U.S. Bioinformatic Coordination Activities
Supported by Allotments of Regional Research Funds, Hatch Act
For the Period 1/1/11-12/31/11
Overview: Coordination of the CSREES National Animal Genome Research
Programs (NAGRP) Bioinformatics is primarily based at, and led from,
Iowa State University (ISU), with additional activities at Mississippi
State University (MSU) and is supported by NRSP-8. The NAGRP is made up
of the membership of the Animal Genome Technical Committee, including the
Bioinformatic Subcommittee.
FACILITIES AND PERSONNEL: James Reecy, Department of Animal Science, ISU,
serves as Coordinator with Susan J. Lamont (ISU), Max Rothschild (ISU),
Chris Tuggle (ISU), and Fiona McCarthy (MSU) as Co-Coordinators. Iowa
State University and Mississippi State University provide facilities and
support.
OBJECTIVES: The NRSP-8 project was renewed as of 10/01/08, with the
following objectives: 1. Create shared genomic tools and reagents and
sequence information to enhance the understanding and discovery of genetic
mechanisms affecting traits of interest; 2. Facilitate the development and
sharing of animal populations and the collection and analysis of new,
unique and interesting phenotypes; and 3. Develop, integrate and implement
bioinformatic resources to support the discovery of genetic mechanisms
that underlie traits of interest.
PROGRESS TOWARD OBJECTIVE 1. Create shared genomic tools and reagents and
sequence information to enhance the understanding and discovery of genetic
mechanisms affecting traits of interest.
See activities listed below.
PROGRESS TOWARD OBJECTIVE 2. Facilitate the development and sharing of
animal populations and the collection and analysis of new, unique and
interesting phenotypes.
Over the past year, partnered with researchers at Kansas State University,
Michigan State University, Iowa State University and U.S. Department of
Agriculture, we have further developed and improved the web interfaced
relational databases to store and disseminate phenotypic and genotypic
information from large genomic studies in farm animals and better serve
the needs by the researchers. For example, we are working with the PRRS
CAP Host Genome consortium to develop a relational database to house
individual animal genotype and phenotype data
(http://www.animalgenome.org/lunney/index.php). This will help the
consortium, whose individual research labs lack expertise with relational
databases, share information among consortium members and thereby
facilitate data analysis.
PROGRESS TOWARD OBJECTIVE 3: Develop, integrate and implement
bioinformatic resources to support the discovery of genetic mechanisms
that underlie traits of interest.
The following describes the project’s activities over this past year.
Poultry
A total of 285 new QTL have been curated into the Chicken QTLdb
(http://www.animalgenome.org/QTLdb/chicken.html). Chicken QTL can be
visualized against the genome at
http://www.animalgenome.org/cgi-bin/gbrowse/chicken/ and aligned with
chicken 60K SNPs along with NCBI annotated gene information
(http://www.animalgenome.org/cgi-bin/gbrowse/chicken/). In addition, we
continue to mirror Dr. Carl Schmidt’s Gallus genome browser
(http://www.animalgenome.org/cgi-bin/gbrowse/gallus/).
NRSP-8 funds were used to support the development of BirdBase resources.
Specifically, Chicken Gene Nomenclature Committee (CGNC) database was
developed, updating records from the Roslin GeneNames effort and providing
access to chicken gene nomenclature. It is now possible for biocurators
and community experts to add nomenclature, download current nomenclature.
In addition this resource is now linked the NCBI Entrez Gene chicken gene
pages (with thanks to Janet Weber). During 2012, we expect to link in with
Ensembl Genes and with the HGNC.
Via BirdBase, a bird comparative genome browser is being developed. This
will initially include the chicken, turkey and zebra finch genomes and
will then be expanded to include all bird genomes (including bird genomes
sequences as part of the BGI-10K Genomes project). Currently we have
accessed funds for this comparative browser (and its set up) and are in
the process of buying the server. We expect the bird comparative genome
browser to be online during 2012.
Cattle
In the past year, 525 new cattle QTL have been added . In addition, cattle
QTL can now be viewed relative to the UMD assembly;
http://www.animalgenome.org/cgi-bin/gbrowse/bovine/) and Btau4.2 assembly;
http://www.animalgenome.org/cgi-bin/gbrowse/cattle. Thanks to efforts by
Steven Salzberg's group at University of Maryland for mapping the STS
Cattle 770K high density SNPs and 4.1M dbSNP data are made available both
in GBrowse to align with QTL and in SNPlotz for genome analysis
(http://www.animalgenome.org/tools/snplotz/).
Porcine
The updated pig genome sequencing information are updated at
http://www.animalgenome.org/pigs/genome/ and a new pig genome database has
been under active development
(http://www.animalgenome.org/pig/genome/db/). 88 new QTL have been added
to the AnimalQTLdb this past year (http://www.animalgenome.org/QTLdb/pig).
The pig gene Wishlist
(http://www.animalgenome.org/cgi-bin/host/ssc/gene2bacs) continue to serve
the pig genome annotation activities throughout the 2011.
