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Pig Genome Newsletter #063
P I G G E N O M E U P D A T E
__________________________________________________________________
A Bimonthly Newsletter of the U.S. Pig Genome Coordination Program
************** No. 63 **************
* *
* <angenmap@db.genome.iastate.edu> *
* November 1, 2003 *
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1. Swine Genome Sequencing Consortium met for the first time in France
2. Livestock genomes: sequence annotation and informatics challenges
symposium was held at Lake Conroe, Texas
3. Pig arrays can be ordered now
4. New NRSP-8 Bioinformatics Coordinator named
5. Release date and deadlines for 2004 NRI RFA to be announced
6. Help us save money - email copy of Pig Genome Update available
7. Your help in sharing microsatellite primers is still needed
8. Next year's PAG-XII will be held January 10-14, 2004
9. Upcoming meetings (3 items)
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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.
o o o o o o o o o o o
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)
o o o o o o o o o o o
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.
o o o o o o o o o o o
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.
o o o o o o o o o o o
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.
o o o o o o o o o o o
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.
o o o o o o o o o o o
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.
o o o o o o o o o o o
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.
o o o o o o o o o o o
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/
Additional items can be found at:
http://www.agbiotechnet.com/calendar/index.asp.
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Contributions to Pig Genome Update 64 including short meeting announcements
are always welcome. Please send by December 10.
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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U.S. PIG GENOME COORDINATION PROJECT
+-----------------------------------+
| Paid for by funds from the NRSP-8 | Web: http://www.genome.iastate.edu
| USDA/CSREES sponsored Pig Genome | Mailing list:
| Coordination Program | angenmap@db.genome.iastate.edu
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