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Pig Genome Newsletter #080
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. 80 **************
* *
* <angenmap@animalgenome.org> *
* September 1, 2006 *
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1. The 8th World Congress on Genetics Applied to Livestock Production
was held in Belo Horizonte, Brazil
2. ISAG 2006 was held August 20-25 in Porto Seguro, Brazil
3. Pig Tales, the newsletter of the Swine Genome Sequencing Consortium
4. The Roslin Bioinformatics Group released the new ArkDB web interface
5. New swine oligo arrays will begin printing October 1
6. Upcoming meetings ( 3 items )
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The 8th World Congress on Genetics Applied to Livestock Production was held in
Belo Horizonte, MG, Brazil. The meeting was an outstanding success with over
1,000 attendees and some excellent plenary, invited and contributed posters. The
talks reflected considerable progress in QTL and gene discovery, examination of
eQTL and the integration of genes and markers into breeding programs across the
world. A large number of pig papers were presented and abstracts and short papers
are available from the organizers in the form of a CD of the proceedings.
ISAG 2006, the 30th International Conference on Animal Genetics, was held August
20-25, 2006 in Porto Seguro, Brazil and kicked off with plenary talks on
Biodiversity from Martin Weitzman, Olivier Hanotte and Fabricio Santos before
breaking into sessions from animal forensics to species specific topics.
Meetings were well attended and the despite the best efforts of Mother Nature to
soak several posters, causing them to be reprinted, the multidisciplinary poster
sessions were also well attended and proved to be very educational. Of special
interest was the Pig Gene Mapping and Applied Genetics session, chaired by Gary
Rohrer. In it Denis Milan gave the status of the current RH map that currently
has over 10,000 markers mapped by IMpRH users, with 5,000+ human-pig ortholog
data points. Hirohide Uenishi updated us on the progress of the 10,000 porcine
full-length cDNA sequences that will be deposited in September/October. From the
section on highlights of the posters, Oliver Couture presented his work on
improving the annotation of the porcine Affymetrix Gene Chip while other research
groups reported on QTL/candidate gene research on topics such as the vitality of
newborn pigs, reproduction traits, and disease resistance. No changes were made
to the organizing committee for this section. Another highlight was the Swine
Genome Sequencing Consortium meeting, chaired by Larry Schook. The group was
handed the inaugural issue of "Pig Tales," the newsletter for the Swine Genome
Sequencing Consortium (SGSC) (see later note below). It was emphasized that the
consortium is willing to push sequencing of important regions (with
justification) to the top of the list with the "Adopt a Gene, BAC or QTL"
concept. Please forward the successes from using the sequence generated from
this project so that it can be used in the First Fruits section to highlight the
usefulness of the pig sequence. The INRA group announced having 500,000 sequence
reads with 200,000 reads from both the Large White and Landrace breeds and
100,000 reads for Meishan. The Korean National Livestock Research Institute
reported the sequencing of 300,000 reads from a shotgun library which generated
~200 Mb of sequence. The Japanese research group, lead by Hirohide Uenishi,
reported on the 10,000 sequence reads of full length cDNA. The Sino-Danish group
commented on the million EST sequences which can be accessed through the
resources link on the SGSC webpage. Sean Humphray gave an overview of the
current status of the pig sequencing efforts at the Wellcome Trust Sanger
Institute. Current status of the sequencing efforts at Sanger can be found at
http://pre.ensembl.org/index.html. A total of 6,984 clones have been selected
for sequencing to date, which represents ~50% of the swine genome. A total of
1302 accessioned clones have generated 226.6 Mb of sequence. Sanger is using a
technique called "Pre finishing" to bridge the contigs of the clones. It was
also announced that automated annotation will not be used on a chromosome until
the entire chromosome has been sequenced (kindly provided by B. Mote).
o o o o o o o o o o o
Pig Tales, the official newsletter of the Swine Genome Sequencing Consortium
(SGSC) is now being published by Larry Schook and colleagues. This quarterly
newsletter will provide updates on the pig genome sequencing project and
communication of the application of the information to addressing agricultural
and animal health issues. It can be found at www.piggenome.org . The website
also provides access to all of the newsletters and permits direct communication
with the Project Directors. There is also an opportunity for users to share
their successes, request specific sequencing to enter the pipeline and to become
a SGSC member.
o o o o o o o o o o o
The Roslin Bioinformatics Group is pleased to announce that the new ArkDB web
interface is now available for general use. The site can be found at
http://www.thearkdb.org/. Underneath the hood, the system has been completely
re-designed with a new database schema running in postgres and a modern
object-oriented interface written in java. They have focused the initial release
of the web interface on a chromosome-centric view which mimics the genome
sequence browsers to some extent. One of the major changes has been in the
map-drawing code. This is now delivered as a java applet - thus you will need a
java-enabled web browser to be able to view the maps. The benefit of this is that
they can build more interactivity into the maps. For example, one can now drag
maps around within the display and position them where you like. It is hoped
that this new version of the system useful. A series of staged additions to the
code are planned for the next few months and they will be announced as they
become available. Feature requests and bug reports can be sent to the
info@thearkdb.org address (provided by Andy Law).
o o o o o o o o o o o
New swine oligo arrays will begin printing October 1. Work continues to get the
materials ready for ordering and printing the arrays and despite some setbacks
they are nearing reality. Details will be provided about October 1 for ordering
and printing. Each investigator can order up to 300 slides for their project and
cost will be about 30 dollars per slide. A revised web page at
http://www.animalgenome.org/pigs/resources/array_request.html will provide
details about October 1.
o o o o o o o o o o o
Upcoming meetings (see: http://www.animalgenome.org/pigs/community/meetings.html)
24th Stadler Genetics Symposium, "Genomics of Disease." October 2-4, 2006.
University of Missouri, Columbia, MO. Please see
http://muconf.missouri.edu/stadler/
Plant and Animal Genome XV, joint with NC-1008 and NAGRP annual meetings,
Jan. 13-17, 2007, Town & Country Convention Center, San Diego, CA. See
www.intl-pag.org/.
Chicken Development and Genomics, April 12-15, 2007, Barcelona, Spain. See
www.lists.bbsrc.ac.uk/mailman/listinfo/chicken-genome
<> <> <> <> <> <> <> <> <> <> <>
Items for Pig Genome Update 81 can be sent to me by no later than October 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 |
+-----------------------------------+--------------------------------------
