The Equine DNA Roadmap

Genetic testing of hair samples by a licensed laboratory can help direct horse owners toward successful breeding.

Photo: Stephanie L. Church, Editor-in-Chief

The equine genome takes us on a journey from prehistoric times to a future of identifying and manipulating individual genes.

"Genome mapping." It's a phrase we hear a lot in the 21st century, an age of scientific advances the likes of invisibility cloaks and bioengineered body parts. But what exactly is this road through a species' heritage, and what do the points along the map tell us about our animals and ourselves?

Before we answer these questions, here’s a quick refresher on DNA in general: Deoxyribonucleic acid is a double-stranded molecule that looks much like a spiraling ladder (Remember those charts on the wall in biology class?). First described in 1953 by Drs. James Watson, Francis Crick, and Rosalind Franklin, the DNA molecule’s double helix contains all of the information that makes up every living organism. 

DNA is comprised of four nucleotide bases (proteins): adenine (A), guanine (G), cytosine (C), and thymine (T). A pairs with T and C with G across the “ladder.” (Is it all coming back to you now, like a 9th grade biology test?) The DNA provides the narrative for every cell in the body, with sections (genes) coding for specific traits. The collection of genes that describes an entire organism is called the genome.

While we’ve known for centuries that parents can transmit certain genetic traits to their offspring—blue eyes in people or coat color in horses, for example—-until fairly recently the genome has been largely uncharted territory.

In 2003 scientists published the sequence of the human genome, followed by complete maps of animal genomes, including that of the horse, a Thoroughbred mare named Twilight, in 2007.

Stephanie Valberg, DVM, PhD, Dipl. ACVIM, Dipl. ACVSMR, a professor and the director of the University of Minnesota Equine Center, in St. Paul, considers this genomic sequencing to be a huge leap forward in the field of equine genetics. She explains that prior to the sequencing of the entire equine genome, scientists only had limited genetic “maps” of the horse. These provided information akin to geographic maps of major cities (think of the detail of pullouts in a state road atlas), whereas the genome sequence shows all the little towns between. 

“Previous (equine) genome maps were not very dense compared to (those for) dogs and humans, so many of the genetic analyses in horses seeking to find disease genes haven’t worked,” Valberg explains. However, now “there is a huge amount of data we can generate. The ability to sequence the entire genome of the horse (genes and everything between) has increased now that we have a reference genome. This makes discovery going forward much more fruitful.”

These genomic “maps” show us far more than the detailed topography, if you will, of an equine individual. The genetic stops along the DNA road also reflect the horse’s journey through time and populations. 

Starting the Journey

Our odyssey begins roughly 6,000 years ago in the steppes of modern-day Ukraine and Kazakhstan. Vera Warmuth, PhD, a researcher in the department of zoology at the University of Cambridge, in the U.K., and colleagues determined that those Eurasian plains might reveal the origins of the horse’s domestication.

Warmuth and her team combined genetic sampling of modern horses, archeologic evidence, and computer modeling to pinpoint this region as the most likely site of initial horse domestication. She and her colleagues looked at previous hypotheses for equine domestication, then simulated the genetics for each model and compared those models to the genetic data they had acquired.What can this tell us about modern horses and humans? Quite a bit, says Warmuth, including early population sizes, population growth rates, and equine and human migration routes. “And then,” says Warmuth, “you can also ... ask which genes or genetic mechanisms underlie certain phenotypic (observable) traits, such as speed and stamina in racehorses.” 

Those phenotypic traits are the ones humans care about most and have sought to influence in horses and, thus, have “selected for” when choosing parents for breeding. As such, during the domesticatation of horses, we shifted the evolutionary road, moved obstacles, and changed the landscape of the equine genome through this selective breeding.

First Stop: Behavior

Today’s horses fill roles most likely unforeseeable to our ancestors. Success in many of these roles—cutting, jumping, and racing, for instance—relies as much on personality or behavior as it does physiology.

Humans try to select for desirable behavioral traits in breeding programs, but often without knowing what is nature (i.e., genetics) and what is nurture (e.g., dam influence, herd influence, training). While it’s quite possible that the ultimate answer is “all of the above,” scientists are making inroads into recognizing genetics’ role in animal behavior.

In 2013 a team of Japanese researchers (Ysuke, et al.) identified differences among horse breeds in the gene coding for a dopamine receptor in the brain. The neurochemical dopamine helps control the brain’s reward and pleasure centers and also helps regulate movement and emotional responses. 


The authors noticed that the frequency of one allele, or variant, on a gene associated with equine behavior differed significantly between Thoroughbreds and native Japanese horses. They found this allele, linked with a propensity for low curiosity (an interest in novel objects and a willingness to approach them) and high vigilance (a horse’s tendency to examine his surroundings) much more commonly in Thoroughbreds. The researchers speculated that the increased frequency of this allele in Thoroughbreds “may be a byproduct of the special breeding history of Thoroughbred horses for racing.” The team concluded that variations in certain genes between each breed could be used to predict behavior and as indicators of the type of training best suited for individual horses.