Sheep
In 2011, 291 new sheep QTL have been added to the Sheep QTLdb. A web site
for NRSP-8 activities continue to be updated as a sheep genome community
information hub (http://www.animalgenome.org/sheep/).
Aquaculture
Many useful links for aquaculture can be found at
http://www.animalgenome.org/aquaculture/. , Thanks to collaborative
efforts by Yniv Palti et all from the USDA National Center for Cool and
Cold Water Aquaculture, rainbow trout is now a new species in the Animal
QTLdb species families. To date 27 QTL data for rainbow trout have been
curated into the Animal QTLdb
(http://www.animalgenome.org/cgi-bin/QTLdb/OM/index).
Multi-species
A local copy of Biomart software has been installed on the
AnimalGenome.ORG server to serve the cattle, chicken, pigs and horse
community (http://www.animalgenome.org:8181/). New data sources and
species are being added.
Ontology development
This past year we continued to focus on the integration of the Animal
Trait Ontology into the Vertebrate Trait Ontology
(http://bioportal.bioontology.org/ontologies/1659). We have continued
working with the Rat Genome Database to integrate ATO terms that are not
applicable to the Vertebrate Trait Ontology into the Clinical Measurement
Ontology (http://bioportal.bioontology.org/ontologies/1583). Traits
specific to livestock products have been incorporated into a new Livestock
Product Trait Ontology (PT;
http://animalgenome.org/cgi-bin/amido/browse.cgi). As the first stage
outcome, we have mapped the cattle, pig, chicken, and sheep QTL traits to
Vertebrate Trait Ontology (VT), Product Trait Ontology (PT) and Clinical
Measurement Ontology (CMO) to help standardize the trait nomenclature used
in the QTLdb. Anyone interested in helping to improve the ATO/VT is
encouraged to contact James Reecy (jreecy@iastate.edu), Cari Park
(caripark@iastate.edu) or Zhiliang Hu (zhu@iastate.edu). We are
collaborating with researchers at INRA (France) and within EADGENE and
SABRE, EU funded projects, to expand the utility of the ATO, including the
development of an ontology devoted to traits of interest in livestock
species. Finally, we have developed a livestock breed ontology based on
the Oklahoma State University Livestock Breeds web resource. This breed
ontology is also found its application in the Animal QTLdb.
Via AgBase, we were recruited by the Phenotype Ontology Research
Coordination Network (NSF DBI 0956049) to develop an avian anatomy
ontology with the goal of integrating this with other, existing ontologies
to describe phenotypes. Using MSU and AgBase funds we have about 650 terms
that cover avian musculoskeletal and integument systems. The information
for these terms includes relationships, synonyms, definitions, and
comments (homologies to mammalian structures; species differences). The
development of this ontology is done in collaboration with Duncan Davidson
(UK Medical Research Council) and in conjunction with the larger Phenotype
RCN Vertebrate Working group. This work will continue with BirdBase
collaborators during 2012 (as funding permits) and will enable poultry
researchers to describe phenotype in a standard way that promotes data
sharing.
Software development
The NRSP-8 Bioinformatics Online Tool Box has been actively kept updated
(http://www.animalgenome.org/bioinfo/tools/). Several major software
upgrades were made to SNPlotz, Gene Ontology CateGOrizer, BEAP, and the
Expeditor. The new addition to the tool box is an online File Sharing
Platform, with which any NRSP-8 members can freely use the tool to share
large data files individually or publicly (e.g. within a consortium).
As a result of collaborations between Iowa State University, the Medical
College of Wisconsin, and University of Iowa, the Virtual Comparative Map
(VCMap) tool has passed its initial development stage and now transferred
to the AnimalGenome.ORG (http://www.animalgenome.org/VCmap/). More
application development will be expected. To improve links between AgBase
and the NRSP-8 website, AgBase now also provides a link to the Virtual
Comparative Map (VCMap). Please feel free to try things out, and send any
feedback to: vcmap@animalgenome.org.
Genome2Seq, an online tool that rapidly retrieves a fasta file of
sequences based on genome co-ordinates generated from RNA-Seq data, was
developed. Users specify either bovine, horse, chicken or pig genomes. The
input file is a tab-delimited text file containing a unique ID, chromosome
number, start location, and stop location in that order. The output is (a)
a list of matching genes and their associated GO annotation; and (b) a
fasta file of sequences for any co-ordinates that do not match any
annotated genes. Genome2Seq is available via AgBase and the NRSP-8
website.
The web site and user forum listserv for CRI-MAP user interactions in
improving the CRIMAP software
(http://www.animalgenome.org/tools/share/crimap/) has been actively used
Minimal standards development
We have worked with the MIBBI project
http://www.mibbi.org/index.php/Main_Page to help define minimal standards
for publication of QTL and gene association data
(http://miqas.sourceforge.net/). See Taylor et al. (2008) for additional
information.
