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Pig Genome Newsletter #107
From: "Rothschild, Max F [AN S]" <mfrothsc@iastate.edu>
To: angenmap@animalgenome.org
Subject: US Pig Genome Newsletter #107
Date: Fri, 01 Apr 2011 09:47:10 -0500
Pig Genome Update # 107:
- PDF version is available at
http://www.animalgenome.org/pigs/newsletter/pdf/No.107.pdf
- Web version is available at
http://www.animalgenome.org/pigs/newsletter/No.107.html
- Plain text version is appended below:
P I G G E N O M E U P D A T E
_________________________________________________________________
A Periodic Newsletter of the U.S. Pig Genome Coordination Program
************** No. 107 **************
* *
* April 1, 2011 *
***************************************
===========================================================================
1. Build 10 of the pig genome sequence continues to be refined
2. Progress in defining genetic resistance to PRRS continues
3. Registration and abstract submission are OPEN for the Swine in
Biomedical Research
4. The Immune Response Annotation Group (IRAG) continues to make progress
5. A data repository was set up by the NRSP-8 Bioinformatics Team
6. New publishing format for Pig Genome Update
7. Upcoming meetings (see:
===========================================================================
Build 10 of the pig genome sequence continues to be refined. The genome
assembly (Sus scrofa 10 / Sscrofa10), on which the analysis and
publication of a draft pig genome sequence will be based, has been
submitted to the public database at NCBI. The NCBI team have worked
together with Nizar Drou and Mario Caccamo to check the assembly. These
important QC checks are now essentially complete. Over the next few days
the assembly will be released through Genbank under the terms of the
Toronto agreement on pre-publication data sharing. The annotation of this
draft pig genome sequence can now be initiated (kindly provided by Alan
Archibald). Additionally in the last week, Martien Groenen discussed the
submission of companion papers of the pig genome paper to the BMC series
with Elizabeth Moylan, Biology Editor of BMC. BMC showed a clear interest
to actively work with the swine genome community to disseminate the
results to a broad audience and they will appoint a main internal contact
at BMC to keep track of all the companion papers. Upon submission, authors
should clearly flag their paper as a companion paper to the pig genome
paper (kind provided by Martien Groenen).
o o o o o o o o o o o
Progress in defining genetic resistance to porcine reproductive and
respiratory syndrome (PRRS) continues. The PRRS Host Genetics Consortium
(PHGC) is a national effort developed with input from PRRS researchers,
NC1037/NRSP8 genome researchers, members of the National Pork Board (NPB)
Swine Health and Animal Science Committees, veterinarians, AASV,
producers, and commercial partners representing breeders, animal health,
feed and diagnostic companies. The PHGC was funded first by NPB in
December 2007. It uses a nursery pig model to assess pig responses to
acute PRRSV infection and for the study of the relationship between host
genes and the resistance/susceptibility of pigs to primary PRRSV infection
and related growth effects. In the last 4 years the PHGC has tested the
responses of 8 groups of 200 commercial crossbred pigs to infection with
one PRRSV isolate using the BSL2 facilities at Kansas State Univ. Pigs
were followed for 42 days post infection (dpi) collecting blood serum
(virus, cytokines, antibodies) and Tempus (RNA) samples with weekly
recording of weights to derive weight gain. All samples are catalogued and
distributed to appropriate testing labs with data collected into a central
PHGC relational database, housed at Iowa State Univ. All pigs became PRRSV
infected with peak viremia from 4-21 dpi, although some have persistent
infections. There is limited correlation of viral load with weight gain.
