Pig Genome Update No. 63angenmap@db.genome.iastate.eduNovember 1, 2003 |
The Swine Genome Sequencing Consortium (SGSC) met for the first time in Jouy-en-Josas, France on September 23 to 26, 2003. This meeting was organized by Larry Schook and Patrick Chardon and hosted by INRA. The meeting included individuals from a number of countries including the US, France, Britain, Denmark, China, Korea, and Japan. Representatives from the USDA, the Alliance for Animal Genome Research and several of the authors of the "Pig Genome Sequencing White paper" participated. Each participant provided updates relating to the state of the art of pig genome research and funding possibilities for the pig genome sequencing project. It was estimated that 50 million dollars would be required but we already have some commitments including a 1X coverage, estimated to be worth 6 million dollars, that was donated by the SinoDanish sequencing project. Korea also agreed in principle to make a donation of 2 million dollars. Strong support was also given by the USDA representatives. A draft mission statement was discussed and will be circulated for comment. The Principles of Cooperation were discussed by the group. The principles of the SNP Consortium and the Human Genome Initiative were reviewed. It was the group consensus that all information would be public and that sequence information would be made public following accepted guidelines used in the Human Genome Initiative. A future meeting is planned early in 2004 to continue to make efforts to acquire the necessary funding for pig genome sequencing project.
Texas A&M and Baylor College of Medicine recently hosted the "The Livestock genomes: sequence annotation and informatics challenges" Symposium at the Del Lago Resort and Conference Center in Lake Conroe, Texas on October 5-7, 2003. There were about 130 attendees from university, government, and industry. The talks of twenty-six invited speakers focused on genome assembly, sequences annotation, bioinformatics resources and challenges. Drs. Richard Gibbs and George Weinstock presented talks on what has been learned from the human genome sequencing project and how this relates to the sequencing of livestock species. In addition, researchers from the chicken (Dr. Jerry Dodgson, Dr. Wes Warren), honey bee (Dr. Hugh Robertson), dog (Dr. Patrick Venta), and swine (Dr. Larry Shook) communities updated the audience with respect to the sequencing efforts genomes sequenced. The symposium also featured talks on the use of bioinformatics tools (Dr. Ewan Birney, Dr. Bryan Dalrymple, Dr. Jim Ostell, Dr. Lisa Stubbs), and the road ahead (Dr. Ruddi Fries, Dr. Leif Andersson) (review kindly provided by J. Reecy and Z. Hu) Pig arrays can be ordered now!! Materials needed to produce a 13,000 element oligo array have been produced. Pig Genome Coordinator funds were used to buy the oligos and will be used to partially fund printing of these oligos on to glass slides. Initial printing of about 400 slides for the community will take place. To ensure that the arrays are not wasted, individual researchers can request 20 free arrays and later up to 50 additional ones but they will be responsible for the printing costs of the additional ones. Printing costs will be $20 dollars a slide and will be billed directly to the researcher from the University of Minnesota facility where they will be printed. Two steps are required to order the arrays. Please go to the following web site: http://www.genome.iastate.edu/resources/array_request.html and place an order. Please note, to get the information on the gene list you must sign the Qiagen non-disclosure agreement (NDA). This likely requires visiting with your purchasing and or intellectual property office on your campus. Shipping will occur after you specify by email when you want the arrays. New NRSP-8 Bioinformatics Coordinator named. In the recent renewal of NRSP-8, a database coordinator position was developed along with the previous species coordinators. Dr. James Reecy at Iowa State University will be taking the lead in this effort. If you have ideas or suggestions please contact him at jreecy@iastate.edu . Release Date and Deadlines For 2004 NRI RFA to be Announced. From the NRI website (http://www.reeusda.gov/nri/ ): "CSREES Administrator Colien Hefferan announced Friday, August 15, that the FY 2004 NRI RFA would be delayed due to changes in the program's size and scope that were authorized by Congress in FY 2003. The changes included increased funding, coupled with an opportunity to use as much as 20% of the total available funding to support integrated research, education, and extension activities. When the added funds became available in FY 2003, the NRI published a supplemental RFA to announce a number of new funding opportunities. In FY 2004, the NRI will publish one consolidated RFA that will include most of the NRI portfolio of programs. The release of additional RFAs for programs offered jointly with other agencies is also planned. Revised submission deadlines will be included in the new RFA, with the earliest deadlines occurring no sooner than six weeks after publication. Help us save money!! If you would prefer to just receive an email copy of Pig Genome Update please email Max Rothschild at mfrothsc@iastate.edu or Ann Shuey at ashuey@iastate.edu and we will remove you from the printed mailing list. You can enroll on Angenmap and receive your newsletter and other interesting information. To subscribe to Angenmap, send an email to angenmap-request@db.genome.iastate.edu and put in the Subject line the key word "subscribe" and you will be one of nearly 1,000 users of this list serve. Your help in sharing microsatellite primers is still needed!! We have been sharing over 11 primer sets world wide for the past 10 years and have run out of them. However, the demand continues from many places around the world. If you have unused sets with current documentation that is still good and you reside in the US please return them to Max Rothschild, 2255 Kildee Hall, Iowa State University, Ames Iowa 50011. Next year's PAG-XII will be held January 10-14, 2004 again in San Diego at the same location. In addition to the outstanding plenary speakers that are scheduled, an excellent joint 2004 PAG Swine Workshop and NC1004 meeting is being planned by chair Dr. Diane Moody. This workshop will be held on Saturday and Sunday morning, January 10-11. Invited speakers will be describing a contig sequence from porcine chromosome 6 (Tosso Leeb), recombineering as a tool for harvesting genomic information (Larry Schook), and the implementation of marker assisted selection in commercial swine populations (Archie Clutter). Invited talks will be followed by coordinator, administrator, and station reports. A Sunday morning session will be devoted to a discussion of priorities, needs, and activities of the swine research community. A preliminary schedule and additional information for the meeting are found at: http://www.intl-pag.org/12/12-swine.htm . Upcoming meetings: (see: http://www.genome.iastate.edu/community/meetings.html )- Swine QTL Workshop and National Swine Improvement Federation annual meeting, December 4-5, 2003, Des Moines IA. For details please contact either Ken Stalder (stalder@iastate.edu), Jack Dekkers (jdekkers@iastate.edu) or Max Rothschild (mfrothsc@iastate.edu).
- Plant, Animal and Microbial Genome XII, joint with the NAGRP annual meetings, Jan. 10-14, 2004, Town & Country Convention Center, San Diego, CA. Please see www.intl-pag.org/ for more information.
- ISAG 2004, 29th International Conference on Animal Genetics, Sept. 11-16, 2004, Surugadai Campus, Meiji University, Tokyo, Japan. For more information see http://www2.kobe-u.ac.jp/~isag2004/
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
cc: Muquarrab Qureshi, CSREES and Caird Rexroad II, ARS
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