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Pig Genome Newsletter #090
From: "Rothschild, Max F [AN S]" <mfrothsc@iastate.edu>
To: angenmap@animalgenome.org
Subject: US Pig Genome Newsletter #90
Date: Wed, 30 Apr 2008 14:12:55 -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. 90 **************
* *
* <angenmap@animalgenome.org> *
* May 1, 2008 *
**************************************
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1. Pig genome sequencing progress continues to move along
2. Registration for the Pig Annotation Workshop July 16-18
3. Dense SNP chip development continues
4. USDA-NRI Grant RFA for FY 2008 is now available
5. Planning for PAG XVII, January 10-15, 2009, is already underway
6. The pig oligo arrays can be ordered
7. Upcoming meetings ( 5 items )
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Pig genome sequencing progress continues to move along. Recent progress is
shown on the graph (http://www.animalgenome.org/pigs/genomesequence/progres1.jpg)
A total of 13,296 clones have been selected and sent for sequencing. The
coverage is now 82.5% of the map. The total sequence now equals 1421 Mb of
which 60.1 Mb is finished quality from 8,999 sequenced clones with 4,741
clones at an improved status. Sequencing appears on schedule but it is clear
more funding is desired.
Registration for the Pig Annotation Workshop July 16-18 at the Wellcome
Trust Sanger Institute is needed. The Sanger institute is organizing an
annotation workshop to bring together researchers from the pig genome
community to participate in the manual annotation of the genome sequence.
The even is sponsored by EADGENE and SABRE. The resulting annotation
from the participants will be eventually displayed in the Ensemble browser.
The aim of the three day workshop is to teach participants how to use
annotation software so they can begin to annotate regions of interest to
them. The organizers will provide support during and after the workshop
to enable participants to work remotely to finish their annotation using
the experience gained at the workshop. Registration is free and there
are a number of grants available to pay for the cost of accommodations.
Registration is limited to 40 participants and the last day of
registration is May 31, 2008. For details see
http://www.sanger.ac.uk/Projects/S_scrofa/workshop_Hinxton08/index.shtml
o o o o o o o o o o o
Dense SNP chip development continues. International efforts to develop
the first large scale (50K) dense SNP chip continue. Several groups in
Europe and the US have been busy making libraries and doing sequencing to
produce SNPs. The overall plan is to attempt to get 30X coverage on about
10% of the genome and to produce about 1 Million SNPs. These will then be
tested using bioinformatics and other tools to come up with a set that are
wide spread across the genome and which work with the technology provider's
platform. The plan also is to have those with validated SNPs to deposit
them in dbSNP. The plan is for ALL SNPs to be deposited by June 1 to be
considered. Members of the consortium from the USDA (ARS, CSREES),
University of Illinois, Iowa State University and the National Pork Board
have met with two technology providers and discussed the technologies and
the possible costs to produce chips. It appears that Illumina will fit
the needs of the community best. To work with them it will be necessary
to have all the sequencing, validation, and bioinformatics completed by
August 22. In addition, all contracts for initial purchase will need to
be executed by August 22, 2008. All interested parties should prepare to
consider how much funding they have available. Cost per chip will depend
on numbers of chips contacted at the date the contract period ends. We
suspect that value could be in the $125 range if sufficient numbers are sold.
o o o o o o o o o o o
USDA-NRI Grant RFA for FY 2008 is now available at
http://www.csrees.usda.gov/ or http://www.grants.gov. Program 43.0, Animal
Genome, contains Translational Animal Genomics, Tools and Resources,
Bioinformatics, and Functional Genomics. The deadline for these is June 5,
2008. However, integrated proposals only for Translational Animal
Genomics and all proposals for Functional Genomics require submission of
a letter of intent by March 14, 2008. Please see the RFA for deadlines
for other animal-related programs. Letters of intent are required for
some programs/elements to insure that proposal aims meet the goals of
the program and to minimize wasted effort in the application process.
o o o o o o o o o o o
Planning for PAG XVII, January 10-15, 2009, is already underway. The new
chairs of the swine genome section are Melissa Ashwell and Cathy Ernst.
Ideas for speakers are gladly being taken by Max Rothschild or Hans Cheng
for plenary talks. Some reorganization of the species workshops on
Saturday and Sunday is likely to take place to avoid overlap and increase
attendance to the NRSP8 meetings. Stay tuned for developments.
o o o o o o o o o o o
The pig oligo arrays can be ordered. Swine oligo arrays can now be ordered
at (http://www.pigoligoarray.org/ ). A validation experiment, funded in
part by the participants and the USDA Pig Genome Coordinator, was reported
on at PAG 2008.
o o o o o o o o o o o
Upcoming meetings (see:
http://www.animalgenome.org/pigs/community/meetings.html)
NC-1037 Genetic and functional genomic approaches to improve
production and quality of pork May 14-15, USDA Beltsville, MD. For
information please contact Joan Lunney at Joan.Lunney@ARS.USDA.GOV
Pig Genome II, The Second European Conference on Pig, June 4-5, 2008
in Ljubljana, Slovenia. For details see http://www.piggenomeii.si/
ASAS 2008 Centennial meeting, July 7-11, 2008, Indianapolis, Indiana,
USA. See http://www.asas.org/100years/
XXXI conference of the International Society of Animal Genetics (ISAG)
July 20-24, 2008 Amsterdam, The Netherlands. See http://www.isag2008.nl
Kennedy Conference on Quantitative Genetics and Animal Breeding, August
11-12, 2008 Guelph, Ontario Canada. For details please contact Larry
Schaeffer at lrs@uoguelph.ca.
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Items for Pig Genome Update 91 can be sent to me by no later than June 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 |
+-----------------------------------+--------------------------------------
