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Pig Genome Newsletter #113
From: "Rothschild, Max F [AN S]" <mfrothsc@iastate.edu>
To: angenmap@animalgenome.org
Subject: US Pig Genome Newsletter #113
Date: Mon, 01 Oct 2012 10:57:15 -0500
Pig Genome Update # 113:
- PDF version is available at
http://www.animalgenome.org/pig/newsletter/pdf/No.113.pdf
- Web version is available at
http://www.animalgenome.org/pig/newsletter/No.113.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. 113 **************
* *
* October 1, 2012 *
***************************************
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1. Funds available for genome community
2. The Animal QTLdb included 633 new pig QTL in its recent #18 release
3. A new custom low density chip is now available for imputation work
4. The PAG XXI and NRSP8 Swine Genome meetings are around the corner
5. USDA National Institute of Food and Agriculture (NIFA) has delayed the
estimated release date for the RFAs
6. A big thanks and best wishes go out to Dr. Qureshi on his promotion
7. The swine genome coordinator is always glad to hear from NRSP-8 members
8. The sequencing and assemblies of genomes are often international
collaborative efforts that conclude upon publication of a reference
sequence
9. Upcoming meetings ( 6 items )
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Funds available for genome community. Funds are available from now until
August 1, 2013 for shared genotyping and phenotyping activities in the pig
community. The best types of projects are those who have not received funds
in the past and who are between two or more stations for genotyping with the
SNP chips (60K or new 10K) or for collection of specialized phenotypes.
Please contact the Swine Genome Coordinator to discuss your requests.
o o o o o o o o o o o
The Animal QTLdb included 633 new pig QTL in its recent #18 release, making
the total number of pig QTL in the database 7,451. With this release, the
NAGRP bioinformatics team has done a number of improvements to the Animal
QTLdb, which includes a procedure to withdraw obsolete QTL data from NCBI,
a new experimental search function for animal breeds associated with QTLs,
a new trait hierarchy navigator, and improved QTLdb curator/editor tools.
Users are encouraged to register an account to enter new QTL data. Find out
more from http://www.animalgenome.org/QTLdb. In addition, the pig genome
build 10.2 annotations are ported to the BioMart
(http://www.animalgenome.org:8181/) for customized downloads; and pig
oligoArray elements are BLAST mapped to pig genome build 10.2, available for
download from
http://www.animalgenome.org/repository/pig/Genome_build_10.2_mappings (kindly
provided by Zhiliang Hu, NAGRP bioinformatics team).
o o o o o o o o o o o
A new custom low density chip is now available for imputation work.
GeneSeek, a supplier of genotyping services has announced the GeneSeek
Genomic Profiler for Porcine LD (GGP-Porcine). This custom low density
BeadChip utilizes Illumina Infinium chemistry and features approximately
8,500 SNPs for high density chip imputation. The GGP - Porcine BeadChip also
includes gene markers from several well-known reproduction, growth, feed
efficiency, and meat quality traits at no added expense. These include the
following markers: EPOR, MC4R, HMGA, CCKAR, PRKAG, and CAST. Details on
these markers will be available from GeneSeek. In addition, researchers can
request additional markers including the HAL, Rendement Napole (RN),
Resistance marker to E.coli (F4 ab/ac), a SNP parentage panel, and the
Estrogen Receptor (ESR) which impacts litter size in Large White or Yorkshire
by paying additional royalty fees for these optional licensed tests. The
chip was developed as a result of a collaborative effort involving leading
academic, USDA, and GeneSeek researchers. The price (per sample) will be $39
per sample for a DNA or $42 for tissue submission.
o o o o o o o o o o o
The PAG XXI and NRSP8 Swine Genome meetings are around the corner. Online
registration is now open for PAG-XXI/NRSP8 at http://www.intlpag.org. The
meeting will be January 12-16, 2013, in San Diego. Speakers include Eric
Perakslis (US FDA), Michael Eisen (UC Berkeley), Daniel Chourrout (Sars
Centre, Norway), Greger Larson (Durham U.), Steve Jacobsen (UCLA), Gonçalo
Abecasis (U. of Michigan), Michele Morgante (U. of Udine, Italy) and Gary
Muehlbauer (U. of Minnesota), see the program at http://www.intlpag.org.
Students can apply for the Jorgensen Travel Award ($1000) at
http://www.intlpag.org/2013/index.php/travelhotel/travel-grants. The poster
abstract deadline and the deadline for reduced registration fees is Nov. 1,
2012.
o o o o o o o o o o o
The PAG XXI and NRSP8 Swine Genome meetings are around the corner. Online
registration is now open for PAG-XXI/NRSP8 at http://www.intlpag.org. The
meeting will be January 12-16, 2013, in San Diego. Speakers include Eric
Perakslis (US FDA), Michael Eisen (UC Berkeley), Daniel Chourrout (Sars
Centre, Norway), Greger Larson (Durham U.), Steve Jacobsen (UCLA), Gonçalo
Abecasis (U. of Michigan), Michele Morgante (U. of Udine, Italy) and Gary
Muehlbauer (U. of Minnesota), see the program at http://www.intlpag.org.
Students can apply for the Jorgensen Travel Award ($1000) at
http://www.intlpag.org/2013/index.php/travelhotel/travel-grants. The poster
abstract deadline and the deadline for reduced registration fees is Nov. 1,
2012.
o o o o o o o o o o o
USDA National Institute of Food and Agriculture (NIFA) has delayed the
estimated release date for the RFAs for the 2013 AFRI Foundational Grants,
Fellowship Grants and most challenge area grants (including Food Security) to
approximately October 1, 2012. Go to
http://www.nifa.usda.gov/funding/rfas/afri.html to get updated information.
