Coordinator's Report for 2006
January 13, 2007
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/); the NCBI Chicken Genome Resources, (http://www.ncbi.nlm.nih.gov/ /); and the EBI's Ensembl Chicken Genome Browser, (http://www.ensembl.org/). The ChickFPC browser at http://www.bioinformatics.nl 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 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://agbase.msstate.edu/cowgo.html), pigs (http://agbase.msstate.edu/PigGO.html), chicken (http://agbase.msstate.edu/chickgo.html), sheep (http://agbase.msstate.edu/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
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.