Archived Post

From  Wed Jun 30 17:28:32 2004
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From: Max F Rothschild <>
Date: Wed, 30 Jun 2004 17:18:18 -0600
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Subject: US Pig Genome Newsletter #67
To: Multiple Recipients of <>

                  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. 67  **************
                  *                                    *
                  *  <>  *
                  *           July 1, 2004             *
 1. Swine Genome Sequencing Consortium continues to try to reach its goal
 2. New array materials likely to become available in the near future
 3. International sequencing consortium launches online resource
 4. The new CSREES web site is up and running
 5. A new funding opportunity within the USDA-CSREES NRI program
 6. A bioinformatics update from the Bioinformatics Coordinator
 7. Upcoming meetings (10 items)

Swine Genome Sequencing Consortium continues to try to reach its goal.
Efforts are progressing to advance the sequencing of the pig genome.  The
most recent meeting for the pig sequencing project was held at Sanger
Institute (Cambridge, UK), June 28th 2004.  This meeting was mainly
devoted to establishing a sound base for the sequencing effort -
integration of the physical maps, fingerprints and BES and to the
definition of a BAC tilling path.  The Consortium consider that the pig is
very well placed for an extremely efficient sequencing effort using the
"hybrid" approach and emphasis can be placed on ensuring valuable
intermediate outputs throughout the project.  This provided the basis for
an encouraging discussion of fund raising.  The next meeting will be held
during ISAG meeting (Tokyo, Japan) September 2004.  It is planned that the
ISAG meeting will focus on the sequencing strategy.  We need to continue
to work towards finalizing a funding plan before October 1, 2004.
Interested parties are encouraged to participate in the future. If you can
help in raising these funds please contact Larry Schook at UIUC or Max
Rothschild, at ISU (kindly provided by Graham Plastow).

           o    o    o    o    o    o    o    o    o    o    o

New array materials likely to become available in the near future.  There
have been a number of requests for arrays from NRSP8 members and others
both inside and outside the United States.  To meet this demand we are
considering buying a set of oligos and selling slides on $60-$65 cost per
slide with minimum orders of 25 required and maximum orders of 150 slides.
This would be available to both NRSP8 members and others both inside and
outside the US.  Slide orders would be on a first come first serve basis.
If you are interested please immediately contact Max Rothschild at

           o    o    o    o    o    o    o    o    o    o    o

International sequencing consortium launches online resource.  The
International Sequencing Consortium (ISC) has launched a free, online
resource where scientists and the public can get the latest information on
the status of sequencing projects for animal, plant and other eukaryotic
genomes.  The new resource can be accessed through ISC's home page, The database enables users to quickly sort
sequencing project information by organism, by sequencing group or by
funding agency.  Information about each sequencing project includes
timetables for completion, along with brief descriptions of sequencing
strategies being employed. In many cases, the database also features links
to the individual sequencing projects' Web sites and the sites of their
funding agencies, such as NHGRI. Also available are links to other
publicly run databases where the actual DNA sequence data is deposited.

           o    o    o    o    o    o    o    o    o    o    o

The new CSREES web site is up and running.  For this page to be effective
it is important that it be kept "current".  Please send any events or
topic information to Dr. Muquarrab Qureshi USDA-CSREES
MQureshiCSREES.USDA.GOV.  You may want to post notices such as meetings
or conferences, as long as they are related to this webpage.  You can
access the web and the page as follows: and then
going to the section on Animals and Animal Products and looking for the
programs on Animal Breeding and Genetics and Genomics.

           o    o    o    o    o    o    o    o    o    o    o

A new funding opportunity within the USDA-CSREES National Research
Initiative (NRI) grants program now exists.  The program is 66.0 Enhancing
the Prosperity of Small Farms and Rural Agricultural Communities
(  Proposals must be
received by October 5, 2004.  Integrated research, education, and
extension project awards for this program are expected to have a total
budget (including indirect costs) of no more than $500,000 for 2-4 years
of support.  Questions regarding the suitability of proposals should be
directed to Dr. Siva Sureshwaran ( or Dr.
Diana Jerkins (

           o    o    o    o    o    o    o    o    o    o    o

A bioinformatics update from the Bioinformatics Coordinator.  For the past
six months, efforts have been involved in two main projects related to
pigs 1) design and creation of a QTL database for pigs, and 2) development
of a bioinformatic tool for primer design.  The QTL database is being
developed and implemented in collaboration with NCBI.  A preliminary
implementation of the database can be found at  Simply query 'QTL and Sus
Scrofa' for entire list of QTLs.  The primer design tool has been designed
and implemented with a perl CGI driven program.  This tool is currently in
beta testing and should be released for public use shortly. In addition,
work to develop a database that researchers can obtain all livestock DNA
sequences without having to query NCBI is underway.  This tool is in the
development stage and should be available to the community shortly. Please
contact with any suggested projects or bioinformatic

           o    o    o    o    o    o    o    o    o    o    o

Upcoming meetings (see:

 The 16th European Colloquium on Animal Cytogenetics and Gene Mapping will
 be held at the Jouy-en-Josas research center of the INRA July 6 - 8.
 Please see:

 American Society of Animal Science- American dairy Science -Poultry
 Science Association joint Meeting, July 25-29, 2004, St. Louis, MO.  For
 details please see

 ISAG 2004, 29th International Conference on Animal Genetics, Sept. 11-16,
 2004, Surugadai Campus, Meiji University, Tokyo, Japan. For more
 information see

 Genome Informatics, sponsored by Cold Spring Harbor Laboratory and the
 Wellcome Trust, September 22-26 in Hinxton Hall, Hinxton, UK. For
 information please contact

 GSAC XVI, sponsored by The Institute for Genome Research, Sept. 27-30,
 2004, Washington, DC. See for more information.

 GO Users Meeting will be held at Northwestern University, Chicago, October
 14, 2004.  For more details contact

 Computational Genomics sponsored by TIGR will be in Reston, VA, October
 21-24.  For details contact

 Ninth DISCOVER Conference on Food Animal Agriculture. "Protecting and
 Managing Animal Genetic Resources for Future Generations: The Next Steps",
 Nov. 2-5, 2004, Cheyenne, Wyoming.  Please see for
 further information.

 Bioinformatics and its Applications in Fort Lauderdale, Florida on
 December 16-19, 2004.  For details please contact

 Plant, Animal and Microbial Genome XIII, joint with the NAGRP annual
 meetings, Jan. 15-19, 2005, Town & Country Convention Center, San Diego,
 CA.  Please see for information.

Additional items can be found at:

           <>   <>   <>   <>   <>   <>   <>   <>   <>   <>   <>

Items for Pig Genome Update 68 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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