Expanded Animal QTLdb functionality
In 2011, a total of 1216 new QTL have been added to the database.
Currently, there are 6432 curated porcine QTL, 5207 curated bovine QTL,
2736 curated poultry QTL, 639 curated sheep QTL, and 27 curated rainbow
trout QTL in the database (http://www.animalgenome.org/QTLdb/). All
included livestock QTL data have been ported to NCBI. With the exception
of the chicken QTL, all QTL data can be visualized relative to the
Illumina SNPchip data. Finally, we have started to curate all SNP
association studies for all livestock species into the database.
In addition, The QTLdb has been revamped to accommodate genome map (map
unit: bp) based QTL and association data (e.g. GWAS data). The map view
and QTL details view have updated to integrate these new data types. A
new user option allows one to view "QTL", "eQTL", "Associations", or
combinations of these data. Some minor but useful improvements continue
to be made. For example users can see a list of references for the QTL
within any chromosomal view window.
Facilitating research
The Data Repository for aquaculture, cattle, chicken and pig community to
share their genome analysis data has been proven to be very useful.
(http://www.animalgenome.org/repository). More species data is being
added. Our helpdesk is here to assist community members. . Throughout
the year, we have helped >88 research groups/individuals with their
research projects and questions. Our involvement has ranged from data
transfer, data assembly, data analysis, software applications, code
development, etc. Please continue to contact us as you need help with
bioinformatic issues.
PLANS FOR THE FUTURE.
OBJECTIVE 2. Facilitate the development and sharing of animal populations
and the collection and analysis of new, unique and interesting phenotypes.
We will seek to partner with any NRSP-8 members wishing to warehouse
phenotypic and genotypic data in customized relational databases. This
will help consortia/researchers whose individual research labs lack
expertise with relational databases to warehouse and share information.
OBJECTIVE 3: Develop, integrate and implement bioinformatic resources to
support the discovery of genetic mechanisms that underlie traits of
interest.
We will continue to work with bovine, mouse, rat, and human QTL database
curators to develop minimal information for publication standards. We will
also work with these same database groups to improve phenotype and
measurement ontologies, which will facilitate transfer of QTL information
across species. We will continue working with U.S. colleagues, as well
as throughout Europe to develop a Bioinformatics Blueprint, similar to the
Animal Genomics Blueprint recently published by USDA-CSREES, to help
direct future livestock-oriented bioinformatic/database efforts.
Publications
1. Zhi-Liang Hu, James E Koltes, Carissa A. Park, Eric R. Fritz and
James M. Reecy (2011). Review: Bioinformatics approaches to livestock
animal genomics research. CAB Reviews: Perspectives in Agriculture,
Veterinary Science, Nutrition and Natural Resources 2011 6, No. 044.
2. Zhi-Liang Hu, Antonio M. Ramos, Sean J. Humphray, Jane Rogers,
James M. Reecy and Max F. Rothschild. (2011). Use of Genome Sequence
Information for Meat Quality Trait QTL Mining for Causal Genes and
Mutations on Pig Chromosome 17. Frontiers in Livestock Genomics, 2:43.
doi: 10.3389/fgene.2011.00043.
3. Xiao-Lin Wu, Daniel Gianola, Zhi-Liang Hu and James M. Reecy
(2011). Meta-Analysis of Quantitative Trait Association and Mapping
Studies using Parametric and Non-Parametric Models. Biometrics &
Biostatistics, J Biomet Biostat 2011, S1. doi: 10.4172/2155-6180.S1-001.
4. Zhi-Liang Hu, Xiao-Lin Wu and James M. Reecy (2011). Extension of
Animal QTLdb: QTL Meta-analysis on the Fly. Poster paper published on ACM
Conference on Bioinformatics, Computational Biology and Biomedicine
(ACM-BCB), August 1-3, 2011, Chicago, IL, USA.
5. Jianguo Lu, Eric Peatman, Qing Yang, Shaolin Wang, Zhi-Liang Hu,
James Reecy, Huseyin Kucuktas and Zhanjiang Liu (2011). The catfish genome
database cBARBEL: an informatic platform for genome biology of ictalurid
catfish. Nucleic Acids Res. 2010 Oct 8. [Epub ahead of print]
6. McCarthy, F.M., Gresham, C.R., Buza, T.J., Chouvarine, P., Pillai,
L.R., Kumar, R., Ozkan, S., Wang, H., Manda, P., Arick, T., Bridges, S.M.,
Burgess, S.C. (2011) AgBase: supporting functional modeling in
agricultural organisms. Nucleic Acids Res, 39, D497-506.
7. Nail, C., Chouvarine, P., Weber, J., Spencer., Kumari, S.,
Burgess, S.C., Schmidt, C, Antin, P., McCarthy, F.M. Manual biocuration to
support standardized chicken gene nomenclature at CGNC. The 6th
International Chick Meeting Roslin Institute, Sept. 17-20, 2011.
(Prepared 1/11/11)