Copy Link
Add to Bookmark
Report
Pig Genome Newsletter #059
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. 59 **************
* *
* <angenmap@db.genome.iastate.edu> *
* March 1, 2003 *
**************************************
===========================================================================
1. Nearly 2000 People Attended PAG-XI in Sunny San Diego
2. The NRSP8 Pig Committee Met Before the PAG-XI Meeting
3. Several Other Workshops at PAG-XI were of Special Interest
4. The Gordon Conference was Again a Success in California
5. Pig Array Planning Moves Ahead
6. Upcoming Meetings (5 Items)
===========================================================================
Nearly 2000 people came to sunny San Diego to attend PAGXI. As in past
years, this year's meeting was another big success. The meetings starred
off with the usual large number of workshops (see below for swine report)
and were followed by some excellent plenary talks, workshops and posters.
For the first time, PAG had a Nobel Laureate speak and the talk was quite
stimulating as well as entertaining. Dr. Sydney Brenner articulated his
thoughts on "The Way Ahead" by emphasizing his theme that biology should
address the organisms of interest and suggested that model organism work
should now be limited. Dr. Sue DeNise of MMI Genomics described their
advanced system of SNP detection and their plans for application to bovine
genome mapping and association studies. A number of other talks were also
quite good. Among them the talk by Lisa Stubbs of Lawrence Livermore
National Lab which was excellent and described comparative sequence
analysis of human chromosome 19 genes in mammals and in the chicken. The
meeting also featured workshops on database development for the animal
genomes, methods to do expression studies and other cutting edge
techniques. Combined with the excellent weather, it was a superb meeting.
Next year's PAG-XII will be held January 10-14, 2004 again in San Diego at
the same location. Plenary speakers will begin to be invited soon. If you
have speaker suggestions or other comments, please contact one of the
organizing committee representatives (Abel Ponce de Leon, apl@umn.edu;
Cathy Ernst, ernstc@msu.edu; Bhanu Chowdhary, bchowdhary@cvm.tamu.edu;
Noelle Cockett, fanoelle@cc.usu.edu; or Martien Groenen,
martien.groenen@alg.vf.wau.nl).
o o o o o o o o o o o
The NRSP8 Pig Committee met the Saturday before the PAG XI meeting and it
was very well attended. A total of nearly 90 people came and listened to
the invited talks by Michel Georges, University of Liege on "Molecular
dissection of an imprinted QTL on SSC2 with major effect on muscle mass"
and Alex Caetano, Embrapa Recursos Geneticos e Biotecnologia Brasil, on
"Using cDNA microarrays to study ovarian follicle development in pigs
selected for increased ovulation rate". Both talks highlighted recent
research on mutation discovery and gene expression research. These
speakers were followed by Alan Archibald, Roslin Institute, who presented a
"Bioinformatics update" that was useful, and some very interesting work by
Joan Lunney, USDA/ARS, on the "Use of Real-time assays of immune gene
expression to assess genetic basis of disease resistance". After these
talks we had updates from the US participants in the NRSP8 project
including reporting from Indiana (Diane Moody), Iowa (Max Rothschild, Chris
Tuggle), Michigan (Cathy Ernst), Minnesota (Lee Alexander, Mike Murtaugh),
Nebraska (Daniel Pomp), Nevada (Craig Beattie), USDA/ARS BARC (Joan
Lunney), USDA/ARS MARC (Gary Rohrer), and Washington (Zhihua Jiang). NRSP8
reports and the Pig Genome Coordinator's report can be found at
http://www.genome.iastate.edu/community/NRSP8/2002_index.html. Also
included is the update from the US Pig Genome Coordinator. The meeting
then discussed at great length the different ideas related to developing a
NRSP8 sponsored array. After the discussion, Max Rothschild asked a
committee of Chris Tuggle, Daniel Pomp (co-chairs), Mike Murtaugh, Diane
Moody and Cathy Ernst. They were to review information and offer a
recommendation by mid February. Dr. Tom Rathje, Danbred North America, was
introduced as the official industry representative to the NRSP-8 Swine
Species Genome Committee. The business meeting included an update from Deb
Hamernik, CSREES. She informed us that the USDA is operating on a
continuing resolution. The draft FY 2004 budget will soon be sent to
Congress but they have yet to pass a FY 2003 budget. Prospects for
increased grant funding are now bleak, and the best that could be hoped for
is funding similar to FY 2003 as was the case in 2002. The business
meeting concluded with Diane Moody elected as chair and Joan Lunney elected
as secretary for the following year.
o o o o o o o o o o o
Several other workshops were of special interest. At the Domestic Animal
Genome Sequencing Workshop (January 13) porcine genome sequencing was
discussed as were other species. We were informed that the recently
written white paper received a "high priority ranking." Thanks goes to the
efforts of many people, including the authors and strong support from our
colleagues abroad in Denmark, China, Scotland and France and the solid
support from industry personnel from many companies and organizations.
