From: "Rothschild, Max F [AN S]" <mfrothsc@iastate.edu>
To: angenmap@animalgenome.org
Subject: US Pig Genome Newsletter #84
Date: Mon, 30 Apr 2007 09:10:55 -0500
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. 84 **************
* *
* <angenmap@animalgenome.org> *
* May 1, 2007 *
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1. The Swine Genome Sequencing Workshop was recently held in St. Croix
2. SNP chip under discussion
3. The new pig oligo arrays are here and can be ordered
4. The NC1004 rewrite was quite successful and the new project NC1037
has been approved for five years
5. PAG-XVI will be held January 12-16, 2008 at Town & Country, San Diego
6. The CSREES FY 2007 National Research Initiative request for proposals
7. CREATE-21 Draft Legislation
8. Upcoming meetings ( 8 items )
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The Swine Genome Sequencing Workshop was recently held in St. Croix.
The meeting was well attended and included specific issues of the
sequencing project, identifying approaches to ensure broad and rapid
utilization of the sequence information, developing educational
programs, and examining ways to find additional financial support.
In this regard there is concern that several million dollars still
needs to be raised to meet the goals of a finished sequence. Funding
sources include ARS which had previously contributed to the cattle
genome project and a number of other sources from other countries. A
full report of the recent meeting will be posted soon at
http://www.piggenome.org/newsletter.php .
o o o o o o o o o o o
SNP chip under discussion. One of the issues being discussed is the
need for a SNP chip in pigs. There has been some development in this
area and a "private" chip of about 7.5K SNPs is under manufacture by
Illumina for a group of European scientists. Max Rothschild and Gary
Rohrer and some of the European research group met with Illumina
personnel. We discussed the possibility of using these SNPs and
others to produce a 10K chip. Gary has agreed to head a committee to
work on this and the committee includes several other swine
researchers. Look for developments to be reported in the future.
o o o o o o o o o o o
The new pig oligo arrays are here and can be ordered. Thanks to
efforts of a number of groups and individuals we have developed a
novel 70-mer oligonucleotide microarray for profiling expression of
the pig (Sus scrofa) genome. The Swine Protein-Annotated
Oligonucleotide Microarray has been developed as an OPEN SOURCE
collaboration between investigators and institutions with an interest
in pig physiology. The sequences of the oligonucleotides, the
consensus sequences they represent, and the annotation of the
consensus sequences are provided at no cost to the entire research
community. New swine oligo arrays ordering can now be ordered
(http://www.pigoligoarray.org/ ). Please note ordering depends on the
source of your funding. Labs associated with agriculture (at US
Colleges or Universities, US government laboratories, or foreign
Universities or governments) please order using the "Arrays for USDA
NAGRP-8 supported activities" button. If you are a PRRS researcher
please order using the "Arrays for PRRS CAP supported activities"
button. Commercial concerns (domestic or foreign) or any biomedical
researchers (domestic or foreign) please order using the "Array for
Biomedical and Commercial Applications" resource button. Validation
of arrays will take place. Thanks to efforts of a number of the
swine genome community a validation experiment, funded in part by the
participants and the USDA Pig Genome Coordinator will take place over
the next few months. The plan is to report the information to the
community at the earliest possible date.
o o o o o o o o o o o
The NC1004 rewrite was quite successful and the new project NC1037 -
Genetic and Functional Genomic Approaches to Improve Production and
Quality of Pork has been approved for five years. The new project
rewrite was successful in large part due to the efforts of Chris
Tuggle and his committee that did the rewrite. North Carolina State
University will be hosting the last NC1004 annual meeting on Friday
June 22nd on the NCSU campus. The next day there will be an event
honoring the career of Dr. O.W. Robison. Details can be obtained by
emailing Joe Cassady at joe_cassady@ncsu.edu
o o o o o o o o o o o
PAG-XVI will be held January 12-16, 2008 at the usual spot, the Town
and Country Hotel, San Diego, CA. The NC-1008 Multistate Research
project committee and the Swine Subcommittee of the National Animal
Genome Research Program, NRSP-8, will meet concurrently. The NRSP-8
project needs to submit a renewal application this year. The NRSP-8
writing team will be coordinated by Mary Delany and include existing
coordinators or their representatives.
