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Pig Genome Newsletter #071
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. 71 **************
* *
* <angenmap@db.genome.iastate.edu> *
* March 1, 2005 *
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1. PAGXIII another success in sunny San Diego
2. The NSRP-8 Swine Sub-committee met at the PAG XIII
3. USDA sets plans for request for proposals for swine genome sequencing
4. Swine in Biomedical Research Conference held in Chicago
5. Interagency Working Group on Domestic Animal Genomics Report is available
6. A pig quantitative trait loci database (PigQTLdb) has been created
7. The 2005 NRI competitive grants program has been announced
8. A small number of pig oligo arrays remain to be printed and released
10. The 3rd International Symposium on Genetics of Animal Health
will convene on July 13-15, 2005
11. Upcoming meetings (3 items)
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PAGXIII another success in sunny San Diego. Great weather and over 2,000
attendees had excellent meetings again this year. Plenary speakers
including one Nobel laureate presented talks on a variety of subjects
including dog genomics and comparison of microarrays platforms. Over 800
posters and some fun evening meetings made for an excellent conference.
Suggestions for next year should be sent to mfrothsc@iastate.edu.
o o o o o o o o o o o
The NSRP-8 Swine Sub-committee met at the PAG XIII meetings on January 15,
2005 at the Town and Country Hotel, San Diego, CA. Joan Lunney, NSRP-8
Swine committee chair, welcomed everyone and then presided over the
session. The morning session included 4 invited speakers. Hirohide
Uenishi (huenishi@affrc.go.jp) Animal Genome Research Program, Natl. Inst.
Agrobiological Sciences, Tsukuba, Japan, spoke on "Swine Immunogenomics:
Resource Of Genomic Data And Its Application To Immunological Research In
Pigs." Randall S. Prather (PratherR@Missouri.Edu) University of Missouri-
Columbia (MU), Columbia, MO USA spoke on "Gene Expression During Pig
Embryogenesis as Determined by Using a Pig Reproductive Tissue-Specific
Microarray." Lucina Galina (Lucina.Galina@PIC.com) from Sygen
International, Franklin, KY USA spoke about "PathoCHIP - A genomics
approach to understanding Haemophilus parasuis infection." Scott
Fahrenkrug (fahre001@tc.umn.edu) from University of Minnesota, St. Paul MN
USA spoke on "Microarray Profiling for Quality Control of Porcine Islet
Isolation."
Dr. Fahrenkrug then led a discussion of plans of the joint NRSP8/NC1004
committee on future swine microarray options. A microarray sub-committee
(Scott Fahrenkrug, Chair, Joan Lunney, CoChair, Chris Elsik, and Cathy
Ernst; Jim Reecy, NRSP8 Bioinformatics Coordinator) was created. This
committee is developing the next array and will be moving forward quickly.
Larry Schook (schook@uiuc.edu) University of Illinois at Urbana-
Champaign, Illinois, provided an update on the swine genome sequencing
consortium's progress. Ronald D Green (rdg@ars.usda.gov), the USDA ARS,
National Program Leader for Animal Production, Beltsville, MD USA spoke
about the "USDA Animal Genomics Workshop." Margaret Dentine, NRSP8 Swine
Technical Committee Advisor explained the new process for project reviews.
NRSP8 received very favorable responses. Muquarrab Qureshi, USDA CSREES
National Program Leader, discussed performance based budgeting. He
mentioned program areas 303 and 304, discussed genome project updates and
the NRI budget increase. Max Rothschild (mfrothsc@iastate.edu) Swine
Genome Coordinator, and James Reecy, Bioinformatics Coordinator, gave
updates. NRSP8 Station Reports were presented by Joe Cassady (North
Carolina State University), Cathy Ernst (Michigan State University),
Max Rothschild and Chris Tuggle (Iowa State University), Gary Rohrer
(USDA ARS MARC), Joan Lunney (USDA ARS BARC), Zhihua Jiang (Washington
State University) and Craig Beattie (University of Nevada). At the
end there was a short NRSP8 swine business meeting. Zhihua Jiang was
elected Swine NRSP8 secretary for the next year. A discussion of whether
NC1006 and NRSP8 would hold a joint meeting in 2005/2006 was left for
Dr. Cassady, 2005 Chair for both groups, to poll members for their
preferences. (kindly provided in part by J. Lunney and J. Cassady)
o o o o o o o o o o o
USDA sets plans for request for proposals (RFP) for swine genome
sequencing. At the Swine Genome Sequencing Consortium meeting at PAG,
USDA Undersecretary Joseph Jen announced that the USDA will issue a RFP to
sequence the swine genome and will provide at least $10 million from the
USDA's competitive grants program. Dr. Anna Palmisano, CSREES, indicated
that the RFP will be issued within the next few months. Dr. Ronnie Green,
ARS, suggested that the ARS intended to provide at least an amount
equivalent to the ARS contribution to bovine ($1 million) and to possibly
provide as much as $2 million for the project. Sequencing could begin in
the fall. This support and all the hard work to get to this point are
appreciated. Page 2 Pig Genome Update 71
o o o o o o o o o o o
A large crowd of over 130 people interested in pig models attended Swine
in Biomedical Research Conference in Chicago on January 27-29. The
conference was hosted by University of Illinois and chaired by Larry
Schook. The outstanding presentations covered a historical perspective,
genomics, transgenesis and cloning in the pig. Examples of biomedical
models using the pig included: eye, obesity, cardiovascular, cancer,
bioengineering, skin and other significant research examples. Reports
form the meeting are expected out in the future and abstracts are
available from www.swinegenomics.com.
