USDA Scientists Rapidly Expand Database of Gene Segments

By Ben Hardin
July 10, 2000

CLAY CENTER, Neb., July 10—Progress by a team of Agricultural Research Service scientists shows that biotechnology’s best shot at improving livestock may be to help conventional breeders identify genetically superior animals.

“This team of 15 scientists is generating a vast amount of new genetic information that’s being shared with researchers around the world,” said Floyd P. Horn, administrator of ARS, the chief research agency of the U.S. Department of Agriculture. The team is based at the Roman L. Hruska U.S. Meat Animal Research Center (MARC) operated by ARS at Clay Center. The team’s findings are accessible through the databases of the National Center for Biotechnology Information (NCBI) Genebank in Washington, D.C., and databases at the Clay Center facility.

In the past year the team has deciphered 50,000 gene sequences in the cattle genome, and more than 30,000 sequences in swine. Within the next three months, the scientists hope to add 30,000 additional sequences from cattle and 10,000 from swine.

The numbers to date represent about 95 percent of the publicly available information on DNA segments called expressed sequence tags (ESTs) for cattle and almost 90 percent for swine, according to Dan B. Laster, who retired as director of the Clay Center facility on June 30. Laster began assembling the Clay Center team in the early 1990s.

ESTs represent significant parts of genes that determine the proteins produced by certain tissues. “Most of an animal’s DNA never seems to do anything,” said biochemist Timothy P. Smith, who leads the ARS team. So the scientists focus on 2 to 5 percent of the DNA that’s turned into RNAs--ribonucleic acids--which are an intermediate step in making proteins.

A similar but smaller effort is also being conducted by an ARS group in Beltsville, Md. That group is sequencing genes that function in the mammary gland of dairy cattle. The Maryland group is working to identify all of the genes responsible for milk productivity traits and the genes that cause superior animals to produce larger quantities of milk proteins in their mammary glands. By using computers to compare gene sequences from different cows, the researchers will sort out the genes that control milk composition. The Clay Center and Beltsville groups work together to deposit the information into the NCBI and Clay Center databases.

According to Steven M. Kappes, a recent member of the MARC genomic team and now ARS National Program Leader for Animal Production and Germplasm, each of many genes may have a small impact on an inherited trait, but when added together they may have great economic importance for a herd and for the livestock industry.

The accelerated pace of gene mapping stems partly from successes by international scientists in the much larger Human Genome Project. Humans and livestock basically have the same genes, but with small differences in sequences and arrangement on chromosomes. Comparisons and contrasts between gene sequences of various species are helping biomedical researchers learn how proteins work and how the human body works, said Kappes.

Scientific contact: Timothy P. Smith, ARS Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, Neb., phone (402) 762-4366, fax (402) 762-4390, smith@map.marc.usda.gov.