Iowa State Animal Scientists Coordinate National Tracking of Animal Genome Research
January 11th, 2006
AMES, Iowa — A team of Iowa State University 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 (DNA) 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, the chicken genome was recently sequenced 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," Reecy said. "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 has been 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. "He's developing computer programs that automate things people used to do by hand," Reecy said.
So far, two programs have been created to handle special data. A quantitative trait locus (QTL) 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.
QTLs have been mapped for some of the most economically important traits in livestock, such as meat quality, fertility and disease resistance.
The Iowa State 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.
"This tool should speed up the search for underlying genes," Reecy said. "Our long-term goal is to make PigQTLdb a part of the genomic information resources for pigs, as well as other species."
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.
The Bioinformatics Coordination Program was initially funded for five years. Reecy said several universities submitted proposals when it was decided to add bioinformatics to the national animal genome program. "At the time, Iowa State easily had the most experience doing this sort of work," he said.
The faculty in this program are part of the Center for Integrated Animal Genomics, one of Iowa State's presidential initiatives. It is made up of an interdisciplinary group of 75 Iowa State faculty from five colleges who use animal genomics, microbial genomics, comparative genomics and bioinformatics to identify, map and understand the function and control of genes.