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 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 infections, and typically succumb to an infection by two months of age. [4]

SCID occurs in Arabian horses and their related breeds. The prevalence of carrier Arabians ranges between 3 – 8% depending on the study. [4]

Efforts to avoid breeding carrier animals together is successfully decreasing the prevalence of carriers and the number of affected foals. Currently, the Arabian Horse Association (AHA) recommends testing of all breeding Arabians for SCID. [4]

Muscle Disorders

Most muscle-related genetic diseases in horses affect Quarter Horses and breeds with similar lineage.

Screening for these diseases is standard practice prior to breeding any stock horse breed.

Hyperkalemic Periodic Paralysis

Hyperkalemic Periodic Paralysis (HYPP) is an autosomal dominant disorder that causes muscle tremors, weakness, and paralysis. [5] Most horses develop symptoms by 2 – 3 years of age. [5]

All horses affected by HYPP descend from a single stallion named Impressive. Estimates suggest that between 1.5% of Quarter Horses and 4.5% of American Paint Horses carry this gene mutation. [5]

Most of the horses affected by HYPP are from halter performance lines, with one study showing up to 56% of halter performance horses carrying the mutation. [5]

In contrast to many genetic diseases that see a reduction in mutation frequency following their discovery, the prevalence of the HYPP mutation has stayed consistent. This is likely due to breeders choosing to breed two HYPP carriers, as they often have a heavily muscled appearance that breeders find desirable. [5]

Currently, the American Quarter Horse Association (AQHA) will not register any horses carrying two copies of the HYPP mutation. The AQHA and American Paint Horse Association also require all breeding stallions to be tested. [5]

Glycogen Branching Enzyme Deficiency

Glycogen branching enzyme deficiency (GBED) is an autosomal recessive disease that causes death in neonatal foals, as well as abortion, and stillbirth. [5] It is characterized by an inability to properly store glycogen, leading to muscle weakness.

The disease primarily affects Quarter Horses and their related breeds. Around 8 – 11% of Quarter Horses are carriers, with Western pleasure, cutting, and working cow horse lines primarily affected. [5]

Currently, the AQHA and APHA requires all breeding stallions to be tested for GBED. [5]

Polysaccharide Storage Myopathy

Polysaccharide Storage Myopathy (PSSM) is an autosomal dominant disease affecting numerous breeds. There are two types of PSSM, however only Type 1 PSSM currently has a genetic test available. [5] Research is ongoing to identify the causative mutation and develop a genetic test for PSSM2. [6]

PSSM1 causes muscle tremors, muscle stiffness, and severe colic-like pain in affected horses. Symptoms usually develop suddenly after exercise, but some horses show chronic symptoms such as poor performance and back pain. [5]

Several breeds carry the PSSM1 mutation, with the highest carrier rate in breeds derived from the Belgian Draft horse. Affected breeds include: [5]

Around 6 – 10% of Quarter horses carry the mutation. Most affected Quarter Horses come from halter performance breeding lines. [5]

Currently, the AQHA and APHA require PSSM1 testing for all breeding stallions. [5]

Malignant Hyperthermia

Malignant hyperthermia (MH) is a genetic disorder in horses that triggers a severe and often fatal increase in body temperature and muscle rigidity, typically in response to anesthesia. Some horses can also develop symptoms due to stress or exercise. [5]

MH is an autosomal dominant disease that primarily affects Quarter Horses and their related breeds. However, it is quite rare overall. Only around 1% of Quarter Horses are carriers, primarily from halter and pleasure horse lines. [5]

The AQHA and APHA require testing for all breeding stallions. [5]

Myosin Heavy Chain Myopathy

Myosin heavy chain myopathy (MYHM) is a relatively new genetic disease that causes two syndromes: [5]

  • Immune-mediated myositis, which results in muscle wasting.
  • Non-exertional rhabdomyolysis, which causes episodes of muscle pain, stiffness, and weakness not associated with exercise.

