Pig Genome Update No. 91

July 1, 2008

  1. The pig SNP consortium is working with Illumina on a whole genome genotyping array
  2. Pig Genome II Conference was held June 4-5 in Ljubljana, Slovenia
  3. The regional project NC1037 met on May 14-15 in Beltsville, MD
  4. Registration needed for the Pig Genome Annotation Workshop
  5. Planning for PAG XVII, January 10-15, 2009, is already underway
  6. The pig oligo arrays can be ordered
  7. Upcoming meetings ( 5 items )

The pig SNP consortium is working with Illumina to offer early access to a whole genome genotyping array estimated to have more than 50K SNPs primarily derived from several breeds including Large White, Landrace, Duroc, Pietrain and Wild Boar. To receive early access and pricing discounts, qualifying orders must be placed by 22nd August 2008 and meet purchase and delivery conditions which can be accessed at (http://www.illumina.com/porcineoffer) using the password: iSelect22AugPDC.

Due to the exceptional offer in pricing and access, delivery of orders greater than 12,672 samples cannot exceed a 1 year period. Since the arrays have a 6 month shelf life, this potentially provides usage over a 1.5 year period if the last shipment is at the end of the 1 year period. Delivery for orders less than 12,672 samples can be for over a 6 month period potentially providing usage over a 1 year period. First available delivery is expected to be in November, 2008. If you are interested in participating, or would like further information please go to(http://www.illumina.com/contactMe.ilmn?CS=1) and an Illumina representative will contact you.

There are many service companies who can provide genotyping using the Porcine SNP BeadChips that you purchase, and each company sets their own pricing for this service. In addition to Illumina's FastTrack Genotyping Services, Illumina Certified Service Providers can be found at(http://www.illumina.com/pagesnrn.ilmn?ID=69 .) Finally, specific service providers will be purchasing the Porcine SNP BeadChip in order to provide services immediately and to those who do not wish to purchase their own Porcine SNP BeadChip. Names can be pro vided upon request by Illumina or by the Pig Genome Coordinator mfrothsc@iastate.edu .


Pig Genome II Conference organized by the European COST action PigNet was held in Ljubljana, Slovenia, from June 4-5, 2008. With emphasis on functional genomics, scientists made presentations covering female reproduction, product quality, pig genome sequencing and 60K SNP chip progress, responses to specific infectious diseases and genetic defects, and bio-informatic strategies to approach non-coding RNAs in the porcine genome. A session on pig models for biomedicine included new efficient and targeted techniques for genetic engineering of pigs. There is an abstract booklet and abstracts are available via Peter Dovc (kindly provided by Barbara Harlizius).


The regional project NC1037, entitled Genetic and functional genomic approaches to improve production and quality of pork, met on May 14-15 in Beltsville MD. Hosted by Joan Lunney the 12 attendees from 9 different stations reviewed project objectives and discussed ways to collaborate extensively. Several projects were discussed including those dealing with performance, reproduction, meat quality and behavior traits. One of the collaborative projects looks at the genetic control of PRRS. It is estimated that the Pig Genome Coordinator will contribute funds to help purchase 500 SNP chips to aid this project as part of the NC1037 collaborative effort. Attendees of this meeting also heard research reports from scientists at BARC on an update on the cattle gene atlas, results on the application of BovineSNP50 for genome-wide associations and an application of Genomic selection in dairy cattle. NC-1037 scientists also presented station reports. Next year's meeting will likely be at PAG or at Washington State University.


Registration for the Pig Annotation Workshop July 16-18 at the Wellcome Trust Sanger Institute is needed. The Sanger institute is organizing an annotation workshop to bring together researchers from the pig genome community to participate in the manual annotation of the genome sequence. The event is sponsored by EADGENE and SABRE. Registration is limited to 40 participants. For details see http://www.sanger.ac.uk/Projects/S_scrofa/workshop_Hinxton08/index.shtml


Planning for PAG XVII, January 10-15, 2009, is already underway. The new chairs of the swine genome section are Melissa Ashwell and Cathy Ernst. Ideas for speakers are gladly being taken by Max Rothschild or Hans Cheng for plenary talks. Some reorganization of the species workshops on Saturday and Sunday is likely to take place to avoid overlap and increase attendance to the NRSP8 meetings. Stay tuned for developments.


The pig oligo arrays can be ordered. Swine oligo arrays can now be ordered at(http://www.pigoligoarray.org/) . A validation experiment, funded in part by the participants and the USDA Pig Genome Coordinator, was reported on at PAG 2008.


Upcoming meetings (see: (http://www.animalgenome.org/pigs/community/meetings.html))
  • 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 http://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.
  • 3rd SABRE Conference - "Welfare and Quality Genomics" - will be held in Foulum, Denmark on 10 and 11 September 2008. For information http://www.sabre-eu.eu

Items for Pig Genome Update 92 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

cc: Muquarrab Qureshi, CSREES and Caird Rexroad II, ARS

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USDA/CSREES sponsored
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