12/05/2025
Understanding Genetics for Performance Horse Success
Producing a great performance horse involves carefully selecting for athletic traits, solid health, and good temperament. This can be a tall order, especially when success hinges on delicate balance between getting what we want and w**ding out what we donโt want, sometimes waiting more than a decade to get results. Historically, breeders have relied on pedigrees, conformation, performance, temperament, and their own personal experience to pair horses likely to produce exceptional foals.
In roughly 4,500 years horses have transformed from wild, Przewalski-like animals into the companion and performance horses we have today. Still, itโs a slow, trial-and-error process, sometimes with more error than breeders would like, says Ted Kalbfleisch, PhD, professor at the University of Kentuckyโs Gluck Equine Research Center, in Lexington. When researchers mapped the first horse genome in 2007, the industry hoped for a more precise breeding system built on gene science. Since then, scientists have sequenced DNA from thousands of horses, uncovering genetic differences linked to coat color, performance, temperament, and dozens of heritable diseases.
Samantha A. Brooks, PhD, of the University of Floridaโs Department of Animal Science, in Gainesville, says this progress has opened the door to a new era of breedingโone driven by precision, improved success rates, and more ethical choices. With education and a blood sample sent to a qualified lab, breeders can understand the genes circulating in their programs and how to combine them in the smartest, healthiest, and most ethical ways possible.
The Genes of Performance in Horses
Within a year of mapping the genome, researchers began zeroing in on the myostatin gene (MSTN). Already studied in human athletes and racing whippets, MSTN variants influence muscle fiber development and musculature, Kalbfleisch says. Scientists found the equine MSTN and started comparing its different variants with racing performance. Over time, they determined that MSTN can work somewhat like a switch, with some variants favoring sprints and others endurance.
โItโs not that one allele is better than the other,โ says Brooks. โItโs just that theyโre giving opportunities to fine-tune.โ
Through genome-wide association studies (GWAS), scientists searched for gene differences in top racehorses. A few candidates emerged, such as COX4I2, involved in mitochondrial respiration, and PDK4, which is thought to influence behavior. But the global picture was complex: genes might work in combination with other genes and multiple other factors, says Kalbfleisch.
Meanwhile, Swedish researchers identified DMRT3, known as the gait keeper gene. Variants caused a truncated protein, altering movement patterns that allow lateral gaits in Icelandics, Saddlebreds, and other gaited horses. Scientists quickly realized that DMRT3 variants also help keep trot-racing horses from breaking into a gallop. Within a few years, theyโd learned that DMRT3 variants can affect gait quality and performance at the trot and gallop across breeds as well.
But more work, such as a recent study in Iceland, led to the same conclusions as for Thoroughbreds: that itโs complicated. DMRT3 appears to work in combination with other genes, such as STAU2 and RELN, to affect tรถlt, pace, trot, canter, and gallop, and RELN seems to influence how trainable young horses are. Genetic regions affecting back and croup conformation also influence gait quality, underlining the role of genes related to neuromotor pathways and skeletal structure, researchers say.
Sports outside racing involve even more complex genetic layers. Show jumpers tend to excel with variants related to mentality, brain signaling, neuromuscular coordination, and muscle development. Cutting horses differ from racing Quarter Horses in genes shaping muscle growth, skeletal development, energy metabolism, cardiovascular traits, and the nervous system.
Temperament genes add another layer, helping horses handle the mental challenges of training and competition. And then thereโs environmental factors such as nutrition, welfare, training, and management, which play a large role. โWeโd all love to have that crystal ball that says, โThis horse will be a great dressage horse, jumping horse, racehorse, or whatever,โโ says Annette McCoy, DVM, MS, PhD, Dipl. ACVS, of the University of Illinois, in Urbana. โBut performance is not a straightforward, simple trait. Itโs a complicated topic.โ
The Genes of Health and Disease in Horses
In contrast, many health-related genes are far more straightforward. Global databases list hundreds of heritable traits in horses and their specific genetic variantsโand the vast majority are about health. That means scientists now know exactly which genetic variants cause disorders such as fragile foal syndrome(FFS), polysaccharide storage myopathy(PSSM1/PSSM2), hereditary equine regional dermal asthenia (HERDA), degenerative suspensory ligament desmitis (DSLD), hyperkalemic periodic paralysis (HYPP), glycogen-branching enzyme deficiency (GBED), and glycogen storage disease type IV. These variants are easily testable, Brooks says.
Thatโs especially important since some of these diseases come hand-in-hand with performance traits, she emphasizes. Connective tissue disorders like FFS and HERDA, for example, might also convey the elasticity of movement weโre looking for in Warmbloods and stock horses. โWeโre putting strong selective pressure that increases the frequency of these issues, because we like the performance,โ Brooks says. โBut whenever you change the elasticity of connective tissue, it impacts other body systems as well.โ
Researchers are also working to identify genetic contributors to musculoskeletal health, aiming to reduce catastrophic racetrack fractures. One promising candidate gene is ZNF804A. Scientists are investigating genetic ties to heart defects, as well, which could help identify horses at risk of sudden collapse.
โI hope the field takes more of an approach of protecting our equine athletes and trying to breed selectively for traits that are associated with a reduced risk of injury,โ says Lynn Pezzanite, DVM, MS, PhD, Dipl. ACVS, of Colorado State University, in Fort Collins.
Still, good health in general can contribute to better performance and welfare. โPerformance is about how all of the systems work together, not just how one system works in isolation,โ McCoy says. โUltimately, breeding for a healthier horse is also going to improve performance.โ
Take-Home Message
Todayโs horse breeders can blend practical experience with modern genomic tools to give future equine athletes their best start. With accessible tests and expanding genetic insight, identifying health risks early and making informed breeding decisions has become easier.
Genetic testing allows breeders to select for desired traits while minimizing the risk of potentially catastrophic and lethal inherited diseases that can have heartbreaking outcomes. โOur biggest gap at the moment is in application and getting the word out to owners and breeders that we have tools that can help them, and they can understand how to use them,โ says Brooks.
With these tools in hand, breeders can make decisions that support not only exceptional performance but also healthier, happier horses, Pezzanite adds. โPromoting welfare should be our highest priority,โ she says.
The Horse
