In Search of Better Beef and a Greener Cow

Posted: May 22, 2009 at 9:39 am, Last Updated: May 28, 2009 at 12:23 pm

By Marjorie Musick

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Working from a computer lab, Mason bioinformatics researchers have entered the virtual barnyard to look for genetic clues about the evolution of cattle. The goal? To find ways to develop cattle that consume fewer resources, produce less greenhouse gases and provide higher quantities of more tender beef and milk in order to create more sustainable food production in a world challenged by global population growth.

John Grefenstette, professor of bioinformatics and computational biology, Lakshmi Matukumalli, research assistant professor, and Rafael Villa-Angulo, a graduate student in bioinformatics, collaborated with 300 researchers from 25 countries to analyze the DNA sequence of a Hereford cow.

The researchers also examined the differences among DNA samples (polymorphisms) taken from 497 cows in 17 different breeds of cattle and two related species. Computational and statistical analyses were performed to understand how modern cattle breeds evolved from the ancient breeds.

Growing the Cattle Family Tree

“This bovine genome sequencing project is important for animal researchers because it serves as a model for all livestock species. This work provides insights about the origin of cattle in relation to other mammals. It also clarifies the relationships and genetic diversity within and across various breeds of cattle,” says Matukumalli.

The team developed new computer algorithms for the analysis of the 30,000 or more variations of genetic data found in the cows and produced a variety of graphical outputs, including charts, graphs, colorful blocks and tree-like diagrams.

“Cattle family trees are substantially different from human ones due to the effects of inbreeding from artificial insemination. We had to modify the data analysis methods that were previously used to study the diversity in the human population so that they would work with cattle DNA,” says Grefenstette.

What did they find? The data supports the hypothesis of two separate domestication events of cattle between 8,000 and 10,000 years ago — one in the Indian subcontinent (indicus) and another (taurus) that formed most of the modern breeds widely used for dairy and beef across the world.

A Decline in Genetic Diversity Spotted

The bioinformatics analysis by the Mason research team suggests that the genetic diversity among taurine breeds is similar to that of humans and that the rapid decline in genetic diversity among cattle is of some concern. Lack of genetic diversity is worrisome because breeds could become less viable and more susceptible to disease. This new data will benefit efforts by the artificial insemination industries and breed organizations to conserve genetic diversity and produce healthier cows.

Although DNA sequencing has been conducted on humans and other animals, such as mice and dogs, the cow is the first livestock animal to be sequenced and the first animal to be sequenced for the purpose of improving the human food supply.

The data is expected to contribute to increased quality and efficiency of meat and dairy production through genomic selection and may even help to protect the environment by creating “greener” cows.

“Certainly, part of the goal is the improvement of global food production. We’ve produced data that people will be studying for years. Scientists will be trying to develop more environmentally friendly cattle that consume fewer resources, produce less greenhouse gases and provide more beef and milk. We’ve helped to lay the groundwork for those future studies,” says Grefenstette.

The findings were published in the April 24, 2009, issue of Science and are available online at

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