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A Scary Lack of Genetic Diversity

The Atlantic:

It started with a bull named Pawnee Farm Arlinda Chief, who had a whopping 16,000 daughters. And 500,000 granddaughters and more than 2 million great-granddaughters. Today, in fact, his genes account for 14 percent of all DNA in Holstein cows, the most popular breed in the dairy industry.
Chief—let’s call him Chief for brevity’s sake—was so popular because his daughters were fantastic milk producers. He had great genes for milk. But, geneticists now know, he also had a single copy of a deadly mutation that spread undetected through the Holstein cow population. The mutation caused some unborn calves to die in the womb. According to a recent estimate, this single mutation ended up causing more than 500,000 spontaneous abortions and costing the dairy industry $420 million in losses....

Amidst this progress, the USDA scientists also noticed something odd. To understand how odd, you just need to know that animals have two copies of every gene, one from each parent. As Chief’s genes took over the Holstein population, farmers would sometimes end up mating a bull and cow both originally descended from Chief. So a resulting calf could sometimes end up with two identical copies of a Chief gene, one inherited via its mother (perhaps a great-granddaughter of Chief) and one via its father (perhaps a great-grandson).

But there was one particular gene from Chief that never, ever showed up twice in any of his descendants. Plenty of cows had one copy of this Chief gene; others none; but never two. This defied probability. All the USDA team knew about this gene is that it corresponded to a series of genetic markers on chromosome 5, which could be traced back to Chief.

The logical conclusion to draw, if you’re a geneticist, is that these genetic markers corresponded to a vital gene that had become garbled. Cow embryos with one faulty copy of the gene and one working copy grew up just fine, but those with two faulty copies died in the womb. They were just never born, which is why the team could never find any. (Chief himself had one copy, which why he was a fine healthy, bull.)...Lewin and his post doc Heather Adams got to work. “Within 48 hours, we had a candidate,” he says. The stretch of DNA in question corresponded to the gene Apaf1, which had been well studied in mice. Brain cells in mice embryos with a faulty Apaf1 would grow out of control, until the embryo eventually died. “The reason we had a candidate so quickly was because of the tremendous investment in mouse genetics,” says Lewin. The scientists trudging through the mouse genome could probably have never known an obscure gene they isolated had such a huge effect on the dairy industry.

Luckily, genetic testing has allowed the dairy industry to get around this problem.  But the fact that so much of the Holstein herd is so closely related is rather scary.  But, in the end, dairy faces many other major issues.