Pig Genome Update No. 97

angenmap@animalgenome.org
July 1, 2009

  1. Join the Swine Genome Sequencing Consortium (SGSC) and Pig Genome III
  2. Swine Genome Community feedback is needed
  3. Illumina and the International Porcine SNP Chip Consortium are pleased to announce that the porcine 50K+ SNP panel is available
  4. The NRSP-8 Bioinformatics Coordination team recently met
  5. PAG XVII, January 10-14, 2009 was a great success
  6. Help our pork producers
  7. Please provide your input
  8. Upcoming meetings

Join the Swine Genome Sequencing Consortium (SGSC) and Pig Genome III meeting to celebrate the completion of the pig genome sequence in Hinxton, UK November 2-4. In anticipation of the completion of the pig genome sequencing project, this workshop will be “SGSC - the genome assembly and annotation Pig Genome III: Exploiting the sequence”. There will be a call for abstracts and registration information in July. Interested parties should contact either Larry Schook (schook@illinois.edu) or Martien Groenen (Martien.Groenen@wur.nl).

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Swine Genome Community feedback is needed: 1) The Ensembl team has taken the Pig assembly and plans to run the automated Genebuild. The timeframe is expected to be 5 months as it is not an easy process. This will add Pig to the list of species found on the Ensembl website. The best QC for the analysis will be feedback from the community and we would like lots of it! Guidance to problematic areas means they can then be corrected in time for a second Genebuild upon completion of the project; 2) Manual annotation for some clones is a possibility, but resources are limited. Therefore, it would be hugely beneficial for the community to identify any sequenced clone that would benefit from increased annotation provided by manual intervention and 3) One advantage of opting for the BAC by BAC sequencing approach was to allow targeted sequencing of important regions first. These regions identified by the swine community are sequenced as "Top Priorities" and allow rapid sequence feedback to the community long before completion of the project. So far, 28 regions of interest have been prioritized spanning 518 clones or ~3% of the genome. If you know of a region that would benefit from prioritized sequencing, please email pig-help@sanger.ac.uk . The deadline is immediate to send a request carol@sanger.ac.uk (kindly provided by Richard Clark and Carol Churcher).

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Illumina and the International Porcine SNP Chip Consortium are pleased to announce that the porcine 50K+ SNP panel is available and being shipped. If you did not place an order please do not hesitate to contact Illumina for further information or questions at (http://www.illumina.com/contactMe.ilmn?CS=1) .

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The NRSP-8 Bioinformatics Coordination team recently met to discuss ways to improve both the tools made available and the opportunities to use them. Please watch the web site (http://www.animalgenome.org/) for new developments including tools to analyze the pig high density SNP chip.

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PAG XVII, January 10-14, 2009 was a great success. The abstracts are now posted on the web. See (http://www.intl-pag.org/) for more information. Planning is well underway for next year and your involvement is encouraged.

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Help our pork producers. Low pork prices and high inputs have made for a bad year for many pork producers. This was further fueled by the so called outbreak of "swine" flu. You can help!! Light up the grill and buy lots of chops, ribs and brats and enjoy the summer.

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Please provide your input The Pig Genome Coordinator is always glad to. hear from NRSP-8 members and other readers about ways to improve the coordination effort or provide resources that are needed and with which the coordination program can help

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Upcoming meetings (see: http://www.animalgenome.org/pigs/community/meetings.html)
  • 2nd Annual NSF-funded Short Course on Statistical Genetics & Statistical Genomics, July 13-17, 2009, Hilton Hawaiian Village Beach Resort & Spa, Honolulu, Hawaii. Register at http://www.soph.uab.edu/ssg/nsfstatgen/nsfsecondannual
  • 7th U.C. Davis Transgenic Animal Research Conf., Aug. 17-22, 2009, Granlibakken Resort and Conference Center, Tahoe City, CA. See http://conferences.ucdavis.edu/transgenic
  • Next generation sequencing: challenges and opportunities. October 1-3, 2009, Casa Convalescencia, Barcelona, Spain http://ngs2009.uab.es
  • Plant & Animal Genome Conference, PAG XVIII, Jan. 9-13, 2010, Town & Country Hotel, San Diego, CA. Information available at http://www.intl-pag.org/)

Items for Pig Genome Update 98 can be sent to me by no later than August 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
USDA/CSREES sponsored
Pig Genome Coordination Program
 http://www.genome.iastate.edu/
Mailing list: angenmap@animalgenome.org

© US Pig Genome Coordination Program