A team of IowaStateUniversity animal scientists coordinates a national project that uses computer technology to manage vast amounts of animal genomic information.

Rapidly improving technologies have made it possible for researchers to make strides in genome research, including the ability to examine the genome of an organism as a whole, rather than just one or a few genes at a time.

As a result of genome sequencing projects, researchers now have access to the complete genome sequence of several species. For example, scientists recently sequenced the chicken genome and the cattle genome will be completed in the next several months, while sequencing of the swine genome has just begun. Now researchers need to determine the role each gene plays within an organism, plus how they interact with each other.
James Reecy, associate professor of animal science, leads the Bioinformatics Coordination Program that is part of the National Animal Genome Research Program. "Bioinformatics is the application of computer technology to the management of biological information," says Reecy. "It's an essential part of the genomics research infrastructure."

The federally funded livestock genome coordination project got underway in 1993, with cattle, sheep, swine and poultry. The project was expanded to include horses and aquaculture species, as well as bioinformatics.

The bioinformatics program began in October 2003 as livestock genome sequence information was first becoming available. Reecy's team works to provide effective data organization and management, plus develops tools and resources that make it possible for other researchers to use and analyze the information.

Also on the Iowa team are Max Rothschild, Charles F. Curtiss distinguished professor of agriculture, and national coordinator of the Pig Genome Coordination project; Susan Lamont, Charles F. Curtiss distinguished professor of agriculture; and Chris Tuggle, professor of animal science. Lamont serves as a liaison to researchers working on the chicken genome, while Rothschild and Tuggle work with others interested in the pig genome.

Reecy is the liaison to all other species in the project. He also handles administrative duties for the bioinformatics project, setting priorities and building alliances with others involved in genomic projects.     

Zhi-liang Hu, associate scientist, does most of the day-to-day computer work, providing assistance to all the national genome coordinators and developing databases, Web sites and tools that help others access the data.

So far, two programs are ready to handle special data. A quantitative trait locus is a region of DNA that is associated with a particular trait. These QTL regions contain genes, one of which contains a mutation that is responsible for a particular trait.

The IowaState team developed a pig QTL database that makes it possible to search and compare results from different studies, derived from different populations and obtained using a variety of methods. Users of the database, which is called PigQTLdb, can electronically confirm or at least narrow down promising chromosomal regions from overlapping QTL results.

Another program, called Expeditor, can be used to combine human gene structure information and animal species sequence information. This comparative analysis can help researchers identify genes associated with economically important traits in farm animals. "This software helps minimize tedious manual operations and reduces the chance of error," Reecy said.

Currently, a computer program is being developed to aid in the generation of a standardized vocabulary to describe animal traits.