US PIG GENOME COORDINATION PROGRAM ACTIVITIES
Supported by Regional Research Funds, Hatch Act for the Period 1/1/12-12/31/12
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:
Max Rothschild, Department of Animal Science, ISU, has served as Coordinator
since 1993 and was last reappointed in 2008. Iowa State University faculty
and staff help support the national pig genome coordination effort as part
of Iowa State University's contribution.
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.
Map Development Update:
New gene markers were identified with the development of the 60K SNP chip.
The 60KSNP chip information can now 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.html)
is an excellent repository for all of these results. New genome wide
association studies (GWAS) are being published in the pigs.
The Swine Genome Sequencing Consortium (SGSC) was pleased to announce the
publication of a high quality draft genome sequence for the pig (Sus scrofa).
The paper entitled "Analyses of pig genomes provide insight into porcine
demography and evolution" describing the sequencing, analysis and annotation
of this draft genome sequence was published in Nature in the November 15
issue. In parallel a series of companion papers has been published in BMC
journals. In addition, this annotation can be visualized in Gbrowse against
version 10.2 of the swine genome at
The Pig Genome Database continues to receive considerable updating. 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
In addition, the pig genome build 10.2 annotations are ported to the BioMart
for customized downloads; and pig oligoArray elements are BLAST mapped to pig
genome build 10.2, available for download from
Shared Materials and Funding:
The Pig Genome Coordinator has recently supported community activities to find
associations with many different traits and has provided nearly 2,000
chips/genotyping for those several projects from 2009-2012. The coordinator
is looking for new projects to support by providing SNP genotyping.
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, 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) is about 40% of the cost of the 60K chip.
Communication with all international groups and individuals is excellent.
The periodic Pig Genome Update has now published 115 issues and has
been distributed electronically to over 2000 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 Activities: The goals are to help support all of the objectives
of this project. Major activities include 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
This coordinator's report marks the last planned yearly report that will be
issued by myself. After 20 years it is time for a change of leadership in
the Swine Genome Coordination program and I will be stepping down September
30, 2013 if a replacement can be chosen. 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 pledge to help the next Coordinator continue to work with our community
and I wish whoever is chosen 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