USDA Grants Awarded to Mason Bioinformatics Researchers

Posted: May 21, 2007 at 1:00 am, Last Updated: November 30, -0001 at 12:00 am

By Jennifer Halpin

John Grefenstette
John Grefenstette

John Grefenstette, professor of bioinformatics and computational biology, and his research associate, Lakshmi Matukumalli, have been awarded two grants to analyze the recently completed bovine genome sequence.

The cow is the first livestock animal to be sequenced, and the data is expected to contribute to improvements in cattle breeding, animal health and human nutrition.

The grants were awarded under the U.S. Department of Agriculture (USDA) National Research Initiative Competitive Grants Program and bring the total current USDA bioinformatics research funding in Grefenstette’s lab to more than $1.1 million.

One purpose of the new Mason research project, titled “Haplotype Analysis from Bovine Genotype Data,” is to determine precisely how various breeds are different on the genetic level. There are more than 800 recognized breeds of cattle and different breeds have been developed to thrive under a variety of environmental conditions.

The human genome project has shown that within any given species, there are many specific places in the genome where individual differences can be detected. This project will help determine the amount of variation in cattle.

Recent developments including the completion of the bovine genome now present the opportunity for large-scale genotyping of cattle. This project addresses the need to evaluate and adapt existing computational tools for the analysis of genotype data from cattle, and to develop new bioinformatics tools as needed.

As part of the project, Mason researchers will create a database of individual genetic data from more than 12,000 animals representing 19 breeds of cattle.

The resulting data will be shared with an international group of researchers who will use the data to further study the genetic properties of individual breeds. The ultimate goals are to improve the process of cattle breeding, promote animal health and improve human nutrition.

The second grant, titled “Bovine MicroRNA Transcriptome Analayses: Discover, Tissue Specific Expression Profile and Target Gene Prediction,” was awarded to Matukumalli, a 2004 graduate of the Mason bioinformatics PhD program. Matukumalli has been working in Grefenstette’s laboratory as part of the USDA-funded bovine genomics project since 2004. The new project will look at how genes are regulated in the bovine genome.

A recent discovery found that small RNA molecules (micro-RNAs) provide a mechanism for “silencing” expression of protein coding genes in the cell. So far there is no published data concerning this important mode of gene regulation in cattle. This project aims to characterize micro-RNA expression in various tissues of cattle and predict the genes that are targeted for silencing.

The study will expand understanding of bovine gene regulation and provide initial data to assist in determining the potential impact of micro-RNAs on animal development, productivity and well-being.

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