U.S. PIG GENOME COORDINATION PROGRAM ACTIVITIES
Supported by Regional Research Funds,
Hatch Act for the Period 1/1/13-12/31/13
*************** January 11, 2014 **************
* *
* Max F. Rothschild *
* USDA/CSREES National Pig Genome Coordinator *
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* 1. Overview *
* 2. Facilities and personnel *
* 3. NRSP-8 objectives *
* 4. Map Development Update *
* 5. QTLs, Candidate Genes and Trait Associations*
* 6. Database Activities *
* 7. Shared Materials and funding *
* 8. Porcine SNP chip update *
* 9. International Efforts *
* 10. Communication *
* 11. Travel and Meeting Support *
* 12. 2013 Research Support Activities *
* 13. Final considerations *
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1. Overview:
Coordination of Pig Genome Coordination Program is under the National
Animal Genome Research Program (NAGRP) and is the effort of personnel at
Iowa State University (ISU). Support is allocated from NRSP-8 and provided
to the Agriculture Experiment Stations by off the top funding. The NAGRP
is made up of the membership of the Animal Genome Technical Committee,
including the Pig Species Subcommittee.
2. Facilities and personnel:
Iowa State University faculty and staff help support the national pig
genome coordination effort as part of Iowa State University's
contribution. Max Rothschild, Department of Animal Science, ISU, has
served as Coordinator since 1993 and was last reappointed in 2008. This
represented the 20th and final year Max Rothschild is reporting.
3. NRSP8 objectives:
Objective 1: Create shared genomic tools and reagents and sequence
information to enhance the understanding and discovery of genetic
mechanisms affecting traits of interest. Objective 2: Facilitate the
development and sharing of animal populations and the collection and
analysis of new, unique and interesting phenotypes and Objective 3:
Develop, integrate and implement bioinformatics resources to support the
discovery of genetic mechanisms that underlie traits of interest. New
objectives were set out for FY 2014.
4. Map Development Update:
New gene markers continue to be identified with the development of the 60K
SNP chip and GWAS and sequencing efforts. The 60KSNP chip information can
be integrated with the development of Build 10.2 as maps now are based on
the pig sequencing efforts.
5. QTL, Candidate Genes and Trait Associations:
QTL and trait associations have continued to be reported on all
chromosomes for many traits. Candidate gene analyses have proven
successful with several gene tests being used in the industry for many
traits including, fat, feed intake, growth, meat quality, litter size and
coat color. The PigQTLdb (http://www.animalgenome.org/QTLdb/pig) is an
excellent repository for all of these results. Several new genome wide
association studies (GWAS) continue to be published in pigs and data
entered into the Pig QTLdb.
6. Database Activities:
The Pig Genome Database continues to receive considerable updating. The
Animal QTLdb included 1468 new pig QTL in during 2013(release #21), making
the total number of pig QTL in the database 8,919., Throughout 2013, the
NAGRP bioinformatics team has continued their efforts to make improvements
to the Animal QTLdb, which includes a new mirror site in China, facilitate
the addition of gene network analysis data, improved search tools and data
analysis 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 continuing to be
updated in the BioMart (http://www.animalgenome.org:8181) and for the
Animal QTLdb.
7. Shared Materials and Funding:
The Pig Genome Coordinator has recently supported community activities to
find associations with many different traits. In FY 2013 several projects
including those for disease resistance, reproduction and meat quality were
supported. This brings the total to well over 3,000 chips/genotyping for
those several projects from 2009-2013.
8. Porcine SNP chip update:
Illumina and the International Porcine SNP Chip Consortium developed a
porcine 60K+ SNP and has shipped it to many researchers worldwide. The
original publication was Ramos et al. 2009. Prices for the chip have been
dropping and are reasonable. 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,ESR, 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, 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) is about 40% of the cost of the 60K chip.
10. International Efforts:
Communication with all international groups and individuals is excellent.
11. Communication:
The bimonthly Pig Genome Update has now published 118 issues and has been
distributed electronically to over 2,300 people worldwide.
12. Travel and Meeting Support:
Some conferences have received support funding from the Coordinator.
Travel of some scientists was partially funded to attend important pig
gene mapping meetings.
13. 2013 Research Support Activities:
The goals are to help support all of the objectives of this project.
Major activities included helping facilitate collection of phenotypes
and sharing use of the 60K and 8 K SNP chips in the future. Further
development of shared populations is ongoing. New bioinformatic tools
will also be developed with help of the bioinformatics team. Constructive
suggestions from researchers to help this coordination and facilitation
program grow and succeed are appreciated. NRSP8 is being revised and
contributions from members of the pig genome community are appreciated.
14. Final considerations:
This coordinator's report marks the last yearly report that will be issued
by myself. After 20 years it was time for a change of leadership in the
Swine Genome Coordination. We as a community should be quite proud of all
we have accomplished. This work has gone from discovering microsatellite
markers, genes and initial QTL to having a pig genome sequence, gene
markers used in industry and a much better understanding of the genetic
control of the traits of interest in the pig. As Coordinator I have tried
to help facilitate these activities and thanks to many, many colleagues
around the US and the world we have been successful. I thank each of you
for your help and support and for your friendship in these matters. I
wish Drs Chris Tuggle (ISU) and Cathy Ernst (MSU) all the success possible
and I will continue to help work with our community. I wish all my
colleagues in our field great success.
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: National Animal Genome Research Program, Lakshmi Matukumalli,
NAGRP Director, NIFA
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U.S. PIG GENOME COORDINATION PROJECT
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| Supported by Multi-State Research Fund | http://www.animalgenome.org
| National Research Service Program (NRSP) |
| Lakshmi Matukumalli, NAGRP Director, NIFA | angenmap@animalgenome.org
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