MYHM affects Quarter Horses and their related breeds. Studies suggest that around 7% of Quarter Horses carry the mutation, with higher prevalence rates in reining, working cow, and halter horses. [5]

At this time, the AQHA and APHA do not require testing for MYHM for breeding stallions. However, there are proposals to add this disease to the required testing panel. [5]

Equine Familial Isolated Hypoparathyroidism

Equine familial isolated hypoparathyroidism (EFIH) is an autosomal recessive condition that results in abnormally low blood calcium levels. Affected foals develop strong muscle contractions and seizures between 4 to 35 days of age. Most foals are euthanized due to their poor prognosis. [7]

EFIH occurs in Thoroughbreds, with around 1.5% of horses carrying the mutation. Foals must have two copies of the gene to develop symptoms. [7]

Testing for EFIH is not currently required by the Jockey Club. However, genetic testing can help prevent breeding carriers together, or confirm EFIH in an affected foal. [2]

Neurologic Disorders

Neurologic diseases affect the brain, spinal cord, or nerves. Most genetic neurologic diseases have a poor prognosis, making genetic testing an important preventative measure for the health of any produced foals.

Lethal White Foal Syndrome

Lethal White Foal Syndrome (LWFS), also known as ileocolonic aganglionosis or overo lethal white syndrome (OLWS), is an autosomal dominant condition that prevents proper formation of the nerves that supply the intestinal tract. [8]

Without these nerves, food material cannot pass through the intestinal tract, resulting in colic and ultimately death of the foal. Foals born with LWFS typically have an all-white coat with blue eyes, and develop colic and abdominal distention shortly after birth. [8]

LWFS occurs when both parents carry the colour gene for overo. With two carrier parents, there is a 25% chance that the foal inherits both copies of overo, resulting in LWFS. [8]

Commonly affected breeds include: [8]

However, any horses carrying the overo coat pattern are at risk of producing a LWFS foal if bred together. Some horses that carry the overo gene do not have obvious overo patterning, making a knowledge of the horse’s pedigree and genetic testing crucial for preventing LWFS. [8]

Currently, only the APHA requires breeding stallions to report their LWFS (OLWS) status. [8]

Lavender Foal Syndrome

Lavender Foal Syndrome (LFS) is an autosomal recessive trait primarily found in Egyptian Arabians. The mutation interferes with the storage components in skin cells and neurons, resulting in cell malfunction. [8]

Foals born with LFS have a pale lavender or pink coat colour. After birth, they develop muscle rigidity, paddling, and seizure-like activity. There is no treatment available, so most foals are euthanized. [8]

Studies show that around 10% of Egyptian Arabian bloodlines carry LFS. [8]

The AHA does not require testing of breeding animals, however if a horse’s LFS status is known, it must be reported to anyone wishing to breed or purchase the animal. Additionally, breeders whose mares produce an affected foal must notify the stallion owner. [8]

Cerebellar Abiotrophy

Cerebellar abiotrophy (CA) is an autosomal recessive mutation that results in damage to the cerebellum, the portion of the brain responsible for balance. Affected foals show symptoms such as irregular gait, head tremors, and spastic or overexaggerated movements. [8]

CA is primarily a disease of Arabian horses, however the mutation is also present in breeds derived from Arabians. Breeds carrying the mutation include: [8]

In Arabians, estimates suggest that between 5 – 20% of horses carry the mutation. [8]

Currently, the AHA does not require testing of breeding animals for CA. However, if an animal is tested, their CA status must be reported to anyone breeding or purchasing the animal. Breeders of foals born with CA must also report their findings to the stallion owner. [8]

Familial Occipitoatlantoaxial Malformation

Familial occipitoatlantoaxial malformation (OAAM) is an autosomal recessive trait found in Arabian horses. The OAAM mutation affects a gene responsible for developing the spinal column, resulting in malformation. [8]

Affected horses show symptoms such as an audible click when moving the neck, uncoordinated movement, and an extended neck posture. [8]

The overall prevalence of the OAAM mutation in Arabian horses has not been reported. The AHA does not currently require testing, however testing of any horses who produce an affected foal is recommended.

