Coat Colour Tests

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.
Accordingly, the interaction of the extension locus and the agouti will create the following situations:

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.

White spotting (also called Dominant White) is a collective term for a variety of piebald patterns caused by different mutations in the KIT gene. So far, at least 30 different mutations (W1-W30) are known, with some of them causing extreme variability in the expression of the piebald pattern. Some of these KIT gene variants occur in certain breeds or families, only.

GeneControl is currently offering genetic testing of following White spotting variants:

Note: Most combinations of two (different or same) White spotting variants cause embryonic death. This means it is very unlikely that a horse will have two copies of White spotting unless it is a combination with at least one copy of W20.

Dun describes the wild type coat colour originally found in all horses. Dun horses (horses carrying at least one copy of allele D) show a diluted base colour together with so-called primitive markings (line on the back, shoulder cross, legs with zebra stripes). Depending on the base colour of the horse, Red Dun (chestnut), Yellow Dun (bay) and Blue Dun (black) horses can be seen.

Another two possible alleles at the Dun locus can influence expression of the dun coat colour:
Nd1 – the non-dun1 allele is caused by a single nucleotide polymorphism in the TBX3 gene. Allele nd1 causes a non-diluted base color in combination with primitive markings of varying degrees (e.g. pseudo- line on the back).
Nd2 - the non-dun2 allele is caused by a complex deletion of bases in the TBX3 gene. Allele nd2 is quite common in most horse breeds, today. It causes a non-diluted base color without primitive markings.
Allele D acts dominant over nd1 and nd2. Allele nd1 is dominant over nd2.

Champagne dilution factor describes a modifier gene which causes dilution of the pigment of coat, mane and tail. Champagne dilution is dominantly inherited. Therefore, it modifies the coat color of horses carrying one or two copies of this gene. Champagne diluted colors are called classic champagne (black), gold champagne (red) and amber champagne (bay).
Champagne colors can resemble other diluted colors, e.g., cream dilutions and can also occur in combination. Horses which are heterozygous for the cream dilution gene will be classic ivory champagne (black), amber ivory champagne (bay) or gold ivory champagne (red) when carrying one or two copies of the champagne gene.
Champagne also modifies the phenotype of dun and silver dapple. For example, bay horses carrying silver dapple will be diluted to amber silver champagne and black dun horses will be diluted to classic dun champagne by the champagne gene.

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.

The pearl gene, also known as Barlink factor, is a recessively inherited dilution factor that modifies pigmentation of coat, mane and tail.
Horses carrying two copies of the pearl gene appear similar to champagne diluted horses. Horses carrying one copy of the pearl gene and one copy of cream will have a diluted color which can resemble champagne dilution or double diluted cream horses.
The pearl gene, originally discovered in Andalusian and Paint Horses, is present in Quarter Horses, Paints and related breeds, today.

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 German Classic 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 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.

Appaloosa spotting or Leopard Complex describes a piebald pattern of very variable expression caused by a mutation in the TRPM1 gene.

Spotted horses with dark body colour and a white "blanket" over hips and back containing coloured "leopard spots" are called blankets. In full leopards, pigmented spots appear on a white body, whereas snowflakes have a coloured body with white spots. Few Spots are born completely white showing only a few coloured spots. Varnish Roans have a coloured body with a white roan pattern, which may increase with age. Those parts of the body where bones lie close under the skin (e.g. forelegs up to the carpal joint, elbow joint, knee joint) will stay dark. This is the same for mane and tail of Varnish Roan horse.
However, some Leopard horses show almost no visible signs of spotting. These horses have a dark body and usually only some leopard characteristics like white sclera of the eyes, mottled skin around eyes, muzzle and genital regions.
Leopard Complex is a trait of incomplete autosomal dominant inheritance. Heterozygous animals (LP/n) show a less pronounced phenotype than animals bearing two mutant alleles (LP/LP). Leopard Complex is associated with the Congenital Stationary Nightblindness (CSNB) in case two copies of the mutant gene are present in a horse. Affected animals can hardly see in darkness.
The phenotype of the Leopard Complex is also strongly influenced by another gene, the so-called Pattern-1 mutation.
Leopard Spotting occurs in many breeds and Appaloosas, Knabstruppers and Ponies of the Americas are well known for this trait.

The Pattern-1 (PATN1) gene modifies the amount and distribution of white coat of horses carrying the Appaloosa spotting gene (LP). In horses lacking the LP mutation, the PATN1 gene has no effects on coat color. So, non-piebald horses can carry the PATN1 mutation, without showing phenotypical effects. Horses which are heterozygous for Appaloosa spotting and carrying the PATN1 gene will have an increased amount of white patterning (typically more than 60%). Horses that are homozygous for LP, will probably become a so-called few-spot when carrying the PATN1 gene. Due to its autosomal dominant mode of inheritance, one copy of the PATN1 mutation will result in modifying effects. The PATN1 mutation is frequently found in breeds such as Appaloosa, Knabstrupper, Noriker, British Spotted Pony or American Miniature Horse.

Mushroom describes a dilution effect with autosomal recessive inheritance, which is known almost exclusively in Shetland ponies. Homozygousity for this trait leads to the lightening of reddish pigment (pheomelanin).
In chestnuts, the gene causes a lightened sepia color of the body as well as a flaxen mane and tail. In bay horses milder gene effects are seen with normally pigmented mane and tail and a sepia diluted body due to lack of red pigment.
Mushroom can show similarities to cream and silver dilutions, although these have different genetic background.