U.S. Database Coordination Activities
Supported by Allotments of Regional Research Funds, Hatch Act
For the Period 1/1/06-12/31/06
Overview: Coordination of Database/Bioinformatics under the National
Animal Genome Research Program (NAGRP) is an effort of Iowa State
University (ISU). CSREES support is allocated via NRSP-8. The NAGRP
is made up of the membership of the Animal Genome Technical Committee,
including the Database Subcommittee.
FACILITIES AND PERSONNEL: James Reecy, Department of Animal Science,
ISU, serves as Coordinator with Sue Lamont, Max Rothschild, and Chris
Tuggle as Co-Coordinators. Iowa State University provides facilities
and support.
OBJECTIVES: 1. Enhance and integrate genetic and physical maps of
agriculturally important animals for cross species comparisons and
sequence annotation, 2. Facilitate integration of genomic,
transcriptional, proteomic and metabolomic approaches toward better
understanding of biological mechanisms underlying economically
important traits, and 3. Facilitate and implement bioinformatic tools
to extract, analyze, store and disseminate information.
PROGRESS TOWARD OBJECTIVE 1. Enhance and integrate genetic and
physical maps of agriculturally important animals for cross species
comparisons and sequence annotation.
The genetic linkage maps of the cattle, chicken and swine have
provided a framework for numerous QTL and other mapping experiments
and a platform on which genome sequences have been assembled and
linked to chromosomes. Over the past year, we have worked to link
linkage maps, BAC fingerprint maps, RH maps, new microsatellites, and
SNPs to the human genome sequence, to allow researchers to seamlessly
transfer information between maps
( http://www.animalgenome.org/QTLdb/ ). As species genome sequences
become available, we are working to tie these different maps together
via species specific genome information.
PROGRESS TOWARD OBJECTIVE 2. Facilitate integration of genomic,
transcriptional, proteomic and metabolomic approaches toward better
understanding of biological mechanisms underlying economically
important traits.
Over the past decade, several hundred manuscripts have been published
in which quantitative trait loci or association tests have been
reported for all livestock species. We have focused on the curation
of cattle, chicken, and swine QTL information
( http://www.animalgenome.org/QTLdb/ ). The database is being expanded
to include all genotype association studies, currently only available
for swine. In addition, we are working with Dr. Jill Maddox
(Australia) to transfer the QTLdb schema so that sheep QTL information
can be included as well. In addition, to inclusion of cattle and
chicken data into the QTLdb, we have worked to link this information
to as many maps as data becomes avilable (Linkage, RH, FPC, SNPs,
human genome, etc). Efforts are underway to integrate gene expression
profiling data into the database as well.
PROGRESS TOWARD OBJECTIVE 3: Facilitate and implement bioinformatic
tools to extract, analyze, store and disseminate information.
Efforts under this objective included communications with curators of
other relevant databases, compilation of information about those
databases, assessment of the content and function of those databases,
and prioritization of the efforts of US coordination efforts in the
areas of highest priority and utility, given the landscape of public
databases already developed and maintained by others. The following
described the publicly available resources, and the Coordinator's
activities.
The chicken genome sequence, along with a variety of options and
tools, can be accessed at three different browsers: the UCSC Chicken
Genome BrowserGateway,
(http://genome.ucsc.edu/cgi-bin/hgGateway?org=Chicken&db=0&hgsid=30948908
); the NCBI Chicken Genome Resources,
(http://www.ncbi.nlm.nih.gov/genome/guide/chicken /); and the EBI's
Ensembl Chicken Genome Browser, (http://www.ensembl.org/Gallus_gallus
/). The ChickFPC browser at
http://www.bioinformatics.nl/gbrowse/cgi-bin/gbrowse/ChickFPC allows
for various searches of the BAC contig map. Similarly, BAC locations
denoted by BAC end sequences can be found on other sequence browsers
noted above. The SNP data generated by the Beijing Genomics Institute
(described above) can be accessed on the UCSC or Ensembl browsers, but
more extensive descriptions are available at the BGI site at
http://chicken.genomics.org.cn/index.jsp .
The latest version of ChickGBASE developed by the Roslin Institute is at
http://www.thearkdb.org/arkdb/do/getChromosomeDetails;jsessionid=B8A6A5EA698B84AF80EE99BE7530B04E?accession=ARKSPC00000004 .
US Poultry Genome coordinator maintains a homepage for the NRSP-8
U.S. Poultry Genome project (http://poultry.mph.msu.edu ) that
provides a variety of genome mapping resources, including the latest
EL maps and mapping data, descriptions of available resources, the
latest cytogenetic map, and access to a host of other information
relating to both genetic and physical maps, including our newsletter
archive.
Roslin Institute maintains the Arkdb, that hosts linkage maps for a
number of livestock species ( http://www.thearkdb.org/), include pigs,
cattle, chicken, sheep, and others.
AgBase developed by Mississippi State University contains information
from their active annotation of Gene Ontologies for cattle (
http://www.agbase.msstate.edu/information/cowgo.html), pigs (
http://www.agbase.msstate.edu/information/PigGO.html), chicken (
http://www.agbase.msstate.edu/information/chickgo.html), sheep (
http://www.agbase.msstate.edu/information/sheepgo.html) and several
aqua culture species, such as catfish, trout, and salmon (
http://www.agbase.msstate.edu/).