It is also important to note that not all forms of OAAM are genetic. OAAM can also occur due to disturbances in fetal growth unrelated to a genetic mutation. [8]

Friesian Hydrocephalus

Friesian hydrocephalus is an autosomal recessive condition causing accumulation of cerebrospinal fluid in and around the brain. Most affected foals are aborted or stillborn. [8]

Studies suggest that 8.5% of Friesians are carriers for Friesian hydrocephalus. [8]

The Friesian Horse Association of North America (FHANA) and Koninklijke Vereniging “Het Friesch Paarden-Stamboek” (KFPS, the Dutch studbook for Friesians) strongly recommend testing for Friesian hydrocephalus, however it is not required. [9]

Ocular Disorders

Ocular disorders in horses refer to a range of eye-related conditions that can affect vision and eye health. Most ocular disorders in horses are associated with genes that determine the horse’s coat colour, and not necessarily linked to a specific breed. [10]

Several of the diseases are not symptomatic when the horse is born, meaning the horse does not show signs until later in life. Genetic testing is recommended to identify which horses have the highest risk of developing these ocular disorders and to make educated breeding decisions. [10]

Multiple Congenital Ocular Anomalies

Multiple congenital ocular anomalies (MCOA) refers to a group of eye abnormalities associated with a genetic mutation. Horses with MCOA can have a range of eye malformations, but the most common is large cysts within the iris and retina. [10]

MCOA is a possible outcome of carrying the silver gene, which dilutes the horse’s coat colour if they have a black base coat. Silver is a dominant gene, and will affect the coat colour with only one copy of the silver gene, as long as the horse does not have a chestnut base coat. [10]

However, the gene’s effects on the eyes are incompletely dominant, meaning horses with two copies of the gene develop severe ocular malformations, and horses with one copy of the gene develop only eye cysts. Chestnut horses who are carriers also develop eye disease, even though their coat colour is not affected. [10]

Horses from breeds who carry the silver mutation should be tested for MCOA, regardless of their colour. [10] All identified carriers should have their eyes examined regularly by a veterinary ophthalmologist, to determine the extent of their eye disease. [10]

Breeds that commonly carry the silver gene include: [10]

Congenital Stationary Night Blindness

Congenital Stationary Night Blindness (CSNB) is a genetic condition that results in severely impaired vision in the dark, which is present as soon as the horse is born. CSNB is a possible outcome of carrying the LP mutation, which is responsible for the leopard spotting found in some breeds. [10]

The LP mutation is an autosomal, incompletely dominant gene. Carrier horses have a white area ranging from a small patch to a completely white coat. Within the white area are patches or spots of the horse’s base coat colour. Horses with two copies of LP typically have no spots in their white area, while horses with one copy have spots. [10]

In horses, the LP gene leads to the absence of a protein essential for the functioning of rod cells in the retina, which play a crucial role in night vision. Horses with two copies of the LP gene will always have CSNB, whereas horses with only one copy typically have functional rod cells. [10]

Commonly affected breeds include: [10]

Equine Recurrent Uveitis

Equine recurrent uveitis (ERU), also called moon blindness, is a disease associated with leopard patterning. Affected horses have repeated episodes of eye inflammation, which can eventually result in blindness, cataracts, and glaucoma. [10]

ERU is a complex disease, and the precise cause is unknown. Current research indicates that its development is likely influenced by a combination of genetic predisposition and environmental factors. [10]

The main gene associated with ERU is the leopard patterning gene, commonly found in Appaloosa horses. However, other non-leopard patterned breeds and horses can also be affected. [10]

Appaloosa horses are eight times more likely to develop ERU than other horses, and four times more likely to develop blindness. Horses who have two copies of the LP gene have the highest risk. [10]

Ocular Squamous Cell Carcinoma

Ocular squamous cell carcinoma (SCC) is an aggressive cancer affecting the tissues within or around the eye. The biggest risk factor for SCC is UV light exposure, but research has also identified a genetic predisposition. [10]