o o o o o o o o o o o
The Interagency Working Group on Domestic Animal Genomics report is now
available and can be obtained by clicking on "Coordination of Programs on
Domestic Animal Genomics" to obtain the PDF at
http://www.ostp.gov/nstc/html/recentnstcdocs.html (click on "Coordination
of Programs on Domestic Animal Genomics" to obtain the PDF). If you may
need a hard copy contact Muquarrab A. Qureshi, CSREES at
mqureshi@csrees.usda.gov
o o o o o o o o o o o
A pig quantitative trait loci (QTL) database (PigQTLdb) has been created
at the Iowa State University. The database and its peripheral tools were
made to compare, confirm and locate on pig chromosomes the most feasible
location for a candidate gene responsible for quantitative trait(s)
important to pig production. To date, 791 QTLs from 73 publications have
been curated into the database at http://www.animalgenome.org/QTLdb/ . The
database content has also been submitted to the NCBI Gene and Map Viewer
resources, where the information about markers are matched to marker
records in NCBI's UniSTS database. Support from NAGRP and NCBI have made
this possible.
o o o o o o o o o o o
The 2005 NRI competitive grants program has been announced
(www.reeusda.gov/nri/). Deadline dates are now May 17, 2005, for Animal
Growth and Nutrient Utilization; and June 15, 2005, for Animal Genomics,
Animal Genome Reagent & Tool Development and Functional Genomics of
Agriculturally Important Organisms. Total 2005 NRI funding remains was
set at $181M.
o o o o o o o o o o o
A small number of pig oligo arrays still remain to be printed and
released. . Some individuals have failed to request a shipping date and
need to do so. Cost is $20/slide plus shipping. Slide orders will be on
a first come first serve basis. Please immediately contact Max Rothschild
at mfrothsc@iastate.edu.
o o o o o o o o o o o
The 3rd International Symposium on Genetics of Animal Health (formerly,
Candidate Genes for Animal Health) will convene on July 13-15, 2005, in
Ames, Iowa, USA. The meeting will feature several invited speakers,
contributed presentations and poster sessions and should be an exciting
continuation of past meetings. Please note the dates on your calendar,
and bookmark the GAH2005 web home page:
http://www.ans.iastate.edu/GAH2005.html. More information will be follow!
o o o o o o o o o o o
Upcoming meetings (see:
http://www.genome.iastate.edu/community/meetings.html)
- The Biology of Genomes, May 11-15, 2005, Cold Spring Harbor Laboratory,
Cold Spring Harbor, NY. See
http://meetings.cshl.edu/meetings/genome05.shtml for more information.
- 3rd International Symposium on Genetics of Animal Health, July 13- 15,
2005, in Ames, Iowa, USA, Please see:
http://www.ans.iastate.edu/GAH2005.html
- Symposium on Integration of Structural and Functional Genomics (14th
Annual Growth Factor and Signal Transduction Conference), September 22-25,
2005, Iowa State University, Ames, Iowa. See
http://www.bb.iastate.edu/~gfst/homepg.html
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Items for Pig Genome Update 72 can be sent to me by no later than April 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
mfrothsc@iastate.edu
cc: Muquarrab Qureshi, CSREES and Caird Rexroad II, ARS
===========================================================================
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 | Mail: angenmap@db.genome.iastate.edu
| Coordination Program |
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