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ARS Scientists Sequence Swine and Cattle ESTs

NEW YORK, Jan 4 – Scientists at the U.S. Meat Animal Research Center in Clay Center, Neb. have sequenced 80,000 ESTs from the beef cattle genome and 40,000 from the swine genome in a livestock genomic pilot project, the United States Department of Agriculture’s Agricultural Research Service announced Thursday.

The sequence tags, which the researchers hope will help livestock breeders to develop better quality animals for beef and pork, are now available on Genbank. Currently, scientists from The Institute for Genomic Research are analyzing and annotating this sequence information.

The project “is designed to look at sequence variation between different animals, and second to provide markers amenable to automated genotyping—the way we determine which genes influence production traits,” said Timothy Smith, a research chemist at U.S. Meat Animal Research Center who worked on this project.

Scientists from the ARS will be working with private companies to develop microarrays based on these sequences.

The practical applications include, for example, discovery of a genetic variation that may be a basis of a variation in meat tenderness, Smith said. If this variation holds true in further investigation, a specific test could be developed to see if an animal has the variation that would make the meat more tender, and breed the animals to have this variation.

Other variations could form the basis of differences in how livestock respond to changes in the environment, or differences in susceptibility to certain diseases.

TIGR has made the cattle gene information available on its website, along with analysis, in a cattle gene index. It is currently constructing a swine gene index.

But this cattle and swine genome project is not the only bull in the pen. Currently, the National Animal Genome Research Program is constructing maps of the chicken and pig genome; there is BovMap, the multinational cattle gene mapping project based at INRA in France; and Japan’s Animal Genome Database that allows inter-species comparison of chromosomal information.

In the private sector, Celera and Austin, Tex.-based Genomic FX are conducting a large-scale project to find SNPs in the cattle genome; Monsanto has began sequencing the genome of swine and aborted a project to sequence ESTs of dairy cattle; and in New Zealand, Ag Research Limited is sequencing the sheep and cattle genomes. But unlike the work of Smith and other public livestock genome researchers, the data generated in these projects is not publicly available.

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