Pig Genome Update No. 93

November 1, 2008

  1. Progress on the sequencing project continues to be excellent
  2. Illumina and International Porcine SNP Chip Consortium announcement
  3. NRSP- 8 was renewed and the Genome Coordinators named
  4. USDA Grant update
  5. The 4th Allerton conference on "Phenotypes" was recently held
  6. PAG XVII, January 10-15, 2009, is already underway
  7. Upcoming meetings ( 7 items )

Progress on the sequencing project continues to be excellent, with 93% of the physical map having been selected from 15,424 BAC clones for sequencing. Some 78% of the map has sequence available which gives 2,207Mb from 12,884 clones. A further 7,453 of these clones have been "improved". More information on specific BAC clones and updates can be found at( www.sanger.ac.uk/Projects/S_scrofa/ .) The aim is to complete the project with approximately 1,500 further clones which will be selected over the next 6-7 months, bringing the total number of sequenced clones for the entire project to 17,000. The average overlap between BAC tile path clones stands at about 40kb. Notoriously, the final stage of sequencing projects can prove more difficult, leading to an increase in redundancy. They are hoping to avoid this by selecting the remaining clones using sequence alignments rather than fingerprint overlaps alone. (kindly provided Lucy Matthew, Sanger)


Illumina and the International Porcine SNP Chip Consortium are pleased to announce that the porcine 60K SNP panel is under production. Thanks to considerable cooperation and work among researchers and Illumina chips were ordered for $99.99 as product. Considerable effort is now underway to organize breed samples and family material for the initial testing of the product. This work will be ongoing and chips should be available by December 1 to those who previously ordered. 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 .)


NRSP- 8 was renewed and the Genome Coordinators named. NRSP-8 was renewed for another 5 years beginning October 1, 2008 with a FY 2009 total budget of $500,000. A modest increase in budget was obtained despite the fact that competition for multi-state research funding has become increasingly intense, reflective of the past success of the NAGRP. Special thanks go to Mary Delany for leading the renewal proposal writing team and Muquarrab Qureshi, who continues as Director, as well as all our CSREES administrative team. Genome coordinators have been reappointed by the USDA-CSREES. These now include John Liu and Caird Rexroad III, aquaculture; Juan Medrano who replaces Jim Womack for cattle, Jerry Dodgson and Hans Cheng, poultry; Noelle Cockett, sheep; Ernie Bailey; Horse; Jim Reecy and a team of ISU researchers (Sue Lamont, Chris Tuggle and Max Rothschild and Shane Burgess), bioinformatics. A special thanks to Jim Womack for his help and cooperation. Many of you were very kind to submit my name for the next five years and I have been reappointed also. The confidence which you have shown in the work we have accomplished together is much appreciated and there are so many people whose help I have appreciated. I hope the next five years will be as much fun and productive as before. Please do not hesitate to suggest ideas, improvements or concerns. Thank you again for your continued strong support.


USDA Grant update. Due to the establishment of the National Institute for Food & Agriculture (NIFA) that consolidates USDA competitive research, education and extension programs, a new competitive grant program will replace the National Research Initiative for FY 2009. An initial alert to include projected program application deadlines is expected to be released in November, 2008. The actual 2009 RFA is expected next January. This means that the earliest application deadlines (e.g., Animal Protection & Biosecurity) likely will not be prior to March, 2009. The Animal Genome deadline is uncertain but will most likely remain in June. The exact amount of funding available also is uncertain, since it is unclear when a FY 2009 budget bill will be passed by Congress.


The 4th Allerton conference on "Phenotypes" was recently held at the University of Illinois. Great talks and a beautiful venue all contributed to an excellent meeting. Eighteen speakers from six countries presented talks centered around the need to collect, analyze and warehouse animal phenotypes. Attendees were provided insights into the use of the latest high density SNP chips based on real data (e.g. Drs. Jerry Taylor, Theo Meuwissen). Dr. John McEwan illustrated the real value to be gained from a central genetic hub or "information nucleus" as a way of linking research to industry populations. Dr. Sussman talked about technology after SNP chips with an exhilarating gallop through 25,000 bp reads from single molecule sequencing to real-time metabolomics of the (mouse) brain. On the swine side, Dr. Martien Groenen presented an update on the Swine SNPchip and Dr. Ming Che (Jay) Wu talked about Taiwan's efforts to conserve swine germplasm. Drs. Larry Schook, Harris Lewin and Jon Beever plan to develop a white paper summarizing the conference. (kindly provided by G. Plastow and J. Reecy.)


PAG XVII, January 10-15, 2009, is already underway. The new chairs of the swine genome section are Melissa Ashwell and Cathy Ernst and the program is now posted on the web. Ideas for speakers are gladly being taken by Max Rothschild or Hans Cheng for plenary talks in 2010. Some reorganization of the species workshops on Saturday and Sunday has taken place to avoid overlap and increase attendance to the NRSP8 meeting which is all Sunday afternoon.. The main PAG meeting runs Sunday night through Wednesday. See (http://www.intl-pag.org/) for more information and to register. Register prior to Nov. 1 for lower rates. Some funds to assist travelers for the swine workshop may be available on request.


Upcoming meetings (see: http://www.animalgenome.org/pigs/community/meetings.html)

Items for Pig Genome Update 94 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

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

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