Learning from Studs

Most dairy farmers treat their heifers like little princesses. Not only are these the potential mothers of more cows, but they’re also the day-to-day producers of a dairy farm’s bounty. Each time a healthy female bears another calf, she’s set to provide a steady supply of marketable milk for months. All heifers are nurtured to adulthood, whereas the vast majority of their bovine brothers meet a different fate.

In an industry where profit margins are slim, there’s tremendous pressure to increase a cow’s production of high-quality milk. Toward that end, scientists scrutinize the genetic inheritance of bulls, looking for indications that they’ll sire daughters capable of reproducing easily and yielding prodigious quantities of milk.

Initially, U.S. dairy breeders screen for potential stud bulls among the calves of only the 1 or 2 percent of cows that are tops in milk production, explains geneticist Curt van Tassell of the U.S. Department of Agriculture. Of the bulls making this cut, he notes, only 1 in 10 will continue into an active artificial insemination program. If a bull’s genetic line looks especially strong and his early offspring are productive, he may eventually be used to father 80,000 or more daughters. In contrast, a bull of just average quality might sire none.

Of course, since bulls don’t produce milk, identifying whether they carry genes for good milk production isn’t easy. In addition to assessing a bull’s heritage, breeders indirectly judge a bull’s genetic value by quantifying the performance of his daughters. Dairy scientists refer to the latter assessment as progeny testing, van Tassell explains. But researchers would like to find a better way to identify bulls that will sire productive cows.

Several research teams are trying to identify genes that mark bulls likely to ace a progeny test. They’re poring over DNA gleaned from semen that has been collected—and often all but forgotten—over the past half century from scores of related animals. The DNA profiles being created are the animals’ genetic pedigrees. The researchers’ goal is to tie genetic anomalies appearing within these pedigrees to various superior traits that have been identified over the years in the bulls’ daughters.

Making this line of investigation possible, explains University of Missouri geneticist Jeremy Taylor, are good records of the backgrounds and milk productivity of cows in the United States, as well as the stored semen samples.

The good news for researchers such as Taylor and van Tassell is that use of these records and samples is free. In fact, Taylor recently acquired a set of decades-old semen samples from USDA’s National Center for Genetic Resources Preservation in Fort Collins, Colo., which he’ll use to determine which genes in a Holstein line play dominant roles in milk production.

Ancestral gene hunts

Geneticist Harvey D. Blackburn coordinates a division of the Ft. Collins facility. Currently, the facility holds more than 150,000 samples from not only cows but also some 65 other mammals, birds, and fish. All the samples are kept frozen at –196 °C in liquid nitrogen. Thus stored, the semen could be viable for decades or even centuries, and the embryos could be kept almost as long and eventually implanted in a surrogate mother.

Included are semen from 850 Holstein bulls and 150 embryos from 25 Holstein cows. Indeed, Blackburn notes, his repository, which he calls a gene bank, currently holds enough Holstein germ plasm and embryos to reestablish a live heard if a catastrophe were ever to wipe out the breed. However, Blackburn says, the frozen vials of sperm and tissue will serve mostly as research tools or for improving existing breeding lines.

USDA maintains an even bigger resource for dairy scientists at its flagship Beltsville, Md., laboratory. There, the Cooperative Dairy DNA Repository houses five –20 °C freezers holding some 100,000 vials of semen from at least 15,000 different bulls. Some of the samples were collected as far back as 1960, notes van Tassell, who oversees the collection.

Van Tassell’s collection continues to grow with contributions of semen that came from bulls now long dead. Where does he find the archived sperm? “You’d be amazed how many tanks of liquid nitrogen [on farms] around the country are sitting around with 30-year-old semen in them” even though such samples are worthless commercially, he says. Van Tassell explains that cattle breeding has become so competitive that whenever a new high-quality stud comes along, the value of sperm from bulls that came before him plummets. “Ten-year-old animals are generally not competitive for breeding purposes,” says van Tassell.

His goal is to retrieve old bull-semen samples from around the country, before they’re discarded, and to collect whatever information is still available on the bulls they came from.

Blackburn’s team is also roaming the countryside in search of a forgotten genetic bounty. However, his gene bank is not as restricted as van Tassell’s is. For instance, he can acquire material not only from dairy cattle, but also from other livestock breeds. Moreover, because most of the semen samples in the Beltsville repository come from artificial-insemination companies that otherwise sell their products, the companies insist that their donations be used for research only, never for projects that would result in live births.

Learning from history

Using statistics on the inheritance of cattle traits, some sophisticated computer software, and comparisons of DNA from animals throughout a pedigree, scientists can trace genes to specific small regions on bovine chromosomes, van Tassell explains. “It’s not a trivial mathematical process, but it’s doable.” Scientists are increasingly gaining access to both old and new bull-semen samples from repositories such as in Beltsville and Fort Collins, he points out.

Taylor is using van Tassell’s gene bank to study a Holstein pedigree for about 1,000 related bulls that go back about 40 years. The collection “is simply unbelievable,” says Taylor. Using registration numbers for each animal, he says, “we can go to the Holstein data base and pull back information on the genetics of each and every animal. In other words, not only do we know who’s the father of whom, but we know genetically what’s the merit of each animal for milk production, fat production, and protein production.”

Taylor looks for DNA variations on chromosome 6 in Holsteins because previous studies have identified that chromosome as a hot spot for genes affecting milk, fats, and proteins. “By doing this, I can identify the locations on the chromosome that harbor genes that cause variations in these economically important traits [in] Holsteins that farmers have intensively bred,” says Taylor.

Theoretically, breeders could screen for beneficial genes in bulls before they’re bred. In other words, this screening tool could be applied months if not years before progeny testing would be possible.

Taylor explains that his research has been aided by the fact the subject is Holsteins. These dairy cows have been intensively monitored, managed and documented for many years. They’re also numerous. Some 90 percent of all U.S. dairy cows—of which there are now roughly 9 million—are Holsteins. They also represent the vast majority of the bulls with semen in USDA’s Cooperative Dairy DNA Repository.

Taylor is also studying the genetics of Black Angus, the nation’s leading beef breed. Because Angus herds tend to be far smaller than dairy herds and are bred less often through artificial insemination, there isn’t as extensive a semen repository for angus-genetics researchers to tap. Still, Taylor has assembled data from some 1,600 bulls into a pedigree spanning more than 50 years and 14 generations.

“I can DNA type an animal born today, look at his pedigree, and identify part of his chromosome that originated in Prince of Malpas, an angus bull born 65 years ago,” says Taylor. The trick is linking the right bits of DNA to the traits he and other livestock breeders most care about—such as growth rate and fat marbling in muscle.

Finding those linkages is tough, he says, but further research will accomplish it.