Pig Genome Update No. 88

angenmap@animalgenome.org
January 1, 2008

  1. PAG-XVI and the swine genome and NRSP8 meetings will be held January
  2. The National Swine Improvement Federation, recently met in Kansas City
  3. SNP chip development underway
  4. The NRSP-8 renewal application is mid stream now
  5. USDA-NRI Grant RFA for FY 2008 is now available
  6. The USDA's Blueprint for Animal Genomics
  7. The pig oligo arrays can be ordered
  8. Upcoming meetings ( 9 items )

Happy Holidays and New Year to you, your families and colleagues!!

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 all day on Saturday, January 12 and the swine genome sequencing meeting will begin at 12:45 pm Sunday January 13. Also of importance on Sunday January 13- from 3:35 pm - 5:45 pm is the NRSP-8 Business Meeting. 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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NSIF - The National Swine Improvement Federation, recently met in Kansas City. About 75 people attended this annual meeting. A number of excellent papers were presented that included updates on the swine genome sequencing project, the use of genetic markers in beef cattle and swine industries, micro RNA technology, eQTL and discovery of markers for growth, disease resistance and meat quality. Other talks also included projects of interest to swine geneticists including the release of new genetic markers for use in the swine industry.

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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 this research tool 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 SNP can be included in the final product. At present, neither the cost per chip or 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 technology. Please write to either Mohammad Koohmaraie (Mohammad.Koohmaraie@ARS.USDA.GOV), Max Rothschild (mfrothsc@iastate.edu) or Larry Schook (schook@uiuc.edu) if you consider your research program / Institution would consider purchasing and using the 50K 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.

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The NRSP-8 renewal application is mid stream now. The NRSP-8 writing team, coordinated by Mary Delany and existing coordinators or their representatives. Be sure to fill out your appendix E to state your participation and please get your director's support for this very important project.

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USDA-NRI Grant RFA for FY 2008 is now available at http://www.csrees.usda.gov/ or http://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 required 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 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))
  • 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. 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 89 can be sent to me by no later than February 15 please.

A special thanks to friends and colleagues for your help and support. Please take some time off to enjoy the holidays!!

                    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
USDA/CSREES sponsored
Pig Genome Coordination Program
http://www.genome.iastate.edu/
Mailing list: angenmap@animalgenome.org


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