max F [AN S]" <mfrothsc@iastate.edu>
To: angenmap@animalgenome.org
Subject: US Pig Genome Newsletter #87
Date: Tue, 31 Oct 2007 13:51:46 -0500
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. 87 **************
* *
* <angenmap@animalgenome.org> *
* November 1, 2007 *
**************************************
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1. The Swine Genome Sequencing Workshop was held October 26th in Paris
2. The International Symposium of Animal Genetics for Animal health was
held in Paris, France
3. SNP chip development underway
4. PAG-XVI and the swine genome / NRSP8 meetings will be held Jan. 12-16
5. USDA-NRI Grant RFA for FY 2008 is now available
6. The NRSP-8 renewal application is mid stream now
7. The USDA's Blueprint for Animal Genomics
8. The pig oligo arrays can be ordered
9. Upcoming meetings ( 6 items )
===========================================================================
The Swine Genome Sequencing Workshop was held October 26th in Paris. It was
attended by 30 individuals from nearly 10 countries. Issues of the sequenc-
ing project, identifying approaches to ensure broad and rapid utilization
of the sequence information, and examining ways to find additional financial
support were discussed. To date about 72% of the map is undergoing
sequencing or in the pipeline with 46MB finished. The goal is to move
beyond the original 3X coverage desired and move to an "improved" coverage
that is actually better than 4X since "improved" sequencing will reduce
the gaps greatly. The progress of sequencing is somewhere in the neighbor-
hood of 500-600 clones a month. This means that there will be an improved
sequence likely completed in Fall of 2009. It is important to remember
that while this appears to be a year later than earlier predicted the
quality of the sequence will be considerably improved. Interested persons
are encouraged to visit the various web sites at Sanger, the piggenome and
the animal genome web site. Further details will be at the International
Swine Genome Workshop meeting on Sunday at 12:45 pm at PAG 2008 in San
Diego. An annotation workshop will also be presented in the summer of
2008 near the time of ISAG. For those further interested please see
progress chart below and recently published papers
http://genomebiology.com/2007/8/7/R139 and
http://genomebiology.com/2007/8/8/R168 and
http://genomebiology.com/2007/8/4/R45 for new information on the progress.
The International Symposium of Animal Genetics for Animal health (AGAH)
was in Paris, France from October 23-25, 2008. It was a large success,
in large part due to the excellent program of talks and posters, and the
large number of participants (over 250 from 33 countries) that attended.
The program chairs, Drs. Marie-Hélène Pinard and Cyril Gay and the
scientific committee should be commended as should OIE for providing
such a nice location. Proceedings will be published in the early spring
and details will follow when available.
o o o o o o o o o o o
SNP chip development underway. A consortium from the USDA (ARS, CSREES),
University of Illinois, Iowa State University and the National Pork Board
is currently undertaking a concerted effort to develop a high density(~50K)
SNP chip for pigs. The consortium is aiming to develop this research tool
by mid 2008. It is envisioned that this chip will be employed widely by the
porcine research community to drive gene discovery and association analyses
and eventually whole genome selection. The SNPs included for this project
will be selected from those in public databases on February 1, 2008. The
consortium would like to invite researchers interested in access to this
technology to join their group. In addition, investigators possessing SNP
information that has not been placed in public databases are encouraged to
submit their information as soon as possible so that the most useful set
of SNPs can be included in the final product. At present, neither the
cost per chip nor the commercial provider of the technology has been
finalized. To help define both of these, the consortium is now seeking
to quantify the likely demand for the finished chip. Please contact
either Mohammad Koohmaraie (Mohammad.Koohmaraie@ARS.USDA.GOV), Max
Rothschild (mfrothsc@iastate.edu) or Larry Schook (schook@uiuc.edu) if
your research program/institution would consider purchasing and employing
the 50K pig SNP chip. Also, please indicate the approximate number of
chips required initially and per year so that we can include you in the
mailing list concerning chip production and supply. Our aim is to achieve
the maximum economy of scale across the pig genomic community and in turn
achieve the lowest unit cost per chip. Please don't hesitate to contact
any of the individuals included in this notice for additional information.
o o o o o o o o o o o
PAG-XVI and the swine genome and NRSP8 meetings will be held January 12-16,
2008 at the usual spot, the Town and Country Hotel, San Diego, CA. The
program is available at http://www.intl-pag.org/16/16-pag.html. The swine
genome meeting NC1004 will be held on Saturday, Jan. 12 and the swine genome
sequencing meeting Sunday January 13. The Swine Genome Coordinator again
have some funds to help with travel support for NAGRP members or their lab
members so please contact the Coordinator as soon as possible.
o o o o o o o o o o o
USDA-NRI Grant RFA for FY 2008 is now available at www.csrees.usda.gov or
www.grants.gov. Program 43.0, Animal Genome, contains five elements:
Translational Animal Genomics, Tools and Resources, Bioinformatics, Func-
tional Genomics and Whole Genome Enabled Animal Selection. The deadline
for the first four elements 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. The
deadline for Whole Animal Genome Enabled Selection is Feb. 14, 2008, and
this section requires a letter of intent by November 26, 2007 (only one
award is likely to be made in this element). Please see the RFA for dead-
lines 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 NRSP-8 renewal application is mid stream now. The NRSP-8 writing team,
coordinated by Mary Delany, includes existing coordinators or their
representatives, and the NC-1008 writing team is being led by Chris Ashwell
(objective 1), Jim Petitte (objective 2) and Sue Lamont (objective 3).
Be sure to fill out your appendix E to state your participation and please
get your director's support for this project.
o o o o o o o o o o o
The USDA's Blueprint for Animal Genomics, a product of several months of
effort of a USDA Animal Genomics Task Force commissioned by Undersecretary
Joseph Jen in 2006, is now available at
http://www.csrees.usda.gov/newsroom/news/2007news/blueprint.html. The
Blueprint outlines needs and goals in the areas of "Science to Practice",
"Discovery Science" and "Infrastructure". The goals of this Blueprint are
closely aligned with the priorities of the NRSP-8 renewal application.
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
(http://www.pigoligoarray.org/). A validation experiment, funded in part by
the participants and the USDA Pig Genome Coordinator, is taking place and
will be 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)
NSIF Annual Meeting and Genetic Symposium being held in Kansas City, Missouri
on December 6 and 7, 2007. For details and program information please contact
Steve Moeller at moeller.29@osu.edu
2nd GSA Model Organisms & Human Biology Meeting, January 5-9, 2008, Town &
Country Convention Center, San Diego, CA. Please see
http://www.gsa-modelorganisms.org/
Plant and Animal Genome XVI, joint with NC-1008 and NAGRP annual meetings,
Jan. 12-16, 2008, Town & Country Convention Center, San Diego, CA. See
http://www.intl-pag.org/.
Midwestern Section, American Dairy Science Association, American Society
of Animal Science, Annual Meeting, Des Moines, Iowa, March 17-19, 2008.
See http://adsa.asas.org/midwest/2008/
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
<> <> <> <> <> <> <> <> <> <> <>
Items for Pig Genome Update 88 can be sent to me by no later than December 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 |
+-----------------------------------+--------------------------------------
