US PIG GENOME COORDINATION PROGRAM ACTIVITIES
Supported by Regional Research Funds, Hatch Act for the Period 1/1/13-9/30/13
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.
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.
Create shared genomic tools and reagents and sequence information to
enhance the understanding and discovery of genetic mechanisms affecting
traits of interest.
Facilitate the development and sharing of animal populations and the
collection and analysis of new, unique and interesting phenotypes and
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.
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.
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.
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.
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.
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.
Communication with all international groups and individuals is excellent.
The bimonthly Pig Genome Update has now published 118 issues and has
been distributed electronically to over 2,300 people worldwide.
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.
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.
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.
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
© US Pig Genome Coordination Program