Equine DNA Tests

DNA Ireland is providing a broad range of services in the field of DNA testing in farm animals. Here, you can find detailed information about our services in horses. Please feel free to approach us, if you require any information on tests not listed below.


Parentage testing/Verification of Identity
As for humans, DNA analysis enables parentage testing and verification of an animal’s identity as well. For that purpose, microsatellite analysis is a commonly used technique. This internationally standardised method allows for verification of parentage or identity of breeding animals at any time. The obtained DNA profile is unique, tamper-proof and unalterable throughout an animal’s life. Even post mortem, such a profile can be established from different tissues or from animal products such as meat or milk.

At present we offer the verification of parentage and identity in horses, cattle, pigs, sheep, goats and dogs.

Parentage testing determines whether the animal’s putative parents can be considered as its genetic parents. In this process the DNA profile of the offspring is compared to those of the presumed parents. Since each parent contributes 50% to an offspring’s genetic information, each allelic variant of an offspring must be detected in either father’s or mother’s profile. Likewise, presumable parentage of a single parent can be tested (e.g. if the second parent is not in doubt or if no DNA profile is available) or multiple potential parents can be included in the analysis.

In addition to parentage verification, DNA profiles play an important role in the identification of animals.

DNA profiles enable unambiguous identification of an animal at any time and therefore are essential in fields of traceability of food and/or animal as well as in the context of judicial cases or insurance claims.

Coat Colour

Red factor
The inheritance of basic horse colours black, bay and chestnut is determined by two different gene loci (the Extension and the Agouti locus). The Extension locus (E) corresponds to the melanocortin-1 receptor gene which accounts for the different melanin types. While the dominant allele E is associated with black pigment (eumelanin) the recessive allele e results in reddish coat colour (pheomelanin). Horses showing some black pigment therefore bear at least one copy of allele E at the Extension locus, either in homozygous (EE) or in heterozygous (Ee) state. Horses lacking black pigment (chestnuts) are reddish in colour and homozygous ee. Depending on the genotype of the mating partner, carriers of the red factor (i.e. animals with gene status Ee or ee) can produce reddish coloured offspring. In contrast, animals that are homozygous EE will never produce red offspring, regardless of the colour of the mate.

Red factor testing can be used to differentiate between black horses carrying Ee and those carrying EE. For further information on the inheritance of colours in horses please visit the section about Agouti testing.

The agouti locus controls the distribution of black pigment: while the dominant allele A confines black pigment to the lower legs, tail, mane and ear rims (e.g. bay horse), the recessive allele a leads to a uniform distribution of black pigment over the entire body (black).

The agouti locus directly interacts with the extension locus (red factor), e.g. horses, which are homozygous ee for red factor are reddish in colour independent of the genetic status at the agouti locus.

The tobiano pattern is caused by the dominant allele TO at the tobiano locus. Homozygous tobianos (TO/TO) pass on the gene independently of the mating partner’s genotype which results in tobiano spotted offspring, exclusively. In contrast, mating of two heterozygous tobianos (TO/to’) will result in approximately 25% solid coloured horses (to’/to’). The underlying genetic mechanisms of this spotting pattern were identified by researchers at the University of Kentucky. A direct PCR based test clearly distinguishes homozygous spotted animals from heterozygous tobianos and therefore enables selective matings according to the breeder’s requirements.

Cream Dilution
Several different genes (e.g. dun, cream, silver dapple and champagne) can dilute the basic coat colour of a horse.

At the cream dilution locus there are two possible allelic states: CCr and C. The semi-dominant allele CCr causes brightening of the basic coat colour which in single dose results in palominos, buckskins or smoky blacks and in double dose causes pale cream colours seen in cremello, perlino or smoky cream horses.

In contrast, the recessive allele C has no influence hair pigmentation. Animals being homozygous for allele C are non-dilute and show basic colours like chestnut, bay or black in the absence of other modifying genes.

