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Scientists Unravel Genome of the Cow
Signs of Human Intervention Seen

By David Brown
Washington Post Staff Writer
Friday, April 24, 2009

The genomes of man and dog have been joined in the scientific barnyard by the genome of the cow, an animal that walked beside them on the march to modern civilization.

A team of hundreds of scientists working in more than a dozen countries yesterday published the entire DNA message -- the genome -- of an 8-year-old female Hereford living at an experimental farm in Montana.

Hidden in her roughly 22,000 genes are hints of how natural selection sculpted the bovine body and personality over the past 60 million years, and how man greatly enhanced the job over the past 10,000.

As with other species, genes governing the immune system, the metabolism of nutrients and social interaction appear to be where much of the evolutionary action has occurred. The result is an animal that lives peacefully in herds and grows large on low-quality food, thanks to the billions of bacteria it carries around.

Selective breeding has exaggerated and spread some of those traits, producing hyper-passive Holsteins and muscle-bound Belgian Blues, and dozens of humpbacked breeds that combine characteristics of both.

"Are there signatures of the human hand in the cattle genome? The answer is plainly and clearly yes," said Harris A. Lewin, head of the Institute for Genomic Biology at the University of Illinois at Urbana-Champaign. He is the author of one of three papers on the cow genome appearing today in the journal Science.

Although sheep and goats were domesticated earlier, cattle are the most important herd animals in the world. There are about 800 distinct breeds, and together they contribute to the nutrition or income of about 6.6 billion people.

The cow is the first livestock animal whose genome has been sequenced, part of an effort to read and analyze the DNA of organisms that have scientific, medical or economic importance. In addition to dozens of microbes and several plants, those sequenced so far include the chimpanzee, mouse, rat, dog, chicken, mosquito, fruit fly, opossum and platypus.

Of a cow's 22,000 genes, versions of at least 14,000 have counterparts in other mammals. Cows appear to have about 1,000 genes that they share with dogs and rodents but that are not found in people.

The most recently evolved genes tend to be clustered in parts of the cow's 31 chromosomes where stretches of DNA have been duplicated, copied and inserted upside down, or added to by invading viruses. Those events are usually catastrophic and often lead to the fatal breakage of chromosomes. Over evolutionary time, however, a few survive and provide the raw material for new genes -- and new functions.

This clear relationship between chromosome instability and gene formation is giving scientists a new view of one way evolutionary change happens at the molecular level.

"Instead of having only a very slow and gradual change by mutation, you have the ability for much larger and dramatic changes because of these rearrangements," Lewin said.

As a practical matter, having the genome is also going to make cattle breeding faster and cheaper.

Traits carried by bulls are important in determining how much milk a cow produces. Because bulls don't make milk, however, a bull's "performance profile" has to be sketched by observing the milk production of his daughters -- a process that takes about six years and costs $25,000 to $50,000. Now, male calves can be tested at birth for milk-enhancing traits using gene-chip technology.

"It doesn't take a rocket scientist to see that makes sense both logistically and financially," said Curt P. Van Tassell, a geneticist at the U.S. Department of Agriculture's laboratory in Beltsville, who was one of the leaders of the project.

There are two types of cattle -- taurine, which have no humps and predominate in Europe, Africa, the Americas and much of Asia; and indicine, which have humps and are in South Asia and East Africa. Both lineages descended from aurochs, a much larger and more aggressive species.

Indicine breeds have much greater genetic diversity than taurine breeds, evidence that they were developed from a larger number of "founder" animals.

Cows have a large number of genes devoted to big-gun, nonspecific defenses called "innate immunity," probably reflecting the fact that the animals rely on a huge variety of bacteria and other organisms to digest the roughage they eat.

"They need an immune system that can deal with that large microbial population in close proximity all the time," said Kim C. Worley, a geneticist at Baylor College of Medicine and one of the leaders of the project.

Both types of cattle show evidence of natural selection in genes that appear to be involved in making the animals -- large, horned and potentially dangerous -- docile. In some breeds, specific variants of behavior-related genes are "fixed," or seen in essentially every animal. Curiously, some of those genes are in regions that in the human genome seem to be involved in autism, brain development and mental retardation.

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