The Swine Genome Sequencing Workshop was held October 26th in Paris. It
was attended by 30 individuals from nearly 10 countries. Issues of the
sequencing 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 neighborhood 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 pig enome 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.
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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-H�l�ne 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.
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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.
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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.
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USDA-NRI Grant RFA for FY 2008 is now available at.
(http://www.csrees.usda.gov/) or www.grants.gov . Program 43.0, Animal
Genome, contains five elements: Translational Animal Genomics, Tools and
Resources, Bioinformatics, Functional 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 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.
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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.
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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.
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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.
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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, Jan. 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
© US Pig Genome Coordination Program