Genetic testing in horses involves analyzing a horse’s DNA to gain information about their genetic makeup. This process can identify specific genetic variations responsible for various traits, as well as predispositions to genetic disorders.

Several common equine health conditions have a genetic basis. This means that these conditions are inherited or caused by specific genetic mutations or abnormalities in the horse’s DNA.

Genetic testing panels for horses are used to detect genes associated with conditions including Polysaccharide Storage Myopathy (PSSM), Hyperkalemic Periodic Paralysis (HYPP), or Severe Combined Immunodeficiency (SCID). Understanding the genetic underpinnings of these diseases allows veterinarians and owners to manage these conditions more effectively.

Furthermore, genetic testing allows breeders to make informed decisions about potential breeding matches. By avoiding breeding known carriers of genetic disorders, breeders can reduce the risk of producing foals with serious health concerns.

Some breed registries also require genetic testing for all breeding animals. Over time, reducing the number of carrier animals can effectively eliminate a genetic disease from the population.

Genetic Testing for Horses

During a genetic test, a laboratory analyzes a horse’s DNA by comparing it to a known “normal” or reference DNA sequence. This comparison is crucial to identify any mutations that are associated with a particular disease. [1]

Most DNA tests use 20 – 30 hair roots collected from the horse as their test sample, but blood tests are also available. [1]

Hair Sampling

The most common method of collecting DNA samples for genetic testing in horses involves using a hair sample. [2] When sampling hair, it is important to ensure that the hair bulbs (roots) are present, as the hair strand itself does not contain enough DNA for testing. [2]

To collect a hair sample from your horse:

  • Grab around 10 hairs close to the base of the hair. For adult horses, mane or tail hairs can be used, while tail hairs should be used for foals.
  • Wrap the hairs around your finger and pull quickly in a downward direction.
  • Check that the ends of the hair have a white bulb present.
  • Repeat until you have gathered 20 – 30 hairs.

Reading a Genetic Panel

Every horse’s genetic material is made up of a set of 64 chromosomes, or segments of DNA, that direct physiological processes in their cells. [3]

These chromosomes are located in the nucleus of all cells within the horse’s body, and are divided into 32 pairs. In each pair of chromosomes, one comes from the horse’s dam, and the other comes from the horse’s sire. [3]

Horses have 31 pairs of autosomes, the primary chromosomes responsible for various bodily functions, along with one pair of sex chromosomes that establish the horse’s gender. [3]

Genes

Genes are segments of DNA that act as instructions to make proteins essential for various biological functions. Every chromosome contains multiple genes, with each responsible for producing a specific protein or enzyme that influences cellular functions.

Genes for the same protein can have a slightly different genetic sequence in different individuals. The “version” of the gene that the horse has is known as an allele. The allele of each gene can vary depending on the genetics of the horse’s parents.

Genetic Diseases

Genetic diseases are health conditions associated with specific gene variants. Instead of having a normal allele at a given gene location, the horse has a mutated allele resulting in adverse health outcomes. [3]

When you receive genetic test results for your horse, they will list the specific alleles found at each tested gene location. This data allows you to determine the risk of genetic diseases not only in the horse tested but also in its potential offspring.

Comprehensive interpretation of these genetic test results requires understanding the significance of the alleles present and their relationship to potential genetic disorders.

Autosomal Disorders

Autosomal diseases are caused by gene mutations on autosomes, the main set of 62 chromosomes. Both sexes are equally affected by autosomal diseases, since both sexes of horses have the same 62 autosomes. There are two main types of autosomal diseases:

  • Autosomal dominant
  • Autosomal recessive

Autosomal Dominant Disorders

Autosomal dominant disorders are genetic conditions that occur when a single copy of a mutated gene from one parent is sufficient to cause the disease, even if the corresponding gene from the other parent is normal. The mutated gene overrides the function of any gene present on the opposing allele.

