US PIG GENOME COORDINATION PROGRAM ACTIVITIES
Supported by Regional Research Funds, Hatch Act for the Period 1/1/10-12/31/10
January 15, 2010
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). CSREES 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.
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.
Map Development Update:
New gene markers were identified with the development of the 60K SNP
chip. These new markers are being integrated with the development of
Build 9 and the new build 10 as maps now are based on the pig sequencing
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.
The Swine Genome Sequencing Consortium (SGSC) continued its efforts this
past year and considerable advances have been made. Build 10 for the
Sus scrofa reference genome sequence was released Monday, September 20
thanks to the efforts of many people and great collaboration across the
world. The sequence and accompanying information was in a final version
and released from TGAC's ftp (FTP site: ftp.tgac.bbsrc.ac.uk; User:
pig10; Password: Sscrofa10). This final version was based on the latest
freeze of the physical map. The assembly is the result of the
integration of all the sequenced clones and contigs produced by
SOAPdenovo and Cortex whole genome shotgun (WGS) assemblies. These WGS
assemblies were generated using Illumina reads sequenced at BGI and the
Sanger Institute (~40X coverage). As part of the release AGP files with
information about the source of every contig were provided. The WGS
contigs were submitted to EMBL/Genbank, and after that the WGS contigs
were to be renamed in the AGP with the corresponding accession numbers.
This assembly provides an almost complete coverage of the pig genome.
Additional details will be presented as they become available. The
"marker" paper has recently been published in which the Consortium sets
outs its plans for the analysis and publication of a draft pig genome
sequence. These plans were presented to participants in the Pig Genome
III conference held at the Wellcome Trust Sanger Institute, 2-4 November
2009 when a series of analysis working groups were established. Please
see BMC Genomics 2010, 11:438
While database activities were transferred to the Bioinformatics
Coordinator, the Pig Genome Database continues to receive considerable
updating. News and updates were set up to report the genome sequencing
progress (http://www.animalgenome.org/pigs/genomesequence/) and to link
to most updated pig genome information resources. New QTL continue to be
curated into the Pig QTL Database. Up to date there are noe 5,986 QTLs
in the database representing 581 pig traits and can be seen at
(http://www.animalgenome.org/QTLdb/pig.html). Efforts are being made to
update the newest pig genome information in several areas including (1)
alignment with pig QTL among other genome features
(http://www.animalgenome.org/gbrowse) and (2) blast service to allow the
community pig gene analysis and annotation activities. The NAGRP
Bioinformatics Team has set up a pig gene Wish List which is seen at
(http://www.animalgenome.org/cgi-bin/host/ssc/gene2bacs) which is
playing an active role to help the pig genome annotation activities.
The last of the microsatellite primers and second generation novel
70-mer oligonucleotide microarray have been shared by the coordination
program. The other shared materials will be SNP chips. The Pig Genome
Coordinator supported community activities to find associations with
PRRS and has provided 800 chips for that activity in 2009-2010 and has
also supported PCV2 shared activities by providing SNP chips for
genoptyping. The coordinator is looking for new projects (meat quality,
sow longevity) to help support by providing SNP genotyping.
Porcine SNP chip:
Illumina and the International Porcine SNP Chip Consortium developed a
porcine 60K+ SNP and have shipped it to many researchers worldwide.
Researchers that did not place an order can contact Illumina for further
information or questions at http://www.illumina.com/contactMe.ilmn?CS=1.
The original publication was Ramos et al. 2009.
Communication with all international groups and individuals is excellent.
The bimonthly Pig Genome Update has now published 100 issues and has
been distributed electronically to over 1,800 people worldwide
Travel and Meeting Support:
Some conferences have received support funding from the Coordinator.
Travel of several 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 in 2010. Further development of a shared population is
ongoing. New bioinformatic tools will also be developed. Constructive
suggestions from researchers to help this coordination and facilitation
program grow and succeed are appreciated.
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