The Federal government will likely operate on a Continuing Resolution that
will hold FY 2013 funding close to that for FY 2012 until at least next year
when a new Congress takes office. The effects on USDA, NIFA and AFRI aren't
yet clear. It's also unclear if and when Congress will pass the Agriculture
Reform, Food, and Jobs Act (2012 Farm Bill) which would reauthorize NIFA and
AFRI through 2017 (at about current funding levels). The Senate Committee
version also includes a provision to establish a non-profit, non-governmental
Foundation for Food and Agriculture Research (FFAR) and provides FFAR with
$100M in funding that must be matched equally with non-Federal funds. The
Farm Bill is currently stuck in the House. Finally, OMB recently released its
Sequestration Report that estimates additional 8.2% cuts to USDA NIFA and ARS
research activities if budget sequestration were to occur according to last
year's budget agreement. (Kindly provided by Jerry Dodgson)
o o o o o o o o o o o
A big thanks and best wishes go out to Dr. Muquarrab Qureshi on his promotion
to the position of Assistant Director, Institute of Youth, Family, and
Community in the National Institute of Food and Agriculture (NIFA) as of June
3. Muquarrab previously served as Director of the Division of Animal Systems
and the National Animal Genome Research Program (NAGRP). He's provided
excellent leadership to the NAGRP as Director and has been a good friend to
all of animal genomics. We wish him the best of luck as he takes on this
challenging new position. Leadership of NAGRP has transferred to Dr. Lakshmi
Matukumalli who was appointed as National Program Leader of Animal Breeding,
Genetics and Genomics in NIFA last year.
o o o o o o o o o o o
The swine genome coordinator is always glad to hear from NRSP-8 members and
other readers about ways that the coordination effort can be improved or
provide resources that are needed. Also, if you have items of general
interest to the swine genetics and genomics communities that can be include
in this newsletter please share.
o o o o o o o o o o o
The sequencing and assemblies of genomes are often international
collaborative efforts that conclude upon publication of a reference sequence.
In order to ensure the continued utility of these assemblies, however, it is
crucial that such projects plan for a means to update reference genomes with
new data as it becomes available. As an assembly matures, this will likely
require focused curatorial efforts rather than whole genome reassembly. The
Genome Reference Consortium (GRC) was organized at the completion of the
human genome sequencing project to perform this curation and oversee future
updates to the reference assembly. GRC experimental work is performed at the
Genome Institute at Washington University, St. Louis (TGI) and The Wellcome
Trust Sanger Institute (WTSI). The National Center for Biotechnology
Information (NCBI), the WTSI and the European Bioinformatics Institute (EBI)
provide the database support and software tools to support this effort.
Funding for the GRC comes from the operating budgets of its members. Since
its inception, the GRC has expanded its role to address the maintenance and
modernization of the mouse and zebrafish reference assemblies. In addition to
publicly released updates to both the human and mouse reference genomes, the
GRC has also developed and published a new assembly model that better allows
for the representation of genome variation and the timely release of
inter-build sequence updates in the form of assembly patches (PLOS Biol. 2011
Jul;9(7):e1001091).
o o o o o o o o o o o
Several of the GRC's curatorial software tools and database support may be
extensible to other groups working to update assemblies. While the human,
mouse and zebrafish reference genomes are all clone-based assemblies, these
tools can be adapted to any assembly for which there are tiling path and AGP
files. The GRC uses a customizable commercial software package to manage
curation of discreet genome regions, while GRC-developed software is used to
manage tiling path updates, produce and store alignments between assembly
components, provide quality assessments and generate AGP files for loading of
an assembly to NCBI's Assembly database. GRC quality assessments include file
validation, component alignment statistics, contig building reports and
monitoring of the effects of assembly updates on annotation. In addition, GRC
software and tools can be used to provide external evidence in support of
component alignments, to evaluate proposed assembly changes prior to database
updates and to produce test assemblies in advance of public releases. Groups
interested in learning more about GRC tools and their applicability to other
assemblies are encouraged to contact the GRC via the "Contact Us" link on
their website: http://www.genomereference.org. (kindly provided by Valerie
Schneider NCBI)
o o o o o o o o o o o
Upcoming meetings (see:
http://www.animalgenome.org/pigs/community/meetings.html)
Innovate 2012: Funding Livestock Research and Outreach in the Future. Oct. 3
to 5, 2012 Shell Beach, CA. For information:
http://asas.org/meetings/innovate-2012
International PRRS Symposium, held in conjunction with the National Swine
Improvement Federation Annual Meeting, Nov. 29-30, 2012, Marriott Hotel
Kansas City Downtown, Kansas City, MO; contact: http://www.prrssymposium.org.
PAG-XXI/NRSP-8 will be January 12-16, 2013, for details see
http://www.intlpag.org/
Gordon Research Conferences: Quantitative Genetics & Genomics, Genetics of
Complex Disease, February 17-22, 2013, Galveston, TX for details see
http://www.grc.org/programs.aspx?year=2013&program=quantgen
PAG Asia to be held in Singapore, March 17-19, 2013. For details see
http://intlpagasia.org/
Human Genome Meeting/International Congress of Genetics: Genetics and
Genomics of Global Health and Sustainability, April 13-18, 2013, Suntec,
Singapore. Details at http://www.hgm2013-icg.org/
<> <> <> <> <> <> <> <> <> <> <>
Items for Pig Genome Update 114 can be sent to me by no later than December 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/pig/
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Supported by Multi-State Research Funds to the National Research Service
Program: NRSP-8. National Animal Genome Research Program, Lakshmi Matukumalli
NAGRP Director, NIFA
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Web: http://www.animalgenome.org/pig | Mail: angenmap@animalgenome.org
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