Mutations in the DDB2 gene increase the risk of developing SCC when exposed to UV light. This gene is responsible for repairing DNA after UV damage. Horses who have two copies of the DDB2 gene mutation have a higher risk of developing ocular SCCs compared to horses with a single copy or no copies. [10]

Horse breeds that are carriers of the DDB2 mutation include: [10]

The genetic test for DDB2 is currently used to screen for horses that have a higher risk of developing ocular SCCs. Carrier horses may benefit from management strategies to reduce UV exposure, such as wearing UV protective fly masks or keeping them indoors during the day. [10]


Distichiasis is an autosomal recessive trait that causes eyelashes to grow in an abnormal position along the edge of the eyelid. These abnormal eyelashes lead to discomfort and damage the surface of the eye, resulting in infections or scarring. [11]

Distichiasis is most common in Friesians. Estimates suggest that around 32% of Friesians carry the mutation for distichiasis, however only horses carrying two copies of the gene are affected. [11]

Currently FHANA and KFPS do not require testing of Friesians for distichiasis, however this may change as research about the disease continues. [9]

Reproductive Disorders

Reproductive disorders affect the fertility and sexual health of horses, potentially impacting their ability to conceive, carry, or birth offspring successfully.

So far, only one genetic disorder affecting the reproductive system is described in horses: androgen insensitivity syndrome.

Androgen Insensitivity Syndrome

Androgen insensitivity syndrome (AIS) is a genetic condition in which male horses have reduced sensitivity to androgens, the male sex hormones, leading to the development of female or ambiguous physical traits.

AIS is an X-linked disease, which means that the mutation occurs on the X chromosome. Female horses have two X chromosomes, but males only have one. AIS only occurs in males who inherit a mutated X gene from their mother. [12]

In normal male horses, androgens stimulate the development of the male reproductive tract. However, in cases of AIS, the genetic mutation prevents the androgen-driven development of male reproductive tissues, resulting in the absence of these structures. [12]

Genetically, horses with AIS are XY (male), but they display female characteristics. In some instances, they might develop external female genitalia, despite being genetically male. [12]

Different mutations causing AIS have been identified, each associated with specific horse breeds. Affected breeds include: [2]

Genetic testing for AIS allows breeders to avoid producing an AIS-affected male foals, who will be sterile. Additionally, the test can confirm AIS in a sterile male horse suspected of having the disorder. [2]

Skeletal Disorders

Genetic skeletal disorders in horses affect bone development, leading to a range of structural and conformational issues. These disorders are caused by genetic mutations that affect the way bone cells grow and organize themselves, resulting in bones that may be improperly formed, weak, overly dense, or misshapen.

Friesian Dwarfism

Dwarfism in Friesian horses is an autosomal recessive trait, causing short limbs and rib bones with a disproportionately long back and large head. [13] Many affected horses also have hyperextension of the fetlock joints. [2]

Studies suggest that around 0.25% of Friesians are affected by dwarfism, with around 12% of the population carrying the mutation. [2][13]

FHANA and KFPS currently recommend testing of all broodmares for dwarfism. [9]

Skeletal Atavism

Skeletal atavism is an autosomal recessive condition that results in abnormal limb development. [14]

Affected horses have overgrowth of the ulna and fibia, the smaller bones next to the radius and tibia, respectively. This ultimately causes angular limb deformities in the knees and hocks, which worsen as the horse ages. [14] Most horses are euthanized by six months of age. [2]

This condition occurs in Shetland ponies and Miniature horses, and only horses with two copies of the gene are affected. Around 12% of Shetland ponies are carriers of the mutation. [2]

Skin Disorders

The formation and maintenance of skin involves many biological processes, each of which is tightly regulated by many genes. As a result, skin is susceptible to many genetic disorders, ranging from skin fragility to tumor growth.


