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Pig Genome Newsletter #072
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. 72 **************
* *
* <angenmap@db.genome.iastate.edu> *
* May 1, 2005 *
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1. Pig genome sequencing is moving forward
2. Swine Oligo Array Committee makes progress
3. The 2005 NRI competitive grants program has been announced
4. Have you tried the pig quantitative trait loci (QTL) database
5. The 3rd International Symposium on Genetics of Animal Health
will convene on July 13-15, 2005, in Ames, Iowa, USA
6. Upcoming meetings (9 items)
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Pig genome sequencing is moving forward. Thanks go to the USDA's
Cooperative State Research, Extension, and Education Service (CSREES) who
issued a request for applications (RFA) to sequence the swine genome. In
January, Dr. Joseph Jen, Undersecretary for Research, Education, and
Economics and Dr. Anna Palmisano, Director of Competitive Programs,
announced their intention to issue the RFA at a meeting of the
International Swine Genome Sequencing Consortium (SGSC) that was held
during the Plant and Animal Genome XIII Conference. Department officials
have indicated that they expect a highly competitive, peer-reviewed
process. The $10 million included in the CSREES RFA is not necessarily
the bottom line of the USDA's commitment. The Agricultural Research
Service of the USDA has indicated that they would provide an additional
$1-2 million for the project. The Alliance for Animal Genome Research,
the nonprofit organization that has led the fundraising efforts, praised
USDA for outstanding leadership in getting the project underway. The USDA
announcement was made possible because of the significant research
collaborations of members of the international Swine Genome Sequencing
Consortium. Many members of the SGSC have contributed to the development
of the resources that will serve as the basis for sequencing the swine
genome. This new USDA program will not be the only source of funding for
the project. Through the SGSC, the ARS-USDA, the Institute for Pig
Genetics of the Netherlands, the INRA of France, Iowa Pork Producers
Association, Iowa State University, the National Livestock Research
Institute of Korea, the National Research Initiative (NRI) of CSREES-USDA,
the National Pork Board, North Carolina Pork Board, North Carolina State
University, the Roslin Institute, the Sino-Danish Consortium, University
of Illinois, and the Wellcome Trust Sanger Institute have contributed
already or have pledged significant support to the swine genome sequencing
project. Information regarding the CSREES RFA can be found
http://www.csrees.usda.gov/fo/porcinegenomesequencingnri.html.
o o o o o o o o o o o
Swine Oligo Array Committee makes progress. The swine NRSP8 genome
committee has started planning the next generation of swine long-oligo
arrays. The Swine Oligo Array committee includes: Scott Fahrenkrug, UMN,
Chair; Joan Lunney, USDA BARC, CoChair; Cathy Ernst, MSU; Chris Elsik,
TAMU; Jim Reecy, IA State, NRSP8 Bioinformatics Chair; Max Rothschild, IA
State, Swine Genome Coordinator, and Joe Cassady, NCSU, Swine NRSP8 Chair.
The swine group will develop the non-redundant sets of sequences on which
to base oligo design, and expects that a set of ~20,000 long oligos to be
produced. To decrease costs the swine group is coordinating efforts with
members of the bovine oligo planning group. Committee conference calls
were held on Feb. 9, Mar. 9, and Apr. 18. For swine sequences to be
included in cluster analyses the Genbank submission deadline was 2/20/05
as affirmed by several Angenmap announcements. Approximately 50,000 new
pig sequences were submitted in 2005. Cluster analyses, that will feed
into the oligo design, are being performed at Chris Elsik's lab at Texas
A&M. Sequence quality assessment has been completed. She expects cluster
analyses to develop the ~20-25,000 non-redundant sets of target sequences
to be completed by early May, 2005. Negative control oligos could include
use of Arabidopsis or Methanococcus (Archaea) gene sequences with no clear
orthology to swine. Alternately random sequence controls could be used but
there have been problems with this approach for the current array control
oligos due in part to the lack of a swine genome sequence. It is unclear
which positive pig sequences to use because of different tissue expression
levels, even for "control genes." An alternate being considered is to use
a spike control, and related oligos, as an index of stringency of
hybridization. The need for post synthesis, amino modification has been
discussed, although all vendors feel that non-modified oligos give great
results on either epoxy or amino silane slides, best results can be
achieved with modified oligos imprinted on epoxy slides. We are
considering no modifications given problems with their
long-term stability and cost (potentially adding >$120,000 to the cost of
$40K per set). Scott Fahrenkrug and Jerry Taylor, UMO, are working with
companies to get competitive bids on oligo production for both swine and
cattle. The Swine Genome Coordinator has set aside funds, $40-45,000, for
this next set of oligos. Each set is expected to contain 10 x 200 pm
aliquots of all oligos; ~1000 slides can likely be printed with 200 pm,
thus yielding up to 10,000 chips for the NRSP8 community. Interest has
been clearly stated by two other groups for purchasing oligo sets. Bids
will be compared for 1) programs for oligo design from the non-redundant
sets of sequences provided; 2) quality assurance for oligo synthesis; 3)
availability of oligo annotation for the user community, as per MIAME
conventions. NRSP8 funds will be used to buy the sets of oligos for the
NRSP8 swine genome community. Each lab will have to pay for slide
printing, bids will be requested later for reduced cost NRSP8 printing
(kindly submitted by Joan Lunney, USDA BARC).
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
Have you tried the pig quantitative trait loci (QTL) database (PigQTLdb)
that was created at 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/ and new data are continually being
added to it. 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 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 see GAH2005 web home page:
http://www.ans.iastate.edu/GAH2005.html.
o o o o o o o o o o o
Upcoming meetings (see:
http://www.genome.iastate.edu/community/meetings.html)
54th Annual National Breeders Roundtable, May 5-6, 2005, Airport Marriott
Hotel, St. Louis, MO. For more info., contact, Larry Brown at
LBrown@poultryegg.org; Tel - (770) 493-9401, or George Ansah, Tel: (607)
257-6591; george.ansah@isapoultry.com
Chicken Genomics and Development Meeting, May 8-11, 2005. Cold Spring
Harbor Laboratory, Cold Spring Harbor, NY. See
http://meetings.cshl.edu/meetings/chick05.shtml for further information.
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.
1st International Cytogenetics and Genome Society Congress, June 14-18,
2005, University of Granada, Granada, Spain. See www.icgs-congress.org
14th Colloquium on Animal Cytogenetics and Gene Mapping, July 3-7, 2005,
Puerto Vallarta, Mexico. See http://www.cucba.udg.mx/14thnacacgm/
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
2005 UC Davis Transgenic Animal Conference, Aug. 14-18, 2005, Granlibakken
Conference Center, Tahoe City, CA. See
http://conferences.ucdavis.edu/TGAC
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
Plant and Animal Genome XIV, joint with the NAGRP annual meetings, Jan.
14-18, 2006, Town & Country Convention Center, San Diego, CA. See
www.intl-pag.org/.
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Items for Pig Genome Update 73 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
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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 | Mail: angenmap@db.genome.iastate.edu
| Coordination Program |
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