Silver Dapple
The autosomal dominant silver dapple gene (Z-locus) causes dilution/brightening of black pigment (=eumelanin) in black and bay horses. This effect can be mainly observed in tail, mane and feathering. In addition to brightening black pigmented parts of the body, silver dapple can also cause other characteristic features such as striped hooves, white eyelashes or dapple markings on the body. All these effects are particularly pronounced in young animals and significantly diminish in the course of aging. As the silver dapple gene has no significant effect on reddish pigment (= pheomelanin), chestnut horses can hardly be recognized as carriers from their physical appearance. In breeds such as Icelandic Horse and Shetland pony, silver dapple is fairly common. Nevertheless, the trait is also known in Quarter Horses, Paints, Appaloosas, Paso Finos, as well as in cold-blooded Belgians, Bretons and Noriker.

The autosomal dominant Grey gene (G) causes premature greying of horses which are born as coloured foals. The progressive loss of pigments usually begins in foals which acquire white hair around the eyes. As the horse ages, more and more white hairs appear throughout the entire body until the animal’s coat becomes more or less white. Due to its autosomal dominant inheritance, heterozygous carriers of the Grey gene as well as homozygous animals become white, albeit in an individual greying process.

Please note: The offered test does not distinguish between homozygous and heterozygous carriers of the Grey gene, but discriminates presence and absence of the Grey gene.

Splashed White
Splashed white horses show a variable white spotting pattern which is characterized by an extremely large blaze, often accompanied by blue eyes and extended white markings at the distal limbs. Some, but not all, splashed white horses are born deaf.

Recent research revealed 3 mutations (SW1, SW2 and SW3) that cause splashed white spotting pattern in horses.

Variant SW1 is found in several breeds, e.g. Quarter and Paint Horse, Trakehner, Miniature Horse, Icelandic Horse and Shetland Pony. Homozygous SW1 splashed horses have been identified, which suggests that this variant is not lethal in homozygous state.

Occurrence of SW2 and the rare SW3 mutation is confined to certain lines of Quarter Horses and Paints. Both mutations are suggested to have a lethal effect in homozygous state. Thus breeding two horses that carry SW2 or SW3 should be avoided due to the risk of generating nonviable embryos.

Horses that carry two or more splashed white mutations or a combination of tobiano or lethal white overo and splashed white may display extensive white markings up to being completely white.

Genetic Disorders

Equine severe combined immunodeficiency is an autosomal recessive immunological disorder found in Arabian horses. It is characterized by a complete absence of B-and T-lymphocytes which results in severe and generally fatal infectious diseases in foals.

A deletion mutation (= loss of base) of the DNA-PK gene has been found to be the cause of that disease.

Affected foals which carry two copies of the SCID gene (SCID-ss) can result from the mating of two carriers of the deletion (SCID-Ss). Those heterozygous carriers themselves can transmit the disease-causing mutation but show no clinical signs of the disease and therefore cannot be distinguished from homozygous SCID healthy horses (SCID-SS).

SCID gene testing allows for unambiguous identification of carriers and is highly recommended for Arabian horses before mating.

Hyperkalemic Periodic Paralysis in horses is an autosomal dominant inherited disease of the muscles. It is associated with episodic muscular paralysis and/or tremor which can lead to collapse and death of the animal. HYPP is also known as ‘Impressive Syndrome’, due to its occurrence in offspring of the American stallion Impressive. Nowadays, the disease can be foundin Quarter Horse, Paint, Appaloosa und US-Pony.

HYPP is caused by a point mutation in the genome of affected animals and leads to dysfunction of the sodium channels of muscle cells. Clinical symptoms of this defect are exaggerated and unintended contractions of the muscles. Such attacks can be stimulated by stress (transportation, convalescence, etc.) and high levels of potassium ions in the blood (low-potassium diet needs to be maintained). Heterozygous animals (h /H) frequently show milder symptoms than homozygous horses (H/H).

Genetic testing enables a clear distinction of affected homo- or heterozygous carriers (H/H and h/H, respectively) from healthy individuals (h/h) for diagnostic, treatment and mating objects.