Efforts now remain to help find funding for this worthwhile effort. The
Animal Comparative Mapping Workshop (January 14) focused on bioinformatics
needs. Dave Adelson summarized the results of the recent USDA Stakeholder
Electronic Workshop on Animal Bioinformatics, organized by Deb Hamernik of
USDA-CSREES. A summary and recommendations report based on that workshop
and the discussion at PAG-XI will be published shortly.
o o o o o o o o o o o
The Gordon Conference was again a success in not so sunny California.
Thanks to an excellent mix of quantitative, molecular and evolutionary
geneticists, the most recent GRC meeting lived up to its usual high
standards. This year's meeting featured many early career scientists and
the discussions were lively and useful. Among the speakers were Clare
Williams (tree genetics), Walter Fontana (RNA folding), Laura Almasy (SNPs
for disease risk), Jaya Satagopa (two stage genome scans), Dan Gianola
(Bayesian estimation), Sally Otto (distribution of QTL effects), Sara Knott
(multi-trait QTL analysis), Christiana Kendzorski and Kathleen Kerr
(microarray analysis), Bill Muir (risk assessment and transgenics), Sue
Denise (SNP associations maps in cattle) and John Quackenbush (using
bioinformatics). A special thanks goes to the chair Bruce Walsh and
co-chair Rebecca Doerge.
o o o o o o o o o o o
Pig array planning moves ahead. Thanks to the activities of a committee
from NRSP (Chris Tuggle, Daniel Pomp (co-chairs), Mike Murtaugh, Diane
Moody and Cathy Ernst) real progress is being made on the development of
pig arrays. The committee tackled the challenge of choosing cDNA arrays
versus oligos and has been comparing vendors. At this point the
recommendations have been to make an array with 10,000 70-mer oligos. The
plan will be to use Pig Genome Coordinator funds (about $40,000) to buy the
oligos and pay for printing between 400-500 slides for the community. Once
the vendor is chosen then more details about timing and availability will
be made public. We owe a big thank you to all that have helped offer
opinions and help, especially the committee for their good work.
o o o o o o o o o o o
Upcoming meetings (see:
http://www.genome.iastate.edu/community/meetings.html)
International Symposium on Animal Functional Genomics, May 9-11, 2003,
Kellogg Center, Michigan State University, East Lansing, MI. Email
rosag@msu.edu for more information.
The John M. Airy Beef Cattle Symposium 2003: Visions for Genetics and
Breeding May 15-17, 2003 in Des Moines, Iowa will be hosted by Iowa
State University. For more information contact James Reecy at
jreecy@iastate.edu.
13th North American Colloquium on Animal Cytogenetics and Gene Mapping,
Louisville Zoo, Louisville, KY, July 13-17, 2003. For more information
please see http://www.uky.edu/Ag/VetScience/NACACGM/ or contact Teri
Lear at equigene@uky.edu.
Plant, Animal and Microbial Genome XII, joint with the NAGRP annual
meetings, Jan. 10-14, 2004, Town & Country Convention Center, San Diego,
CA. Please see http://www.intl-pag.org/ for more information.
ISAG 2004, 29th International Conference on Animal Genetics, Sept. 11-16,
2004, Surugadai Campus, Meiji University, Tokyo, JAPAN. For more
information see http://www2.kobe-u.ac.jp/~isag2004/
Additional items can be found at:
http://www.agbiotechnet.com/calendar/index.asp.
<> <> <> <> <> <> <> <> <> <> <>
Items for Pig Genome Update 60 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: Deb Hamernik, 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 | Mailing list:
| Coordination Program | angenmap@db.genome.iastate.edu
+-----------------------------------+
============================================================================