If a horse tests positive for an autosomal dominant disease, the genetic panel will display the alleles as either X/x or X/X, with the capital letter indicating the mutated allele. [3]

  • X/x: When a horse has X/x, it means it has one mutated allele (X) and one normal allele (x), and this single mutated allele is enough to cause the disease.
  • X/X: If the horse’s genetic makeup is X/X, it indicates that both alleles are mutated, which also results in the disease. [3]

Some autosomal dominant diseases are “incompletely dominant”, which means that horses carrying one copy of the mutation (X/x) have different or less severe symptoms than horses carrying two copies (X/X). [3]

Horses affected by an autosomal dominant disease are very likely to pass the disease onto their offspring. When bred to a healthy animal, the likelihood of an affected foal is 100% of X/X horses, and 50% for X/x horses. [3]

Autosomal Recessive Disorders

Autosomal recessive disorders are genetic conditions that occur when a horse inherits two copies of a mutated gene, one from each parent.

Unlike autosomal dominant disorders, having just one copy of the mutated gene does not cause the disease. This is because the normal allele masks the effect of the mutated one.

  • x/x: Horses affected by autosomal recessive disorders will have x/x reported on their genetic panel, with the lowercase letter indicating the mutated allele in these diseases. [3]
  • X/x: Horses that are X/x for the allele are carriers. They can pass the disease onto their offspring despite not showing symptoms themselves. [3]

In breeding scenarios, an x/x horse paired with a non-carrier (X/X) will produce only carrier offspring (X/x). These horses will not be affected by the disease. [3]

When two carriers breed together, there are several possible outcomes: [3]

  • 25% chance of a non-carrier (X/X) foal
  • 50% chance of a carrier (X/x) foal
  • 25% chance of an affected (x/x) foal

Autosomal recessive diseases are challenging to eliminate without genetic testing, as carriers usually show few or no symptoms. [3]

X-linked Disorders

Some genetic disorders affect the sex chromosomes, particularly the X chromosome. The X chromosome is a large chromosome that has many genes, compared to the relatively small Y chromosome. [3]

The specific pairing of sex chromosomes in a horse dictates whether it is male or female:

  • Horses with two X chromosomes are genetically female.
  • Horses with one X and one Y chromosome are genetically male.

X-linked disorders are genetic conditions that are caused by mutations on the X chromosome. Most X-linked disorders are recessive, meaning that a normal allele on an opposing X chromosome can prevent symptoms of disease.

However, since males have only one X chromosome (XY), a mutation on their X chromosome can cause these disorders. Females, having two X chromosomes (XX), typically must have the mutation on both X chromosomes to express the disorder, making these conditions more commonly expressed in males. [3]

On a genetic panel, affected males will show x/Y or simply x, with the lowercase letter indicating the mutated gene. Affected females would show x/x, and carrier females would show x/N, with N indicating the “normal” allele. [3]

Many X-linked disorders affect fertility, with mutated X chromosomes causing sterility in affected males. This phenomenon naturally limits the transmission of such mutations to subsequent generations.

In specific X-linked diseases, it is highly unlikely for a mare to inherit two mutated copies of the gene. This is because to carry two copies, a mare would need to receive one mutated X chromosome from her father. However, if the father is sterile due to the mutation on his X chromosome, he cannot reproduce and pass the mutation to his offspring. Thus, the likelihood of a mare having two copies of such a mutation is extremely low. [2]

Immune Disorders

Genetic disorders that impact the immune system can lead to immunodeficiency, a condition where one or more types of the horse’s immune cells fail to function correctly.

Horses with such conditions face a heightened risk of infections and related health complications.

Foal Immunodeficiency Syndrome

Foal Immunodeficiency Syndrome (FIS) is an autosomal recessive disorder that causes anemia (low red blood cells) and septicemia (blood infection) in young foals. [4] Affected foals develop severe infections within the first few weeks of life, ultimately resulting in death or euthanasia. [4]

FIS primarily occurs in Fell ponies and Dales ponies. Approximately 39% of Fell ponies and around 18% of Dales ponies are carriers. [4]

Ongoing efforts to reduce the number of FIS-affected foals in these breeds have been successful, with very few affected foals born just two years after the development of the genetic test. [4]

Due to the limited number of breeding animals in both breeds, many breeders choose to continue to breed carrier animals to avoid limiting the gene pool. With careful selection that avoids breeding two carriers together, it is expected that FIS can be completely eliminated from these breeds in the future. [4]

Severe Combined Immunodeficiency

Severe Combined Immunodeficiency (SCID) is an autosomal recessive disease that prevents proper development of white blood cells. Affected foals are highly susceptible to infection