o o o o o o o o o o o
The CSREES FY 2007 National Research Initiative (competitive grant
program) request for proposals can be found at
http://www.csrees.usda.gov/funding/rfas/nri_rfa.html . The FY 2007
budget was finally passed as a continuing resolution, allocating $189
million to the NRI. FY 2007 NRI applications require electronic
submission through http://grants.gov/. The deadline for both Animal
Genome and Animal Growth & Nutrient Utilization programs is June 5,
2007. This year, the Animal Genome program will not offer Functional
Genomics grants (but expects to resume these in FY 2008). Applied
Animal Genomics, Tools & Resources and Bioinformatics grants will be
awarded this year. The President's proposed 2008 budget allocates
$257M to the NRI, but the increase would come at the expense of
deleting $157M in earmarked projects and grants, and Congress can be
expected to cut the NRI in order to save much of the earmarked
funding (kindly provided by Jerry Dodgson).
o o o o o o o o o o o
CREATE-21 Draft Legislation. Create-21 is a proposal by the National
Association of State Universities and Land Grant Colleges to increase
USDA's organizational flexibility and budgetary efficiency through
greater program integration, increased competitive grant funding and
enhanced stakeholder involvement as part of the 2007 Farm Bill
reauthorization. The CREATE-21 proposal has two "integral" elements:
(1) creation of a new "National Institute" through the consolidation
of agencies, programs, and activities currently within the USDA's
Research, Education, and Economics Mission Area (REE) and U.S. Forest
Service R&D; and (2) authorization of new funding to increase the
intramural capabilities of the Institute and its land-grant and
related university partners and to increase competitive research
programs to address critical food, agriculture, and natural resource
problems. Draft legislation has been proposed that encompasses all of
the provisions recommended by CREATE-21 Executive Summary:
www.create-21.org/documents/PDF/Print/A_Bold_Proposal.pdf (kindly
provided by jerry Dodgson and Jeff Armstrong).
o o o o o o o o o o o
Upcoming meetings (see:
http://www.animalgenome.org/pigs/community/meetings.html)
Symposium on Epistasis: Predicting Phenotypes and Evolutionary
Trajectories, May 31to June 3, 2007, at Iowa State University, Ames,
IA. For details please see
http://www.bb.iastate.edu/~gfst/PSIframeset.html
NC1004 meeting and O.W. Robison meeting at North Carolina State
University on June 22-23, 2007. For details please email Joe Cassady
at joe_cassady@ncsu.edu
American Society of Animal Science annual meetings in San Antonio,TX
on July 8-12. For details please see
http://adsa.psa.ampa.asas.org/meetings/2007/
3rd International Conference on Quantitative Genetics, August 18-24,
2007, Zheijiang University, Hangzhou, China. Conference Organizers:
Jun Zhu (jzhu@zju.edu.cn) and Zhao-Bang Zeng (zeng@stat.ncsu.edu)
Convergence of Genomics and the Land Grant Mission: Emerging Trends
in the Application of Genomics in Agricultural Research, September
10-12, 2007, Purdue U., West Lafayette, Indiana. Please see
www.entm.purdue.edu/conference/
International Symposium on Animal Genomics for Animal Health, October
23-25, 2007, OIE Headquarters, World Organization for Animal Health,
Paris, France. For information contact Cyril Gay,
cyril.gay@ars.usda.gov, or Marie-H�l�ne Pinard,
pinard@dga2.jouy.inra.fr
2nd GSA Model Organisms & Human Biology Meeting, Jan. 5-9, 2008, Town
& Country Convention Center, San Diego, CA. Please see
http://www.gsa- modelorganisms.org/
Plant and Animal Genome XVI, joint with NC-1008 and NAGRP annual
meetings, Jan. 12-16, 2008, Town & Country Convention Center, San
Diego, CA. See www.intl-pag.org/.
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Items for Pig Genome Update 85 can be sent to me by no later than June 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
http://www.animalgenome.org/pigs/
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.animalgenome.org/pig
| USDA/CSREES sponsored Pig Genome | Mail: angenmap@animalgenome.org
| Coordination Program |
+-----------------------------------+--------------------------------------