Genomic DNA has been genotyped with the Porcine SNP60 SNPchip for genome
wide association studies now underway at Iowa State University. Gene
expression work is being led by Michigan State University and protein
expression work by BARC. It is expected that the PHGC will provide
producers and breeders with tools to identify pigs that are more
resilient, that resist PRRSV infection and continue to grow well. It
should provide animal health and vaccine companies with new targets to
develop improved therapeutics and vaccines. The PHGC is funded by the
NPB, USDA ARS, USDA NIFA PRRS CAP and functional genomic grants, Genome
Alberta, NRSP8 Swine Genome and Bioinformatics Coordination programs, and
private companies (kindly submitted by Joan Lunney, PHGC Coordinator, USDA
ARS BARC).
o o o o o o o o o o o
Registration and abstract submission are OPEN for the Swine in Biomedical
Research Conference 2011. It will take place from July 17th to 19th, at
the Chicago Mart Plaza Holiday Inn. If you are interested in learning
more about the utility of pigs as biomedical models, please plan to
attend. Go to http://www.dbs.illinois.edu/comparativegenomics/ for all
the details on the meeting and to www.conferences.illinois.edu/sbr for
registration and abstract submission. See you in Chicago.
o o o o o o o o o o o
The Immune Response Annotation Group (IRAG) which was formed soon after
the 2009 Pig Genome Workshop in Hinxton continues to make progress. The
purpose of IRAG is to annotate the pig genome sequence for genes and gene
families known to be involved in the immune system and its response to
pathogens. Our approach is to select a large list of genes and use gene
sequence data to find and manually annotate the genome and predicted
transcript structure of IR genes in regions predicted to contain these
genes. We are using software Otterlace in collaboration with Jane Loveland
and Jen Harrow at the Sanger Institute, and have provided annotations for
over one thousand loci thus far. We are also providing evidence for
changes in genome content (gene additions/loss) for immune response (IR)
genes in the pig, and reported early results at the ISAG meeting in
Edinburgh in 2010. To functionally validate these annotations, we are
using global transcriptomics data. We have two companion papers being
organized from our group; a paper on the IRAG gene list annotation and
functional verifications, and a second paper on a meta-analysis of the
porcine response to PRRS virus. If interested please contact Chris Tuggle
(ISU) or Claire Rogel-Gaillard (INRA-Jouy-en-Josas) (kindly provided by
Chris Tuggle).
o o o o o o o o o o o
A data repository was set up by the NRSP-8 Bioinformatics Team for the pig
genome research community to share data. It can be seen at
(http://www.animalgenome.org/repository/pig/).
Currently available data sets are the Illumina 60K SNP locations for build
10 contributed by Martien Groenen. The data repository is part of the
NAGRP Data File Sharing Tool, with which you can upload large files to
share, either privately with your collaborators, OR with a community you
designate. Please contact the Helpdesk for any problems or suggestions
using the tool (http://www.animalgenome.org/bioinfo/services/helpdesk.php).
o o o o o o o o o o o
New publishing format for Pig Genome Update. Starting January 1, 2011 the
Pig Genome Update are now published 4 times a year instead of 6. Your
input and ideas are always welcome. Please contribute.
o o o o o o o o o o o
Upcoming meetings (see:
http://www.animalgenome.org/pigs/community/meetings.html)
Advances in Reproductive Biology and Genetics Conference, University of
Missouri, May 16th and 17th, 2011, for more information see
http://muconf.missouri.edu/reproductivebiology/index.html
British Pig Breeders Roundtable 2011: 21-23 June 2011. For further details
and to register, please visit:
https://ktn.innovateuk.org/web/british-pig-breeders-round-table
American Society of Animal Science and American Dairy Science joint annual
meeting, July 10-14, 2011, New Orleans, Louisiana. For details please see
http://adsa.asas.org/meetings/2011/
Swine in Biomedical Research, July 17-19, 2011, Chicago IL, for details
contact Larry Schook at schook@uiuc.edu
Plant & Animal Genome Conference, PAG XX, Jan. 14-18, 2012, Town & Country
Hotel, San Diego, CA. Information available at http://www.intl-pag.org/ .
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Items for Pig Genome Update 108 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, NAGRP Director, National Animal Genome Research Program, NIFA
===========================================================================
U.S. PIG GENOME COORDINATION PROJECT
+-----------------------------------+
| Supported by USDA/NIFA NRSP-8 | Web: http://www.animalgenome.org/pig
| National Animal Genome Research | Mail: angenmap@animalgenome.org
| Program |
+-----------------------------------+--------------------------------------
