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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.
FACILITIES AND PERSONNEL: James Reecy, Department of Animal Science,
ISU, serves as Coordinator along with Sue Lamont, Max Rothschild and
Chris Tuggle, Department of Animal Science, ISU, as Co-Coordinators.
Iowa State University provides facilities and support.
OBJECTIVES: 1. Develop high-resolution comparative genome maps aligned
across species that link agricultural animal maps to those of the human
and mouse genomes, 2. Increase the marker density of existing linkage
maps used in QTL mapping and integrate them with physical maps of
animal chromosomes, and 3. Expand and enhance internationally shared
species genome databases and provide other common resources that
facilitate genome mapping.
PROGRESS TOWARD OBJECTIVE 3: Database and other map resources.
Researchers at universities and other research institutions are
conducting multifaceted research to develop bioinformatics programs and
database resources for livestock species and this research is supported
in part by the NAGRP. Continued efforts to inform scientists and lay
persons about genome databases have been made and many new entries are
now available at www.animalgenome.org. The NAGRP genome databases were
accessed over 2.2 million times by over 140,000 users world-wide.
QTL database. The NAGRP database has a newly developed Porcine QTL
database that graphically displays QTL from over 70 experiments and can
be used at
http://www.animalgenome.org/QTLdb/ . All information has
been cross-listed at NCBI and can be viewed at
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&term=pig+QTL.
Over the past year, links have been added to the viewer allowing
researchers to visualize QTL on the human genome. In addition, we will
expand this visualization option to additional sequenced organisms,
such as the mouse, rat and dog. The database can now be used for any
species. We are currently working with the Aquaculture community to
enter their data into the QTL database.
PCR Primer Design. A bioinformatics program (Expeditor) was developed
to design primers for livestock species. This program takes advantage
of the information from the human genome and applies it to livestock
cDNA. This program can be used at
http://www.animalgenome.org/hu/expeditor .
Blast Analysis of Livestock and Aquaculture DNA sequence. Programs
were developed to automatically download livestock sequence data from
and synchronize them with NCBI. The available sequence databases
include: (1) EST sequence from all non-human, non-mouse animals; (2)
Whole genome shotgun (WGS) sequences from all livestock animals; (3)
TIGR gene indices for 6 species, and can be used at
http://www.animalgenome.org/blast/ .
Phenotype Ontology Editor. With the dramatic increase in sequence
information in livestock and aquaculture species, it will be imperative
to be able to link phenotype, genotype, proteomic, and gene expression
data in a queryable format. Development of a formal phenotype ontology
will complement on-going gene and anatomy ontology efforts. However,
due to the small size of the livestock and aquaculture species
communities, it will be important to do so in a cooperative manner.
Toward this end, we have developed an ontology editor that can be used
simultaneously by several annotators. We anticipate that this resource
will be shortly available to the livestock community.
Porcine EST Cluster and Annotation Analysis. Over the course of the
past year, funds were used to support work by Dr. Chris Elsik's lab
(Texas A&M) to cluster and annotate porcine EST clusters. This work
was to support the development of a new porcine long-oligo array in
collaboration with the Swine Genome Coordinator.
Genetic Program Database. With the rapid progress in genetics and
genomes, there are an increasing number of genetic analysis software
programs. Each program has its own pre-defined scope, assumptions, and
applicability. With the large number of available programs, it can be
a challenge to identify suitable options. Thus, we have created a
database and related tools to effectively archive, annotate, and manage
the wealth of the software information so that researchers can easily
identify, locate, and retrieve appropriate software. We have also
introduced ontology concepts and tools to manage the proper
classification and feature annotation of this resource. To date, there
are 331 software programs listed in the category of "genetic analysis".
We plan to add other genomics and computational biology software in the
near future.
http://www.animalgenome.org/soft
Database Activities: As in past years, the Livestock Genome Databases
have received considerable updating.
ArkDB statistics (December, 2005)
| | cattle | pig | chicken | sheep | horse | salmon | tilapia |
| loci | 2725 | 4081 | 2530 | 2030 | 1470 | 230 | 243 |
| (genes) | 746 | 1588 | 765 | 543 | 465 | 10 | 1 |
| (linkage) | 2209 | 5141 | 3400 | 14909 | 0 | 0 | 163 |
| (cytogenetic) | 659 | 1927 | 307 | 843 | 688 | 0 | 0 |
| clones | 1 | 602 | 316 | 206 | 153 | 27 | 0 |
| library | 0 | 96 | 32 | 0 | 5 | 3 | 0 |
| experiments | 6020 | 5680 | 2529 | 2934 | 1851 | 293 | 135 |
| references | 509 | 1254 | 573 | 518 | 217 | 86 | 243 |
These activities help to promote cooperation and facilitate progress in
livestock genomics.
Newsletter: The Bioinoformatics Newsletter is published and distributed
through our Homepage, and electronically on the AnGenMap email
discussion group.
Meetings: In the past year, we helped support the Third International
Symposium on Genetics of Animal Health, July 13-15, 2005, at Iowa State
University. There were over 120 participants from 14 countries. Many
livestock and aquaculture scientists attended the joint Plant and
Animal Genome XIII meeting held last January, held jointly with the
annual NAGRP meeting. Coordination funds helped support attendance at
PAG-XIII and will do so again for the upcoming PAG-XIV in January,
2006.
FUTURE ACTIVITIES. Suggestions from researchers to help this
coordination and facilitation program grow and succeed are always
appreciated. (Please send them to jreecy@iastate.edu). We will continue
our efforts on QTL database curation and expand these efforts to
additional species. To aid in this effort we are developing a
submission editor so that labs can directly deposit QTL data into the
database. Furthermore, we will link new maps and sequence information
to QTL as new information becomes available. In addition, we will
continue phenotype ontology development, BLAST tools development, and
software curation. In the next year, we will develop a genome sequence
assembly program that will allow researchers to develop genomic contigs
in species with incomplete genome sequence information.
There is an incredible need for species-specific genome databases,
which can serve as central repositories for integrated genomic data.
For instance, as livestock genomes are sequenced there is a preliminary
level of annotation that will be completed by Ensembl and NCBI, but
there is not consensus on what annotation is correct. Furthermore,
continued annotation efforts are necessary to realize the full power of
the genomic sequence. Although these efforts are well beyond the scope
of the currently funded NRSP-8 project, the database coordination
program plans to support community efforts toward this end. The recent
USDA-NRICGP RFA presents a wonderful opportunity in its call for
bioinformatics proposals. However, the funds available to support this
effort are not adequate to meet the immediate needs of the avian,
bovine, and porcine communities.
Items for the next update can be sent to me by no later than February 15
please.
(Prepared 01/06/06)
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