Melanomas are tumors arising from melanocytes, the cells the produce the skin’s pigment. These tumors can be very aggressive, and can metastasize from the skin to other organs. The tumors are most common around the perineum, on the tail, and on the head. [15]

Gray horses have significantly higher risk of developing melanomas, due to the genetic mutation that results in their gray coat colour. Up to 80% of gray horses will develop melanomas during their lifetime. [15]

Horses who carry two copies of the gray gene are more likely to develop melanomas than those with one copy. [2] Even though all carriers of the gray gene are visibly gray, genetic testing can still be helpful to assess their risk of developing melanoma.

Hereditary Equine Regional Dermal Asthenia

Hereditary equine regional dermal asthenia (HERDA) is a form of Ehlers-Danlos Syndrome, a disease which results in extremely fragile collagen. HERDA has an autosomal recessive inheritance, and is primarily found in Quarter Horses and their related breeds. [15]

Affected horses have a poor attachment between their skin and the deeper tissues, resulting in peeling or sloughing of the skin in areas that come into contact with tack or blankets. Affected horses have a diminished capacity for skin healing, potentially resulting in disfiguring scars. [15]

Around 3.5% of Quarter Horses are carriers, with higher prevalence rates in cutting horses and working cow horses. [15] HERDA is currently part of the “5 panel” or “6 panel” test required by AQHA for all breeding stallions.

Warmblood Fragile Foal Syndrome Type 1

Warmblood fragile foal syndrome (WFFS) is another type of Ehlers-Danlos syndrome that primarily affects Warmblood horses and derived breeds. The disease is autosomal recessive; foals carrying two copies of the gene are unable to survive beyond a few days. [15]

Studies show that around 11% of the Warmblood population are carriers. [15] Some warmblood registries now require WFFS testing as part of their registration process for foals or breeding animals.

Junctional Epidermolysis Bullosa

Junctional epidermolysis bullosa (JEB) is a disease of newborn foals causing large skin blisters and ulcers on the hocks, stifle, and mucous membranes. [15] In some cases, the hooves may slough off. [16] There is no treatment available, so affected foals are euthanized due to poor welfare. [15]

JEB occurs primarily in draft horses and the American Saddlebred. The disease is autosomal recessive, so horses must carry two copies of the gene to develop symptoms. [15]

Between 8-27% of horses in many draft breeds carry the mutation for JEB. Affected draft breeds include: [16]

  • Belgians
  • Bretons
  • Comtois
  • Vlaams Paard
  • Belgische Koudbloed Flander horses

Naked Foal Syndrome

Naked foal syndrome (NFS) is an autosomal recessive disease unique to the Akhal-Teke breed. Affected foals have little to no hair, and typically die shortly after birth. [17]

Some foals also exhibit abnormal tooth development, gastrointestinal disorders, diarrhea, and laminitis-like issues. [17]

The genetic mutation causing NFS was first identified in 2017, and commercial genetic tests are now available. [2] The Akhal-Teke Association of America currently offers discounted genetic testing for NFS, and recommends testing of all breeding animals. [18]

Hoof Wall Separation Disease

Hoof wall separation disease (HWSD) is an autosomal recessive disorder that causes fragile hoof walls. Affected horses have cracking, splitting or loss of the hoof wall starting within the first 6 months of life. Severely affected horses may have no hoof wall for weight-bearing, and walk exclusively on their hoof sole. [19]

HWSD occurs in Connemara ponies, with studies showing around 15% of ponies carry the mutation. Ponies must have two copies of the gene to develop symptoms. [19]

Currently, the Connemara Pony Breeders Society requires testing for HWSD in all horses, unless they are from non-carrier parents. [19]

Summary Table

The following table offers an overview of genetic health testing guidelines for various horse breeds. It outlines tests that are essential for all individuals of a specific breed before breeding, as well as those recommended only for certain subgroups within the breed.

Breed All Horses Some Horses
All breeds
American Saddlebreds
Connemara ponies
Dales ponies
Draft breeds
Fell ponies
Icelandic horses
Kentucky Mountain horses
Miniature horses
Quarter horses & related breeds (Paint horses, Appaloosas)
Rocky Mountain horses
Shetland ponies
Tennessee Walking Horses

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