Cattle sequence, along with a variety of options and tools, can be
accessed at three different browsers: the UCSC Cow Genome Browser
Gateway ( http://genome.ucsc.edu/cgi-bin/hgGateway?org=cow), the NCBI
Cow Genome Resources (
http://www.ncbi.nlm.nih.gov/projects/genome/guide/cow/), and the EBI's
Ensembl cattle Genome Browser (
http://pre.ensembl.org/Bos_taurus/index.html). In addition, cattle
genome browser is set up at Texas A&M to aid the annotations at
http://bovinegenome.org/ and in Australia
(http://www.livestockgenomics.csiro.au/perl/gbrowse.cgi/bova3/).
Cattle BAC contigs can be visualized at
http://www.livestockgenomics.csiro.au/perl/gbrowse.cgi/baccontig/.
Ruminant-human genome comparison can be visualized at
http://www.livestockgenomics.csiro.au/perl/gbrowse.cgi/rumhum/.
Bovine SNPs can be visualized at
http://www.livestockgenomics.csiro.au/ibiss/. Cattle QTL information
can be found at 3 databases: Texas ( http://bovineqtl.tamu.edu/), Iowa
( http://www.animalgenome.org/QTLdb/cattle.html) and Australia (
http://www.vetsci.usyd.edu.au/reprogen/QTL_Map/).
NCBI announced the release of its annotation of the bovine genome
assembly, build 3.1. This build includes annotation of the Btau_3.1
genome assembly from Baylor and a complete mitochondrial genome. The
data can be viewed in Map Viewer:
http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=9913
downloaded by ftp:ftp://ftp.ncbi.nlm.nih.gov/genomes/Bos_taurus/ and
searched by BLAST:
http://www.ncbi.nlm.nih.gov/genome/seq/BlastGen/BlastGen.cgi?taxid=9913
A guide to bovine genome resources is availablet:
http://www.ncbi.nlm.nih.gov/projects/genome/guide/cow/
Please note two new items in this release: 1 -The Map Viewer includes
a new BAC-end sequence map for build 3.1 (BES clone),
e.g.:http://tinyurl.com/y3mehr 2 - The previous build, 2.1 based on
Btau_2.0, is still available for display in Map Viewer:
http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=9913&build=prev
The pig genome sequencing is actively carried out at Sanger Institute
( http://www.sanger.ac.uk/Projects/S_scrofa/) and preliminary sequence
results can be found at Ensembl site (
http://pre.ensembl.org/Sus_scrofa/index.html) and regularly updated
into the NCBI database (
http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=9823). Pig
QTL information has been actively updated at the AnimalQTLdb (
http://www.animalgenome.org/QTLdb/pig.html).
Sheep genome information can be found at several databases: NCBI sheep
genome resources ( http://www.ncbi.nlm.nih.gov/genome/guide/sheep/),
International Sheep Genomics Consortium (
http://www.sheephapmap.org/). Sheep BAC clone and FPC information can
be found at http://bacpac.chori.org/library.php?id=162 , and sheep
virtual genome at http://www.sheephapmap.org/isgc_virtualgenome.htm .
A number of on-line tools have been developed
http://www.animalgenome.org/bioinfo/tools/. Tools have been developed
to generate PCR primers across livestock exon or between two conserved
sequences. A Gene Ontology term counter has been developed to aid in
the determination of the number GO parent and sibling numbers. Graph
drawing tools can also be accessed as well.
Meetings: Over 2000 scientists attended the joint Plant and Animal
Genome XIV meeting held last January, held jointly with the annual
NAGRP meeting. Coordination funds helped support attendance at
PAG-XIV and will do so again for the upcoming PAG-XV in January, 2007.
We will host a bovine genome annotation meeting in conjunction with
Chris Elsik at PAG on January 15th in the Towne Room. In addition, we
will host a QTL database meeting to discuss minimal information
necessary for publication of QTL data, development of a phenotype
ontology, and sharing of curated data.
PLANS FOR THE FUTURE.
OBJECTIVE 1. Enhance and integrate genetic and physical maps of
agriculturally important animals for cross species comparisons and
sequence annotation.
We will begin to develop links between species genomic sequence
(Cattle, Chicken, Human, and Mouse) so that QTL information can be
transferred across species, such that QTL from cattle can be
visualized on pigs or human or mouse.
OBJECTIVE 2. Facilitate integration of genomic, transcriptional,
proteomic and metabolomic approaches toward better understanding of
biological mechanisms underlying economically important traits.
We will expand the QTL database to house individual animal genotype
and phenotype data. This will help research labs that lack expertise
with relational databases and will facilitate comparison of QTL
information across experiments. In addition, we will work to expand
the QTL database to house microarray data, which will facilitate the
identification of candidate genes when researchers are searching for
causal mutations.
OBJECTIVE 3: Facilitate and implement bioinformatic tools to extract,
analyze, store and disseminate information.
We will work with bovine, mouse, rat, and human QTL databases to
develop minimal information for publication standards. In addition,
we will work with these same databases to develop a phenotype
ontology, which will facilitate transfer of QTL information across
species.
(Prepared 1/05/07)