One In A Million: Part 1

An incredible genetic circumstance creates a unique DNA puzzle: a chimeric horse.

From The American Quarter Horse Journal

“Excluded.” For the second time Denise Charpilloz had sent in hair from her 2004 foal out of her mare Sharp One for DNA testing and parentage verification. And for the second time, the Veterinary Genetics Laboratory at the University of California, Davis, had excluded not only the stallion Dunbars Gold as the foal’s sire, but also Sharp One as the foal’s dam.

Every now and then, people make mistakes when they submit mane (or tail) hair samples for DNA testing on a foal. It usually happens when people accidentally mix hair if they’re collecting samples from more than one horse. Although very rare, sometimes mares can actually switch foals or the wrong stallion’s semen is unintentionally shipped and used to breed a mare. All those scenarios result in a DNA test that “excludes” a mare or stallion as a foal’s parent. Usually it doesn’t take long to figure out what went wrong. But “I saw it being born!” Denise says. “I didn’t mix it up with any other foals; there were no other foals!” And Dunbars Gold’s owner, Carole Dunbar, had only one stallion to ship semen from. AQHA’s registration department turned back to the lab’s geneticists: could they please give the case another, much closer, look?

Puzzling Pattern

The case landed on the desk of Dr. Cecilia Penedo, the lab’s associate director of service and genomic research and development. Dr. Penedo immediately noticed that Dunbars Gold and Sharp One are brindles. “It’s a very rare coat pattern in horses,” she says, though it is common in dogs and cattle. “People have not been very successful reproducing this pattern through breeding, and we’ve never really had much information on the genetics of it because it is so rare.”

Do you have coat color questions? Get your answers with AQHA’s Quarter Horse Coat Colors report, a full-color, 20-page report that is packed with easy-to-understand information about all 17 recognized colors.

In fact, of the more than 4.7 million American Quarter Horses registered with AQHA (excluding appendix horses), the registration department has a list of only 15 horses who have exhibited some form of the brindle coat pattern. Dr. Penedo began reviewing the lab’s testing on the horses. “When I looked up the stallion, Dunbars Gold, I found that we had tested him three times before we established his (DNA) type,” Dr. Penedo says. The first two tests the lab ran were on mane and tail hair samples. “At that time, there was something odd about his type,” she continues. “It looked like the hair samples came from two different animals, like the hair had been mixed together. We requested a second sample and had the same problem.” Convinced the hair samples were getting contaminated, for the third test, the lab requested a blood sample from the horse. “When the blood sample came in, we got a perfectly good type that would be consistent with one animal,” she said. The blood test results also had some things in common with the hair results. The lab used the DNA type obtained from blood for the parentage verification on Sharp One’s 2004 foal (the first of the stallion’s foals to be tested for parentage verification). But in her review, something else caught Dr. Penedo’s attention.

“The oddest thing about the stallion’ blood sample results was that the DNA types for sex-linked markers were typical of a female and not a male,” Dr. Penedo says. “There was no evidence of a Y chromosome.” Penedo decided to retest Dunbars Gold. “We went back to the original hair samples and used a single hair for the DNA test,” she says. “And we performed several of these single-hair tests. “Some of the tests yielded a perfectly good type for a male individual and some a good type for a female individual.” Some of the results also showed two DNA types within a single hair root. “At that point, I thought, ‘This horse is chimeric,’” Dr. Penedo says. Stay tuned for the last half of this story.

You'll learn to name all 17 recognized American Quarter Horse colors, be able to pick each of them out in a pasture full of horses, and better yet, you will know how each color is genetically derived. Learn all of this and more with AQHA's Quarter horse Coat Colors report.