Monday, December 01, 2014

Cows, clones, and genomic selection

Via Gwern. See also Genomic Prediction: No Bull and It's all in the gene: cows.
National Geographic: ... The ideal rib eye in the American market is a marriage of opposites: It's richly marbled with internal fat to give it flavor, but it has only a thin layer of the back fat that no one wants. In the parlance of the U.S. Department of Agriculture, it's both "prime" and "yield grade 1." Cows that produce such beef are rarer than nose tackles who are great dancers. Only three carcasses in 10,000 make the grade.

But that night in the packing plant, Lawrence watched two go by in close succession—it was like being struck twice by lightning, he said, but in a good way. He pulled out his cell phone and called Dean Hawkins, the head of the animal sciences department at WTAMU. "It's time we cloned one of these things," he said.

... Though it's more expensive, there's a way to spare both cow and rancher the experience of artificial insemination: in vitro fertilization, or IVF. It's 90 percent of Trans Ova's business now, Crow says. The company does about 20,000 cattle IVF procedures a year, including 15 or 20 on the best cows at 44 Farms. ...

"We had a female in our herd—a foundation female," Slattery recalls. "She's deceased now. She lived to 13 years old, and she was very fertile. She had over a hundred progeny—well over a million dollars' worth of progeny in her lifetime. And it never really affected her. She had a wonderful life."

These days 44 Farms has a good idea that it has found such a prizewinner even before she has offspring, because the farm tests its calves' DNA when they're six months old. Just a couple drops of blood taken from the thin skin under the tail suffice. From that blood, Zoetis, a subsidiary of Pfizer, can determine how the animal compares with other Angus cattle at 50,000 points in the genome where Angus cattle are known to vary.

It's unclear what specific effect those individual mutations, or the genes they're part of, have on the animal. But by gathering data on thousands of Angus, Zoetis has established statistical correlations between each variation and traits that cattlemen care about—traits such as birth weight, weaning weight, marbling, and so on. The test assigns the animal a genetic score on each trait.

For the past five years 44 Farms has been using those scores to select animals to breed—and the results are in the beef, Slattery says. Though it's primarily a seed stock producer, 44 Farms also markets its own 44 Steaks to consumers online and to fancy restaurants. Since the farm began using genomic testing, it has seen a 20 percent increase in the number of carcasses that are graded prime or choice, the USDA's second-best grade for beef. Such carcasses fetch premiums of up to $500 a head. "It's absolutely huge," Slattery says.

There's an environmental upside too. The 44 Farms cattle are fattened at a feed yard in Hereford, Texas, but 44 Farms retains ownership of them—and they're given no hormones, antibiotics, or other additives. And thanks to the improved genetics of its herd, it no longer has to fatten them to 1,400 pounds to get meat that has prime or choice marbling. It's slaughtering them at 1,250 pounds, saving more than a month's worth of feed.

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