US PIG GENOME COORDINATION PROGRAM ACTIVITIES
Supported by Regional Research Funds, Hatch Act for the Period 1/1/11-12/31/11
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, serves as
Coordinator and was 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 10.2f 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) continued its efforts this
past year and considerable advances have been made. The "marker" paper
has been published in which the Consortium sets outs its plans for the
analysis and publication of a draft pig genome sequence. Please see BMC
Genomics 2010, 11:438 (
Sequencing efforts by the SGSC continue with build 10.2f being released.
There are two preliminary annotation resources for the swine genome. The
first is work conducted by Henrik Hornshøj Jensen. This annotation can be
obtained at the following site
. The second, is work
developed by the Ensembl team and is
. Please keep in mind that
these efforts are part of the Swine Genome Sequencing Project and all
rules and rights of community sequencing projects apply. 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. News
and updates were set up to report the genome sequencing progress
). New QTL continue to be
curated into the Pig QTL Database. The database is available at
. Efforts are being made to align
the current genome assembly against pig QTL among other genome features
). Database activities were
transferred to the Bioinformatics Coordinator.
Shared Materials and Funding:
The Pig Genome Coordinator has recently supported community activities to
find associations with many different traits and has provided nearly 1600
chips/genotyping for those several projects from 2009-2011. The
coordinator is looking for new projects help support by providing SNP
Porcine SNP chip update:
the International Porcine SNP Chip Consortium developed a porcine 60K+ SNP
and has shipped it to many researchers worldwide. Researchers that did not
place an order can contact Illumina for further information or questions
http://www.illumina.com/contactMe.ilmn?CS=1. The original publication
was Ramos et al. 2009. Prices for the chip have been dropping.
Communication with all international groups and individuals is excellent.
The bimonthly Pig Genome Update has now published 110 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.
The goals are to help support all of the objectives of this project.
Major activities include helping facilitate and sharing use of the 60K SNP
chip and in 2012. 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
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