The Overo Lethal White Syndrome describes an autosomal recessive lethal defect in Overo dappled American Paints caused by a mutation in the endothelin-B receptor gene. In homozygous animals (OO) the mutation leads to congenital dysfunctional innervation of certain sections of the intestine (intestinal aganglionosis). Due to the impaired intestinal motility, affected foals suffer from severe colic and die within the first days of life. The available DNA test detects the mutation of the endothelin-receptor B gene and identifies possible carriers. Breeders can use the test to avoid affected offspring in Overos but also in Tobiano Paints, Quarter Horses and Thoroughbreds.

Equine Cerebellar Abiotrophy (CA) of Arabian thoroughbreds is a hereditary neurological disorder with autosomal recessive inheritance. Affected animals appear normal at birth; however develop neurological symptoms within of a few weeks or months due to abnormal death of cerebellar neurons.

Affected foals may show a variety of cerebellar deficiencies, e.g. head tremor (intention tremor), ataxia or tendency for a higher startle response.

In addition, those horses often have difficulties in rising and/or moving backwards or may collide with other horses or obstacles due to an insufficient coordination. Finally, affected horses have a higher risk for severe accidents and injuries and thus often need to be euthanized.
Genetic testing of a specific mutation in the TOE-1 gene which is associated with CA, allows identifying affected animals as well as potential carriers of the disease gene.

The terms “Lavender Foal Syndrome” (LFS) or “Coat Colour Dilution Lethal” (CCDL) describe a hereditary neurological disease of the Arabian horse which is most commonly thought to be inherited in an autosomal recessive manner.

Lavender foals typically show a brightened coat colour (dull lavender) and suffer from a variety of neurological symptoms, such as opisthotonos, nystagmus as well as convulsive seizures. All clinical signs manifest shortly after birth. Due to the massive neurological deficits, LFS-affected foals usually are unable to stand or to ingest colostrum. Therefore, they often die within a few days after birth or have to be euthanized.

According to the autosomal recessive inheritance of this trait, heterozygous carriers do not show any neurological deficits but can produce homozygous LFS-affected foals. LFS results from a specific mutation of the MYO5A gene in horses. Genetic testing for this mutation enables a clear distinction between homozygous non-carriers and clinically normal LFS-carriers.

Hereditary Equine Regional Dermal Asthenia (HERDA) describes a degenerative skin disease in American Quarter Horses which is inherited in an autosomal recessive manner.

Horses suffering from HERDA are usually born without any clinical signs. However, at a later stage affected animals develop localized skin defects which often appear along the horse’s back. In most cases, on the course of the disease, progressing lesions prohibit any further use of affected animals for riding purposes.

The diagnostic DNA test for HERDA detects the causal mutation in the cyclophilin B (PPIB) gene and thus enables identification of horses that are affected or carry the mutation.

Junctional epidermolysis bullosa (JEB) is an autosomal recessive inherited trait which is observed in Belgian Draft as well as in American Saddlebred horses. JEB-affected foals are born with moderate to severe skin defects like blisters, erosions or ulcera on the skin (fetlocks, hips, etc.) and mucocutaneous epithelia (mouth, anus, vulva, etc.). In the long run, affected foals are not viable and usually need to be euthanized at an early age.

Due to its autosomal recessive inheritance, JEB foals can arise from mating of two JEB-carriers, which themselves do not show any clinical signs of the skin disease.

JEB gene testing provides the possibility to distinguish not only between clear and affected animals, but also enables identifying carriers for this disease. Therefore, gene testing offers an instrument for avoiding production of affected and unviable foals.

Please note: The offered test detects the mutation associated with JEB in American Saddlebred horses, only. In Belgian Draft horses, JEB originates from a different mutation not located in the LAMA3 gene.

Contact DNA Ireland

If you have any questions or concerns please Lo-Call 1890 989 556 or phone 021 4965809 or email us at info@dnaireland.ie or lucy@dnaireland.ie. Alternatively you can use our enquiry form here or Tweet us @ DNAIreland.