One Bull Sired 14 Percent of U.S. Dairy Cows. Buried in His Genes, a Deadly Mutation

Two percent of dairy cows contain a mutation that leads to spontaneous abortions. David Gray / REUTERS

In 1962, the Arlinda farm in Northern California purchased a milk cow from Nebraska named Beauty. The manager bought the cow because she produced a lot of milk, but there was a big bonus: Beauty was pregnant. It would prove to be one of the most significant purchases in the history of the dairy industry.

That's because her male calf turned out to be quite special. Named Chief—Pawnee Farm Arlinda Chief, to be exact—the young bull had an enormous appetite, fierce strength, a broad chest, a large muzzle and a thick body, all sought-after traits. He had "a front end like a bulldozer," remembers Rus Shortridge, a Holstein fieldman in California at the time. The farm used Chief to breed, and that's when they noticed something magical: His daughters—who had wide rumps and udders—produced huge quantities of milk. Chief's daughters also began to produce milk at a very young age and in such large amounts that many couldn't believe it would last. Some attributed the plenitude to their good diet of California alfalfa, a nutritious food to which most cows didn't have access.

The farm started leasing out Chief for breeding, and his daughters began to appear around the country. Soon thereafter, "you could find [them] just about everywhere you could find cows," according to Progress of the Breed: The History of U.S. Holsteins. "To see them was to want them. To milk them was to want more."

Chief's daughter Beecher Arlinda Ellen produced 55,600 pounds of milk in her life, a world record that stood for more than a decade. His sons were strong and virile; many ranked among the world's top studs. Over the course of his life, Chief produced enough sperm to yield more than 16,000 daughters, and he has more than 500,000 granddaughters and 2 million great-granddaughters. In all, 14 percent American dairy cattle can trace their lineage to Chief.

The burly bull's outsized legacy was made possible in part by careful record-keeping and, later, applied genetics, in which farmers select cattle whose genes—like Chief's—are linked with high milk production and other valuable attributes. The dairy industry is adept at selecting for such positive traits, while also recognizing and weeding out problematic ones. Chief's offspring would test both abilities, by being off the charts in both directions.

Decades after he passed, breeders noticed that the miracle bull wasn't perfect. When two animals in his line bred with one another, some cows would spontaneously abort fetuses at elevated rates. A team led by Paul VanRaden at the U.S. Department of Agriculture eventually tracked this abortive variant back to Chief. The mutation would prove responsible for more than half a million spontaneous abortions in dairy cattle worldwide, which cost the industry about $420 million. (This is a significant figure, although one could say it pales in comparison to the estimated $30 billion in income Chief's genes have churned for dairy farmers around the world over the past 50 years.)

The USDA team took this information to Harris Lewin, a scientist at the University of California, Davis, who along with colleagues identified the exact source of the mutation. As described in a study published in the current issue of the Journal of Dairy Science, Lewin and colleagues found it arose because of a change in a single nucleotide, one of the building blocks of DNA. To find it, Lewin and colleagues collaborated with the genotyping company Neogen GeneSeek, one of the largest in the world, to sequence the genetic code of 246,000 animals.

Lewis explains that this mutation prematurely stops the production of a protein that's essential for cell death. This may sound counterintuitive, but to keep growing, especially at the intense pace seen during fetal development, cells need to know when to stop dividing. "Many tissue have to be modeled by death—parts die to form right structure," Lewin says. So when fetuses arise with this mutation, parts of them grow out of control, leading to abortion.

Dairy farmers are already applying this information in the field. Neogen GeneSeek developed a test based on VanRaden's 2011 paper that identified cattle that might be carriers; they have since updated it to search instead for the exact mutation from Chief that the new study pinpointed. Already, the frequency of cattle carrying this trait has been reduced to 2 percent. But with the new test, that percentage could one day reach zero, Lewin says: Problematic traits can be removed by not letting carriers breed.

When a carrier—like Chief—breeds with a noncarrier, half of the offspring pick up the mutation. About 7 percent of bulls, or half the 14 percent that trace their lineage back to Chief, carried this mutation just a few years ago. However, by selecting against these carriers and not letting them pass on their genes, farmers are pruning out this problem, while keeping Chief's nonmutated descendants and their milk-friendly DNA.

Chuck Sattler, the vice president of genetic programs at Select Sires, an artificial insemination company in Plain City, Ohio, says they run this test on every bull they consider purchasing. (They own 1,700 dairy and beef bulls, which produce 15 million breeding units of semen each year.) If a bull tests positive for this mutation, "it would be a strong negative." Sattler says he has turned down bulls who have tested positive and hasn't brought in a carrier since 2013.

Having a more precise test, which this study has made possible, also saves people like Sattler a lot of time and money.

This episode is just one example of how the dairy industry is the most advanced area of agriculture, in terms of incorporating genetics, says Jeremy Walker, with Neogen GeneSeek. All bull semen is tested for a variety of genetic defects, so problematic traits can be isolated and good ones can be recognized even before a bull has offspring. But sometimes, as in Chief's case, it takes years to unravel the good from the bad.