Scientists have identified similar genetic links to behavior in other species. Variations in dopamine receptor genes, for instance, appear to be associated with “novelty seeking” in humans (think of individuals you know who gravitate toward extreme sports) and aggression/impulsiveness in dogs. 

Next Stop: Performance

Humans have bred horses over many generations for certain physical traits—for example, specialized gaits, such as those exhibited by Paso Finos, Tennessee Walking Horses, and pacing Standardbreds, and performance traits, such as speed in Quarter Horses and Thoroughbreds. 

The so-called “sprinting gene” is a particular variant of the myostatin gene that influences muscle development (Hill et al. 2010). While breeders have selected for this gene through generations of racehorses, its identification means that owners can now test to see if their horse carries it so they can perpetuate that gene through breeding, says Valberg.

The desire for a faster horse hasn’t changed much over time, but the way we utilize and manage horses has. “When we used (horses) all the time, a full day’s work was at least six hours a day,” says Valberg, noting that horses prior to the Industrial Revolution were fed and exercised differently than they are now. The shift to a largely recreational lifestyle means that once-desirable traits might now contribute to modern-day problems. Valberg says muscle conditions such as type 1 polysaccharide storage myopathy (PSSM) might be a byproduct of human selection for equine traits that were ideal at one time. “Storing glycogen in muscle may have been an advantage then when horses worked constantly, but not now,” she says.

Hitchhikers and Highwaymen

Valberg further explains that unintended consequences of trait selection over time can even be deadly. 

“In general,” she says, “sometimes when we try to concentrate the genetics to pull out one trait we can have a hitchhiker effect—for example, overo coat color. It looks great when the horse is heterozygous for the trait (has the overo allele only on one chromosome), but it’s lethal in the homozygous form (when the trait is present on both chromosomes). This has opened questions in some countries as to the ethics of breeding for that.”

Cutting horses, along with the genes that make them ideally suited to work cattle, says Valberg, can carry mutations that lead to conditions such as the fatal muscle disease glycogen-branching enzyme disorder (GBED) and potentially fatal skin disease hereditary equine regional dermal asthenia (HERDA). 

Valberg says the goal of a breeding program should be to try to “understand what you’re selecting for and to maintain enough diversity to avoid concentrating deleterious traits.”

Surveying the Road

Genetic testing can help direct horse owners toward successful breedings. Valberg says researchers have already used genome mapping to build useful genetic tests for easy-to-recognize conditions such as HERDA and the fatal neurologic disease in Arabians, lavender foal syndrome. “For more subtle traits moving forward,” she says, “being able to sequence the entire genome of affected horses will help.”

The American Quarter Horse Association (AQHA) requires genetic testing for all breeding horses and offers a five-panel test for HYPP, PSSM1, MH, GBED, and HERDA. “Results of this test must be on file for many breeding stallions beginning with the 2014 breeding season and all breeding stallions beginning in 2015,” states the AQHA website. Other breed organizations, such as the Arabian Horse Association, are also promoting genetic testing of its members’ horses.

Sarah Davisson, senior manager of publicity and special events for the AQHA, says that “disease panel results are public information if we have them on file for the horse.”

Valberg applauds this testing policy: “Mare owners need to know what results are to choose the right mate,” she says.

However, even testing does not guarantee a smooth ride along the genetic highway. Says Valberg, “One thing that is hard for owners to understand—and it’s true for humans and other animal species—is that genetic tests look for a predisposition to genetic diseases,” and not necessirily a confirmed diagnosis. 

For example, she says, a horse might test positive for a disease such as type 1 PSSM without showing clinical signs. This is, says Valberg, “in part because there are 20-30,000 other genes that may influence whether the horse ever shows disease.” As examples, she lists signs of diseases such as HYPP that can range from no symptoms at all to daily episodes of muscle trembling, or the condition shivers that only shows if the horse is taller than 16.3 hands.

With gene mapping becoming even more detailed and the availability of whole genome sequencing, Valberg believes “we will develop more genetic tests. But those tests always need to be interpreted in light of the clinical signs seen and the environment,” she cautions. 

Valberg points out that horses are complex beings and while genetic testing is unlikely to provide absolute answers, we can become better equipped to address individual animals’ needs. “We may be able to target individual susceptibilities and treat them,” she says. “For muscle conditions that won’t incapacitate a horse but may not make horse as strong, we may be able to manage them differently when we have a better idea of their individual genetic susceptibilities.

“That’s just biology,” says Valberg. “And biology is not black and white.”

About the Author

Christy Corp-Minamiji, DVM

Christy Corp-Minamiji, DVM, practices large animal medicine in Northern California, with particular interests in equine wound management and geriatric equine care. She and her husband have three children, and she writes fiction and creative nonfiction in her spare time.

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