Cracking the Horse's Genetic Code

Genetic research is today's scientific frontier, disclosing information that will affect future equine health and help correct genetic defects. By Jack Moore for EQUUS magazine.
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It all begins with a single horse, usually in the earliest embryonic stages, with one mistake in a single piece of DNA. As that DNA fragment, or gene, is replicated in all the cells in his body, so is the "typographical error" in his genetic code.

A foal usually inherits a genetic defect from a mutant gene passed on by each parent. |

A foal usually inherits a genetic defect from a mutant gene passed on by each parent. |

The result is a different set of instructions for building one protein that becomes part of that developing embryo. From the individual's standpoint, this clerical mistake may not amount to much. After all, he has some 70,000 genes on his 32 pairs of chromosomes, and the vast majority of them work just as intended. Most likely he'll be born apparently healthy, lead a productive life and die from an unrelated cause, taking the mutation with him.

But let's say this horse grows up to become a popular stallion whose "error" produces a potentially debilitating abnormality that's controllable through medication or surgery. As the horse sires offspring, his genes--"typo" and all--are passed to the next generation. That single genetic error can multiply and appear in thousands of individuals over the course of several generations.

Even if the new defect causes severe problems, it could be years before the pattern is suspected as genetic in origin. By then it will be difficult, if not impossible, to erase the error. Many owners will be involved, few of whom are able and willing to sacrifice valuable breeding stock for the greater good of the breed. As the politics drag out, the genetic mutation becomes part of the biological heritage of more and more horses.

Over the past several years, however, researchers have used new and better tools to unlock the mysterious world of equine genetics. Helped greatly by groundbreaking studies of human and other mammalian genetic makeup, these researchers expect to develop a working "dictionary" for the horse's chromosomal lexicon--known as a genetic map. With it, researchers can develop the necessary tests to identify specific mutations and, in theory, selectively eliminate them. The science of horse breeding is about to undergo a transformation.

Genetic Spell-Checking
Genetic defects tend to be recessive, meaning that for a horse to be affected by a given disorder, both parents must possess the mutant gene and pass it along to their foal. If these carriers are never bred, the typo can't be passed on to the next generation. Putting such eugenics into practice is not as easy as it sounds: Unapparent carriers of the gene are physically indistinguishable from noncarriers, and until recently, pedigree research was the only tool breeders had to trace heritable conditions in a horse's family tree.

But pedigree analysis uses statistical probabilities for establishing the heritability of a trait. "You have to have a study of a large enough number of horses and their offspring, normal stallions and affected stallions and look at all their offspring," says Kansas State University researcher Judy Cox, PhD, who has studied the heritability of hyperkalemic periodic paralysis (HYPP) and of retained testicles (cryptorchidism).

Breeders' cooperation and honesty are essential to the success of a study passed on pedigree analysis, and interpreting pedigree information is tricky. "You're going to get an answer, but you have to know how good your data is to know whether to believe the answer or not," says Gus Cothran, Ph.D., a geneticist at the University of Kentucky's Gluck Equine Research Center. "You have to be really careful that you're not just seeing what you want to see."

A much more definitive, but also much more expensive, approach is a controlled-breeding program conducted at a research facility. "It requires a significant research budget," says Cox. "The biggest cost would be the maintenance of the horses. For chryptorchid study, you probably have to keep the offspring around for two years." Typically, controlled-breeding projects take three years and cost $100,000, says Ann Bowling, Ph.D., equine geneticist at the University of California's veterinary genetics laboratory in Davis.

Enter DNA testing. In October 1992, Eric Hoffman, Ph.D., a human geneticist at the University of Pittsburgh, and Sharon Spier, DVM, Ph.D., a UC-Davis equine researcher, published a landmark paper on HYPP in the journal Nature Genetics. Long suspected to be a familial disease, HYPP causes muscle tremors in horses, sometimes leading to "dog sitting," complete paralysis and even death.

Hoffman and Spier discovered a defect in a protein that regulates the flow of sodium into muscle cells, much as a light switch regulates the electricity that reaches a lamp. They further traced the mutation to a single nucleotide error that produced the wrong amino acid (leucine instead of phenylalanine), which in turn produced the faulty sodium-channel gene. In short, one misplaced letter in the genetic sequence--one typo--causes HYPP.

A Universal Alphabet
What made the HYPP test possible, and what promises to unlock the doors to many other equine genetic disorders, is the breathtaking pace of human genetic research. "The human map is progressing at an incredible rate. That's going to be our encyclopedia. So much money and effort have been spent on finding these diseases in humans; now we just have to correlate them," says Cothran.

That correlation depends on finding "linkage groups"--pieces of DNA that are common to more than one species, rather like similar words in the Indo-European "family" of languages derived from common roots. By a happy circumstance of mammalian evolution, Cothran says, "there is a high degree of conservation of blocks of the genetic information, so if you know of a gene for whatever characteristic occurs in man, you know where to look for it in any other vertebrate."

The geneticist hopes to apply that model to several equine disorders he's studying, including epitheliogenesis imperfecta (EI), a fatal condition in which foals are born with large areas of skin, oral membranes and sometimes hooves missing. People suffer from a similar defect called epidermolysis bullosa. "Based upon the pathology of the disease, it appears that EI is equivalent to the disease that occurs in humans," says Cothran. "What we want to find is a marker for the gene so that carriers can be detected."

Correcting The Error
Finding a mutation is one thing; eliminating it is another matter entirely. Even if researchers manage to crack the equine genetic code and locate the errors responsible for inherited diseases, defects and deficiencies, breeders and breed registries are the ones who must put those discoveries to good use.

For breed registries, genetic defects pose a real quandary. How much pressure can they afford to apply to effectively blacklist a group of horses on the basis of one bad gene? How conclusive must the evidence be that this gene, and not another, is the cause of the disorder?

"Registries don't exist to tell people what to do," says Ralph Clark, executive director of the International Arabian Horse Association. If a CID test ever becomes available, "we would certainly recommend that people use it," says Clark; anything stronger than recommendation is "a ticklish subject."

Lisa Hale, DVM, has seen dozens of EI cases in her practice in Arthur, Ill., and says that breeder inaction is an important accomplice in the spread of a genetic disorder. "Everybody needs to be up front about it. If it's something that's hurting the breed and we stick our head in the sand, it's not going to go away."

The American Saddlebred Horse Association (ASHA) supported EI research by openly soliciting blood samples from afflicted foals for Cothran's research. "Until we have a diagnostic test, we can't label horses as being carriers," says ASHA executive director Pat Nichols. "This is going to be a moment of truth for our association once we have a diagnostic tool. There are no easy answers, but I feel that we're going to have full disclosure."

This article originally appeared in the December 1995 issue of EQUUS magazine.