Pig Genome Update No. 82

angenmap@animalgenome.org
January 1, 2007

  1. PAG-XV will be held January 13-17, 2007 at the Town and Country Hotel
  2. QTL database Workshop is planned at PAG in San Diego on January 16th
  3. The new pig oligo arrays are here and can be ordered
  4. Pig Genome Update goes electronic only beginning January 1
  5. Swine Sequencing Committee met recently in Toulouse France
  6. The Alliance for Animal Genome Research met in Washington, DC
  7. The National Swine Improvement Federation met in Nashville, TN
  8. The CSREES FY 2006 National Research Initiative (competitive grant)
  9. Upcoming meetings

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

PAG-XV will be held January 13-17, 2007 at the usual spot, the Town and Country Hotel, San Diego, CA. The program is available at www.intl-pag.org/. See the PAG website for more information or to register on-line. The deadline for reduced fee registration is Nov. 1. The program for porcine genomics can be found at http://www.intl-pag.org/15/15-swine.html and looks quite good. Hope to see you there.

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QTL database Workshop is planned at PAG in San Diego on Tuesday January 16th at 1PM. The bioinformatics coordinator and his team will be hosting a workshop involving databases actively curating QTL data from rat, mouse, chicken, cattle, and swine. The goals of the workshop are 1) Define the minimal amount of information needed for QTL publication. Can we develop MIAME guidelines for QTL publication? 2) Integration of phenotype ontologies; and 3) Exchange of curated QTL information. At 3PM, they would like to invite all users of QTL databases to come and discuss with us what they would like QTL databases to be able to do. This is your chance to help set priorities for future development of QTL databases.

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The new pig oligo arrays are here and can be ordered. Thanks to efforts of a number of groups and individuals we have developed a novel 70-mer oligonucleotide microarray for profiling expression of the pig (Sus scrofa) genome. The Swine Protein-Annotated Oligonucleotide Microarray has been developed as an OPEN SOURCE collaboration between investigators and institutions with an interest in pig physiology. The sequences of the oligonucleotides, the consensus sequences they represent, and the annotation of the consensus sequences are provided at no cost to the entire research community. New swine oligo arrays ordering can now be ordered (http://www.pigoligoarray.org/ ). Please note ordering depends on the source of your funding. Labs associated with agriculture (at US Colleges or Universities, US government laboratories, or foreign Universities or governments) please order using the "Arrays for USDA NAGRP-8 supported activities" button. If you are a PRRS researcher please order using the "Arrays for PRRS CAP supported activities" button. Commercial concerns (domestic or foreign) or any biomedical researchers (domestic or foreign) please order using the "Array for Biomedical and Commercial Applications" resource button. Validation of arrays will take place. Thanks to efforts of a number of the swine genome community a validation experiment, funded in part by the participants and the USDA Pig Genome Coordinator will take place over the next few months. The plan is to report the information to the community at the earliest possible date.

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Pig Genome Update goes electronic only beginning January 1. For those who used to get the hard copy version of this newsletter, this issue will be the first to be distributed in email format only though Angenmap (http://www.animalgenome.org/community/discuss ) Acrobat .pdf versions (with graphics) are also posted on our website at http://www.animalgenome.org/pigs/newsletter/index.html .

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Swine Sequencing Committee met recently in Toulouse France. Progress on the sequencing continues at an excellent pace and was reported to those attending by the project directors. Minutes of the latest meeting are posted at www.piggenome.org . The website also provides access to all of the newsletters and permits direct communication with the Project Directors. There is also an opportunity for users to participate more fully and to become a SGSC member. Be sure to attend the international swine genome sequencing meeting on Sunday at PAG (http://www.intl-pag.org/15/15-swine-seq.html).

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The Alliance for Animal Genome Research met in Washington, DC in late November. This was the first meeting of the year for the Alliance. The accomplishments have been many and Alliance members reviewed options for moving forward. It is clear that new members are needed and that the focus will be more towards functional genomics. More details will be made available in the future.

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The National Swine Improvement Federation met in Nashville, TN in early December. Several talks covered genetic markers, swine genome sequencing and other topics of interest. The meeting was well attended and most producers and company people were interested in the progress made through genomics. Paper can be seen at www.nsif.com.

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The CSREES FY 2006 National Research Initiative (competitive grant program) request for proposals can be found at http://www.csrees.usda.gov/funding/rfas/nri_rfa.html . Total FY 2006 NRI funding was $181.7M. The House FY 2007 budget and the Senate Appropriations Committee allocate about $190M for next year's NRI, but almost all appropriations bills failed to get through by the Oct. 1 deadline and it seems likely that another Omnibus Appropriations Act will be required, and one can never tell what that may contain. Note: next year's FY 2007 NRI applications will require electronic submission through http://grants.gov/ (provided by Jerry Dodgson).

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Upcoming meetings (see: http://www.animalgenome.org/pigs/community/meetings.html )
  • Seventh International Long-oligonucleotide Microarray Workshop, January 7- 12, 2007, Univ. of Arizona, Tucson, AZ. See http://ag.arizona.edu/microarray/workshopJan2007.html .
  • Plant and Animal Genome XV, joint with NC-1008 and NAGRP annual meetings, Jan. 13-17, 2007, Town & Country Convention Center, San Diego, CA. See www.intl-pag.org/.
  • Chicken Development and Genomics, April 12-15, 2007, Barcelona, Spain. See www.lists.bbsrc.ac.uk/mailman/listinfo/chicken-genome
  • 3rd International Conference on Quantitative Genetics, August 18-24, 2007, Zheijiang University, Hangzhou, China. Conference Organizers: Jun Zhu(jzhu@zju.edu.cn) and Zhao-Bang Zeng (zeng@stat.ncsu.edu)
  • Convergence of Genomics and the Land Grant Mission: Emerging Trends in the Application of Genomics in Agricultural Research, September 10-12, 2007, Purdue U., West Lafayette, Indiana. See= www.entm.purdue.edu/conference.
  • International Symposium on Animal Genomics for Animal Health, October 23-25, 2007, OIE Headquarters, World Organization for Animal Health, Paris, France.For information contact Cyril Gay, cyril.gay@ars.usda.gov, or Marie-Hélène Pinard, pinard@dga2.jouy.inra.fr

Items for Pig Genome Update 83 can be sent to me by no later than February 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


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