The Future of Genetic Testing

Written By: Pat Griffin, DVM, PhD, DACT

Written By: Pat Griffin, DVM, PhD, DACT

Genetic testing can have a positive impact on any horse owner, from the owner of the backyard companion animal to the serious breeder. There is a (false) assumption that genetic testing only affects breeding barns, but genetic testing can enlighten any horse owner about what medical challenges may affect your horse in the future, what predispositions he may struggle with, and how you can manage those genetic challenges by making critical decisions regarding your horse’s nutrition, levels of stress, exercise, and environment. For example, if you know your horse is HYPP heterozygous positive, you’re going to make different, and more intelligent, decisions managing that horse. Responsible breeders need to be even more aware of the genetic status of their broodmare and stallions in order to decrease risks to future offspring. The end goal of genetic testing is four-fold: eliminate genetic disease; breed sounder, more fit horses; “know and assess risks”; and improve herd and individual health care. Irongate Equine held a seminar for our clients who were interested in the basics of genetics, testing, & conditions that occur in different breeds (see video at the end of this article in order to answer many of the questions you will find in this article.

History of Equine Genetic Testing

The beginning of genetic testing really came about as the advancement of equine assisted reproduction hit its stride. As shipped semen, embryo transfers, artificial insemination, etc. became more common, breeders across the globe were really able to tap into the possibilities of a great genetic pool, but we also shrank the genetic pool. A dozen American Quarter Horse stallions, for example, were bred to thousands of mares. It propagated the great characteristics of those stallions, but it also sent along those negative characteristics. This is really why we’re seeing so many genetic diseases among those most popular breeds (Arabians, Quarter Horses, etc), and why there are so many advancements in genetic testing.

Prior to 2006, some genetic testing already existed, primarily with the testing of single gene diseases. In 2006, the horse’s genome was almost completely mapped – it is about 97-98% complete. This set the stage for equine veterinarians and researchers to become very sophisticated with genetic testing. The genome is just the complete set of DNA of any species. The equine genome, consisting of over 25,000 genes, was mapped by an international cooperative effort of many laboratories across the world. Because of this project, there is now an explosion of information coming forward about the genetic basis of many of equine diseases. Currently, there are ten genetic diseases that we test for commercially, and these are the easy, single gene diseases. What’s coming down the pipeline is information about a genetic predisposition to diseases, how environmental factors can aggravate that disposition, and how we turn those genes off.

The Basics of Genetics

Let’s jump back to high school biology for a minute here. There are 31 pairs of autosomal chromosomes, or non-sex chromosomes. Each chromosome has thousands of genes, and each gene has two alleles, one from Mom, and one from Dad. If there’s a mutation in any of those genes, the DNA sequence is altered, and you can get an abnormal biologic process that may or may not result in a disease. The testing protocol is also very simple.

There are a few different laboratories that are testing for genetic diseases at this point – Gluck Center of University of Kentucky is very popular; University of Minnesota is testing muscle associated diseases (PSM, etc); University of California – Davis is probably the most popular, and has a well done, informative website to read through. To run the test, the lab needs anything with cellular content. That can be anything from hair to frozen semen. In fact, labs are now testing the frozen semen of stallions that are long since deceased.

We can also complete embryo biopsies, which is testing on a small section of cells from an embryo.  We take a small sample of cells from what will eventually become the placenta, not the foal. We’ll then freeze the embryo during testing, and if the results come back clear, we go ahead and use that embryo to get a pregnancy. This is often called pre-implantation testing in human medicine, and is frequently used by older women who are worried about genetic issues due to age. Because we’re using the cells from the placenta, there is no harm done to any future foal.

Genetics Vocabulary

Autosomal Dominant Genes – You need only one copy of the bad gene to produce the affect

Autosomal Recessive Genes – You need two copies of the bad allele, or gene, to produce the affect. One copy of that allele would be considered a “carrier state,” in which you may or may not see a clinical effect, depending on the condition.

Single Gene Diseases – This is what we’re testing for now, and is the field of genetic testing at its most basic.

