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Pig Genome Newsletter #085
From: "Rothschild, Max F [AN S]" <mfrothsc@iastate.edu>
To: angenmap@animalgenome.org
Subject: US Pig Genome Newsletter #85
Date: Sun, 08 Jul 2007 22:04:38 -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. 85 **************
* *
* <angenmap@animalgenome.org> *
* July 1, 2007 *
**************************************
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1. The Biology of Genomes Meeting was held at Cold Spring Harbor May 8-12
2. The Symposium on Epistasis held May 31 to June 3 at Iowa State Univ.
3. The CSREES-USDA NC-1004 meeting was held June 22-23 at North Carolina
State University
4. The Swine Genome Sequencing Workshop was recently held in St. Croix
5. SNP chip under discussion
6. Improvements to the Animal QTLdb have recently been made
7. The new pig oligo arrays are here and can be ordered
8. Upcoming meetings ( 6 items )
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The Biology of Genomes Meeting was held at Cold Spring Harbor May 8-12th to
present and discuss recent findings in the area of genome analysis. Numerous
new approaches to genomic studies are showing us that DNA still contains a
lot of surprises. For example, the diversity of organisms that live in the
oceans and in our own mouths is absolutely amazing. There are thousands if
not millions of new genes to be discovered. Several talks focused on whole
genome analysis studies designed to elucidate genes involved in human
diseases. Furthermore, with the advent of new high-throughput genome
sequencing technologies, new avenues for genome analysis will come on-line
shortly. However, these new technologies present new challenges with respect
to data handling and mining. Some so called "junk DNA" may be just that.
Surprisingly, when 2 megabases DNA that is highly conserved across species,
but lacks known genes, was deleted from the mouse no phenotype was observed.
This raises the question were the wrong phenotypes measured or is this
conserved DNA actually an artifact? Next years meeting will be held in early
May. (kindly provided by J. Reecy)
o o o o o o o o o o o
The Symposium on Epistasis: Predicting Phenotypes and Evolutionary
Trajectories was held, May 31 to June 3, 2007, at Iowa State University,
Ames, IA. The meeting was extremely interesting in that it brought together
two groups, evolutionists, and plant and animal breeders to discuss
epistasis. While no consensus was reached on the best way to estimate and use
such effects the discussions were lively and useful.
o o o o o o o o o o o
The final meeting of the CSREES-USDA multistate project NC-1004 on Genetic
and Functional Genomic Approaches to Improve Production and Quality of Pork
was held June 22 and 23 at North Carolina State University. Research stations
in attendance presented results on ongoing research and discussed plans and
opportunities to collaborate under the new 5-year multistate project NC-1037,
which was recently approved. The NC-1037 project carries the same title as
NC-1004 and will have a substantial focus on genetic aspects of health.
Details can be found at http://nimss.umd.edu/homepages/home.cfm?trackID=8917
. The meeting was followed in the afternoon of June 23 by a symposium in
honor of Dr. O.W. Robinson, with presentations by several of his former
students. Dr. Robinson recently retired and has made many contributions to
swine genetics during his career (kindly provided by J. Dekkers).
o o o o o o o o o o o
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. 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. Gary Rohrer has agreed to head a committee of
interested researchers to work on developing a 10K chip and a group of
scientists led by the University of Illinois put in a proposal for a 50K chip
to be funded in part by USDA. Look for developments to be reported in the
future.
o o o o o o o o o o o
Improvements to the Animal QTLdb have recently been made by the
Bioinformatics Coordinator and his team. New data including mapping of Affy
array elements to QTL maps for pigs and cattle and SNPs stored in Genbank to
the respective chicken, pigs and cattle QTL maps have been added to the QTLdb
(http://www.animalgenome.org/QTLdb). If they is any additional
information that you would like added, please contact James Reecy at
jreecy@iastate.eduus.
o o o o o o o o o o o
The new pig oligo arrays are here and can be ordered. New swine oligo arrays
can now be ordered (http://www.pigoligoarray.org/ ). Validation of arrays is
taking place. Thanks to efforts of a number of the swine genome community
members, 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
Upcoming meetings (see:
http://www.animalgenome.org/pigs/community/meetings.html)
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
http://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-Héne
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
http://www.intl-pag.org/.
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Items for Pig Genome Update 86 can be sent to me by no later than August 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 |
+-----------------------------------+--------------------------------------
