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Pig Genome Newsletter #077
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. 77 **************
* *
* <angenmap@animalgenome.org> *
* March 1, 2006 *
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1. The PAG XIV and the swine genetics and genome committee meetings
2. Awarding of the $10 million USDA grant for sequencing the pig genome
3. Other activities at PAGXIV were quite varied
4. Pig Genome I was held at Lodi Italy
5. USDA CSREES FY 2006 National Research Initiative information
6. Upcoming meetings ( 8 items )
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The PAG XIV meeting and the swine genetics and genome committee meetings
again were held in sunny San Diego. Despite the cooler than normal
weather the meetings were well attended. Saturday the joint NRSP8 and
NC1004 committees met with over 75 people attending the invited talks
which highlighted reports from younger scientists. Mr. Tsai (NC State)
examined epigenetics involving porcine clones based on gene expression
profiling using Affymetrix Porcine, Affymetrix Human, and spotted glass
oligonucleotide microarray platforms. Their work revealed a number of
differentially expressed known imprinted genes among their clones. Dr.
Wang (Iowa State) presented their work on the host transcriptional
response to infection with S. enterica serotype Choleraesuis (SC) and
Typhimurium (ST) in pigs. Mr. Ramos (Iowa State) reported fine mapping of
QTLs for meat quality on SSC17. A contig of ~7.1 Mb was assembled and
used for developing high density markers for narrowing down the QTL
intervals. Dr. Grapes (Monsanto Choice Genetics) reported a construction
of an ultra high-density linkage map in pigs with a total of 6,000 single
nucleotide polymorphisms (SNP) and microsatellite (SSR) markers. Dr.
Damgaard (Danish institute for Ag Sci) showed how to use survival models
to infer phenotypic and genetic aspects of longevity in sows. Dr. Hu
(Iowa State) presented their continued research on the Pig QTL Database
(PigQTLdb) that include its new data collection/curation/editing/release
functions, alignment of QTL maps to pig RH maps, pig BAC FPC maps, human
maps, and tools for pig trait ontology management. Ms. Demars (INRA)
reported new micro rearrangements between the porcine and human genomes in
the region surrounding the MHC that contains QTL influencing many traits.
Administrative reports by Dr. Hamernik, Dr. Qureshi, and Dr. Stromberg
covered budget items and reports due. The swine genome coordinator
discussed resources and materials available to the swine genome community.
These were then followed by station reports from several stations on QTL
and expression research. The efforts of the two chairs, Joe Cassidy and
Zhihua Jiang in organizing this very good program are much appreciated.
o o o o o o o o o o o
Awarding of the $10 million USDA grant for sequencing the pig genome took
center stage on Sunday at the International Swine Genome Consortium
workshop organized by Larry Schook. Several speakers including Larry
Schook, Jon Beaver (University of Illinois), Jane Rogers, Sean Humphray
(Wellcome Trust Sanger Institute), Craig Beattie (University of
Nevada-Reno), Patrick Chardon (INRA), Gary Rohrer (USDA-MARC), Max
Rothschild (Iowa State) and Kellye Eversole, (Alliance for Animal Genome
Research) presented the plans for sequencing, SNP detection, map results
and plans for informing the public and acquiring additional funds for
future research. Undersecretary Dr. Joseph Jen announced the grant being
awarded to the University of Illinois and their collaborators from US and
foreign labs. Sequencing has already begun and updates can be seen daily
at http://www.animalgenome.org/pigs/genomesequence/ . These updates are
provided as part of the Bioinformatic Coordinator's team effort. Other
information about the sequencing can be seen at that page and web pages at
the Sanger Institute and the University of Illinois.
o o o o o o o o o o o
Other activities at PAGXIV were quite varied. The main PAG-XIV meeting
opened with a plenary talk from Ari Patrinos, head of the Office of
Biological and Environmental Research at the Department of Energy's Office
of Science and a key player in the human genome project. A recurring
theme of the plenary talks was higher order systems biology and
integration of genomic information with other data pipelines. Among the
highlights were talks by Ariel Darvasi (mouse QTL searches), Bernhard
Palsson (multidimensional genome annotation/prokaryotic genome evolution),
and Rob Martienssen (RNAi/heterochromatin silencing). In addition to
plenary talks and industry workshops, a poster session with nearly 1000
posters was held. There will likely be several changes to improve the
meeting next year. In order to meet the ever-growing demand for workshop
space, plenary lectures will be reduced to two each on Tuesday and
Wednesday, with an earlier start (8 a.m.), and workshops will be added
between 10 a.m. and lunchtime. A single keynote/plenary speaker will be
added to the program after the opening reception/poster session on Sunday
night. Anyone with suggestions about PAG-XV speakers or other aspects of
PAG should contact PAG animal reps, including Hans Cheng, Max Rothschild,
Claire Gill, Mary Delany, Michel Georges and Jim Reecy.