Polygenic Diseases – These are the interesting things we’re seeing and researching now. These have multiple genes involved. They can also be genes that are altered by the environment – nutrition is the number one factor there, followed by levels of stress, exercise, etc. These are much more difficult to have a black and white test for, and we need to continue to expand our sophistication in understanding the equine genome in order to meet these needs.

Homozygous Results – Your horse has two alleles that are the same for a single gene. This would be indicated by an N/N or a D/D, where N stands for “normal”, and D stands for “defective”, or mutated.

Heterozygous Results – Your horse has two different alleles for a single gene. This is indicated by an N/D.

Autosomal Dominant Diseases – You only need one bad allele for your horse to be “affected”.

Autosomal Recessive Diseases – You need one bad allele to be a “carrier”, and two bad alleles to be “affected”.

Interpreting the Results

After we receive the results from the laboratory, the classification of your horse allows us to use basic probability to determine if they’re going to be affected, if their foals would be affected, or if their foals would be carriers. Remember, for Autosomal Dominant diseases, you only need one bad allele in order to have an affected horse. As such, there is no such thing as a “carrier” horse. However, for Autosomal Recessive conditions, you need two bad alleles to be “affected”, and only one bad allele to be a “carrier”. See the tables below to understand the likelihood of a “carrier” or “affected” foal out of various genetic statuses of dams and sires.


Factors to Consider in Genetic Testing

  • The purchase and breeding of animals at risk

    • Consider their genetic background – does this animal have a propensity to develop a complex genetic disease?

  • Quality of life

    • As you’re considering your breeding options, can you avoid a certain stallion, and thereby avoid a condition that may not be life-threatening, but could affect their quality of life? If you avoid a certain stallion to pair with your mare, can you avoid Ocular Anomaly Syndrome or EMS?

  • Degree of lethality

    • Some of these genetic diseases are fatal – consider Overo Lethal White Syndrome. Does it make sense to breed heterozygous carriers of this allele for the foal you want?

  • Effects on heterozygote carriers

    • While some of these horses may not suffer the full affects of the disease if they’re only heterozygous, they may still suffer some affects of the illness.

  • Intended use of animal

    • Particularly in light of the goals to eliminate genetic disease, the horse we truly need to monitor is the carrier. All horses homozygous for a condition will have the scarlet letter on them, alerting potential breeders to the problem. However, many of the heterozygous horses still end up in the breeding pool. If you’re breeding and get a heterozygous foal, are you committed to keeping them out of the breeding pool?

  • Willingness of owner/breeder to test

    • Financially, the tests are not at all prohibitive. However, many owners and breeders may not want to test their stallion or mare for genetic disease. While the AQHA has started requiring testing for five major diseases, most registries do not have a similar requirement. Many owners may find it preferable to keep their heads in the sand and breed or sell without knowledge of any problematic genetic disease.

  • Ethical/Legal considerations in disclosure

    • Related to the willingness of the owner or breeder to test, what are the ethical and/or legal considerations that come into play when you do test for a genetic disease? There needs to be more discussion about any required disclosure during sales and breeding agreements of genetic disease, or even propensity to disease.

Role of Assisted Reproduction

Assisted reproduction includes any of the advanced reproductive tools that we use today to produce foals – this includes artificial insemination, freezing semen, embryo transfers, cloning, etc. The advancements in assisted reproduction have been a great boon to the breeding industry, and have helped us maximize performance and quality of our foals. However, we should also be using it to maximize genetic diversity. Instead, we’ve seen an amplification of these genetic diseases due to the popularity of certain lines. We’ve passed on the brilliant performance attributes, conformation and temperament, but there’s always the flip side of the coin. Luckily, as genetic testing becomes more widely available and cost effective, people are making smarter decisions regarding the genetics that we’re passing on.


Genetic testing is making a lot of gains now, and we’re learning more about the complex diseases every day. The goals of genetic testing include decreasing/eliminating deleterious alleles, maintaining genetic diversity, enhancing the health and welfare of the horse, and identifying and curtailing propagation of “new” genetic disease. As a horse owner and/or breeder, you have the opportunity to take part in those goals.

Dr. Pat Griffin held an educational seminar at Irongate Equine Clinic in Wisconsin covering the impacts genetic testing can have on horse owners.