Published August, 2009

The horse industry in the United States is diverse. Horses are used for racing, competitive riding, showing, recreational riding, and working cattle. Today the number of horses in the United States is estimated at 9.2 million, down from 21 million around 1900, when horses were a primary source of power and transportation, but up from 4.5 million in 1959 (the last time the United States Department of Agriculture counted horses). According to an American Horse Council study, in 2004 the horse industry had a $102-billion impact on the U.S. economy and provided 1.4 million jobs. The horse industry is growing and important. More than ever, we need each horse to be athletically sound and healthy. Consequently, the thrust of equine genetics research on horses during the last half century has been related to health and physiology.

Advances in biotechnology have provided powerful new tools. In 2006, the entire DNA sequence was determined for a Thoroughbred mare. That sequence was assembled and can be viewed online at several Web sites,,

In addition, scientists performed partial DNA sequences on seven more horses, including another Thoroughbred, as well as an Akal-Teke, Andalusian, Arabian, Icelandic, Quarter Horse, and Standardbred. Comparing the DNA sequences led to the discovery of more than 1 million genetic differences among these horses. The significance of this work is apparent. Prior to 1990, only 50 genes had known genetic variation; following more than a decade of molecular genetics work on horses, variation had been discovered for an additional 3,000 sites by 2005.

The DNA sequencing work was done by the National Human Genome Research Institute to aid the investigation of human gene function. This work is the largest--ever--single contribution to equine research. DNA sequencing enables studies in all areas of equine research. Those of us working at the University of Kentucky Gluck Equine Research Center played major roles in the development of this resource, and we are well-situated to use the tool and solve problems which have resisted earlier technologies.

Coat Color Genes

Our initial studies focused on hereditary traits that were well understood, such as coat color. We wanted to determine if our gene map was sufficiently powerful to find the precise molecular cause for these traits. These studies also formed the basis for training graduate students to use the new molecular tools.

Among the discoveries made during this period:

  • Rebecca Bellone, PhD, former graduate student and now a faculty member at the University of Tampa, mapped the gene for Appaloosa spotting;
  • Samantha Brooks, PhD, former graduate student and now a faculty member at Cornell University, identified the molecular basis for tobiano, sabino, and several forms of dominant white (she is currently using molecular genetics to investigate laminitis); and
  • Deborah Cook, MS, a current graduate student, identified the molecular basis for champagne dilution of coat color.

Collectively, these studies demonstrated the power and efficacy of the gene information to discover the molecular basis of these traits. Commercial tests are available for horse breeders interested in selecting for these traits.

Simple Disease Genes

Following the success of the hair color investigations, we investigated health traits that were easily characterized and thought to have a simple hereditary basis. The work was conducted through funding from interested breeders and breed registries. We have had three successes in this area:

Junctional epidermolysis bullosa (JEB) Kathryn Graves, PhD, director of the Animal Genetic Testing Laboratory at the Gluck Center, discovered the molecular basis for this skin disease of American Saddlebred horses. This research was done based on having samples from fewer than 10 affected foals. The work was recently reported and commercial tests are available to detect the trait and allow breeders to avoid this disease.

Swayback among Saddlebred horses Cook has mapped a DNA region that appears to contain the gene for this trait. She is currently conducting investigations on the mutation involved and determining what other effects this gene might have on performance. The most significant aspect of this work was mapping the gene based on testing 40 American Saddlebred horses selected for their back conformation and not on the basis of complete family studies.

Dwarfism among Miniature Horses John Eberth, a current graduate student at the Gluck Center, has mapped a gene for this trait. Again, the discovery was made on the basis of testing 40 Miniature Horses, 20 with dwarfism and 20 without, but not using family studies. He is currently sequencing a gene in the region that is known to cause dwarfism in other species. Hopefully, genetic variants will be identified which are responsible for the dwarfism trait and breeders can select against that gene.

Success with such a small set of samples was remarkable. About 10 years ago, such genetic studies required the collection of dozens to hundreds of samples and amassing pedigree records that would demonstrate the mode of inheritance and implicate founding stallions and dams. Since breeders avoid matings of horses known to carry disease genes, this is not a viable approach to study horse diseases. However, with the advent of the whole genome sequence for the horse and associated genetic tools, we have new approaches that require fewer samples, and in some cases, do not require families.

Future Genetic Marker Work

Studies are currently being designed for more complex traits with suspected hereditary influences. Some of these are listed below.

Contracted Foals Teri Lear, PhD, is collaborating with scientists at the University of Kentucky Livestock Disease Diagnostic Center (LDDC) to investigate the condition often referred to as contracted foal syndrome. This condition is one of the most common sources of foal loss. Sometimes the condition is minor and can be corrected by splinting or surgery. Other times the contractures are so severe they cause dystocia and even death of the broodmare. The condition might have multiple causes, so the challenge to Lear and her collaborators is to divide the affected foals into several categories based on pathology and pedigree, then investigate each category for a discrete genetic basis. They might all have one common cause or each category might have some combination of nutrition, genetic, or other environmental cause. But today, Lear can use the whole genome sequence and associated molecular tools to parse out the genetic component.

Parrot Mouth Dysmorphology of the mouth is another cause of foal loss that is thought to have a hereditary component. There are a wide range of problems that can occur to the mouth of the horse, and there might also be a diversity of genetic and environmental causes. As with contracted foal syndrome, we are devising studies to evaluate the hereditary contribution to the condition in these foals. We are collaborating with Jack Easley, DVM, MS, Dipl. ABVP, to evaluate affected horses, categorize them, obtain DNA samples, and initiate genetic investigations.

The work on these conditions is under way, but only at preliminary stages; we need funding from private donors and agencies that fund equine research.

In the future we anticipate investigating variation in response to infectious diseases, variation leading to developmental bone diseases, nutritional responses, hoof quality, and aspects of physiology including reproduction and performance.

What Does This Mean?

Does it mean that horse owners need to become molecular geneticists? Absolutely not! After all, we do not need to become mechanics to drive a car. These tests will simply be one more tool a breeder can use in addition to advice from bloodstock agents and veterinarians who, in turn, use radiographs, pedigree analyses, and other tools.

Molecular genetics information is already being used in agriculture and medicine. When bull studs have two attractive bulls but can keep only one, they use DNA tests to determine which one has the better genetic potential. Physicians treating human diseases make a preliminary diagnosis based on all available clinical tests; then they might add a DNA test to include or exclude a hereditary condition.

We want to provide the horse breeder with the same opportunities for success.

Ernie Bailey, PhD, is a professor in the Veterinary Science Department at the Gluck Center.