o o o o o o o o o o o
Pig Genome I was held at Lodi Italy. The meeting was attended by over
130 people and brought together primarily individuals from the European
team working on the pig genome. Invited talks, presentations and posters
provided for a very stimulating meeting and the organizers and hosts
should be thanked for an outstanding meeting. While Pig Genome II has yet
to be planned it is likely there will be follow-up meetings.
o o o o o o o o o o o
USDA CSREES FY 2006 National Research Initiative (competitive grant
program) information can be found at
http://www.csrees.usda.gov/fo/fundview.cfm?fonum=3D1112 . Total FY 2006
NRI funding was estimated at $183M, but this will likely be reduced by
across the board cuts of 1% (to end up at about the same level as last
year). Note that there are some changes in the FY2006 NRI. The Program
43.0, Animal Genome, has been divided into Applied Animal Genomics, Tools
and Reagents, Bioinformatics, and Functional Genomics. (Functional
Genomics will appear on alternate years beginning in FY 2006.) The due
date for all is June 15, 2006. As mentioned in the last issue and
discussed again at PAG-XIV, CSREES officials are concerned about the low
overall NRI success rate (14 of 73 proposals funded in the 2005 Animal
Genome Program or 19%). Efforts (sometimes controversial) have been made
to focus the NRI RFA to reduce the effort going into preparing and
reviewing unsuccessful proposals. However, we all agree that, absent a
significant increase in Federal and other sources of financial support for
agricultural research, the scientific community will have little choice
but to compete as best they can for all those funds that remain available.
Most of us also agree that a fair and open competition, followed by
rigorous peer review and careful allocation of resources, is the best way
to ensure the future of animal genomics and agricultural research, in
general. A report provided by CSREESs Peter Burfening at PAG-XIV showed
that, over the last 7 years, the success rate by species emphasis area has
been remarkably close to the overall average of 23% for all species for
which enough applications were submitted to be statistically meaningful
(kindly provided by Jerry Dodgson)
o o o o o o o o o o o
Upcoming meetings (see:
http://www.animalgenome.org/pigs/community/meetings.html)
Pig Breeders Roundtable, March 29-31 in Wye, Kent, England. For details
please contact chris.haley@bbsrc.ac.uk
Workshop on Chicken Genomics & Development, May 7-10, 2006, Cold Spring
Harbor Laboratory, Cold Spring Harbor, NY. See
http://meetings.cshl.edu/meetings/chick06.shtml
The Biology of Genomes, May 10-14, 2006, Cold Spring Harbor Laboratory,
Cold Spring Harbor, NY. See
http://meetings.cshl.edu/meetings/genome06.shtml
2nd International Symposium on Animal Functional Genomics, May 16-19,
2006, Henry Center, Michigan State U., East Lansing, MI. See
http://www.isafg.msu.edu
17th European Colloquium on Animal Cytogenetics and Gene Mapping, June
18-21, 2006, Lisbon, Portugal. See http://www.realvitur.pt/17_ecacgm.php
The 8th World Congress on Genetics Applied to Livestock ProductionBelo
Horizonte, MG, Brazil, August 13- 18, 2006. For information please
contact Fernando E. Madalena at iprociencia@terra.com.br
ISAG 2006, 30th International Conference on Animal Genetics, August 20-25,
2006, Porto Seguro - Brazil. See http://www.cbra.org.br/eventos/XXXisag.do
24th Stadler Genetics Symposium, "Genomics of Disease." October 2-4, 2006.
University of Missouri, Columbia, MO. Please see
http://muconf.missouri.edu/stadler/
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Items for Pig Genome Update 78 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.animalgenome.org/pig
| USDA/CSREES sponsored Pig Genome | Mail: angenmap@animalgenome.org
| Coordination Program |
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