Equine Coat Color Genetics
Base Coat Color
The basic coat colors of horses include chestnut, bay, and black. These are controlled by the interaction between two genes: Melanocortin 1 Receptor (MC1R) and Agouti Signaling Protein (ASIP). MC1R, which has also been referred to as the extension or red factor locus, controls the production of red and black pigment. To date, there are three versions (alleles) of this gene that have been identified at the molecular level: E, e, and ea. The e and eaalleles are recessive to E and are considered to be loss of function mutations in MC1R. In homozygous individuals (e/e or ea/ea) only red pigment is produced, hence the name red factor. ASIP, also known as Agouti, controls the distribution of black pigment. The dominant allele (A) restricts black pigment to the points of the horse (mane, tail, lower legs, ear rims), while the recessive form (a) distributes black pigment uniformly over the body.
Variability exists among the three basic coat colors. This variability has been described as shade. For example, some horses are a very dark chestnut known as liver chestnut while others are a much lighter yellow shade. While, over 300 different genes have been identified that contribute to mammalian pigmentation, for many of these their contribution to equine pigmentation variation remains unknown. The genetics behind the variability in shade in horses is something we still have a lot to learn about.
There are several genes that that have been shown to reduce the amount of pigment produced and/or reduce the amount transferred from the pigment cell to the hair follicular cells, and these are know as dilution genes. Some of these dilution genes affect only one type of pigment (red or black) while others affect both (red and black). Some dilute both the coat and the points (mane, tail, lower legs, ear rims), while others primarily dilute the points, and still others leave the points unaffected and only dilute the coat. Molecular characterization of six different dilution phenotypes in horses include Cream, Champagne, Dun, Pearl, Silver, and Mushroom. Cream is dominant and has a dosage effect in that a single copy of the cream allele (N/Cr) produces palominos on a chestnut background and buckskin on a bay background. Two doses of the Cream allele (Cr/Cr) produce cremellos on a chestnut background, perlinos on a bay background, and smoky creams on a black background. Pearl is an allele at the same locus at Cream (SLC45a2) but is recessive; two copies of the Pearl allele (Prl/Prl) or one copy of Pearl and one of Cream (Prl/Cr, this is known as a compound heterozygote) are needed to see the dilution effect on the coat.
Champagne, Dun, and Silver are all dominant traits, and therefore only one copy of dilution causing allele is needed to produce the respective phenotypes. Silver is interesting because it primarily affects black pigment of the points (black and bay horses). Chestnut horses with the sliver mutation do not show a different coat color phenotype than those chestnut horses without the silver mutation, as silver does not dilute red pigment. Horses with the silver mutation, regardless of base coat color, have an ocular condition known as multiple congenital ocular anomaly or MCOA for short. Horses with two copies of silver (Z/Z) have a more severe phenotype than those with one (N/Z).
The mushroom allele (Mu) is recessive and dilutes red pigment. Chestnut horses who are homozygous for Mu will have a dilute sepia coat phenotype. Bay horses homozygous for the mushroom phenotype have a lighter shade of red body with black counter shading, suggesting that Mu increases black pigment production having the opposite effect on black pigment as it does on red.
Current genetic tests for dilution mutations in the horse include:
White Spotting Pattern Genes
There are several genes responsible for white coat patterns in horses. These can occur on any base color and in combination with any dilution mutation. White spotting patterns can be divided into distributed white or patch white patterning. Distributed white patterns, in which white hairs are intermixed with colors hairs, include classic Roan and Gray. Both classic Roan and Gray are caused by dominant mutations. Classic Roan horses have fully or nearly fully pigmented faces but white hairs are distributed throughout the coat. Grey horses will progressively loose pigment distributed in the coat as they age. Gray horses are at risk for melanoma. Patch white spotting patterns include Appaloosa, Dominant White, Sabino 1, Splashed White, Tobiano, and Overo. These all vary in the location of the white pattern. For example, Appaloosa white patterning tends to be symmetrical and centered over the hips, but the amount of white can vary from just a few white flecks on the rump to a horse that is almost completely white. Patch white patterns identified to date have all been caused by dominant mutations. Some of these, like gray and silver described above, have pleiotropic effects; that is, a mutation in one gene can affect more than one body system. Homozygosity for the frame-overo allele (O/O) is lethal (Lethal White Overo syndrome). Horses with two copies of the Appaloosa mutation (LP/LP), also known as leopard complex, have an ocular condition known as congenital stationary night blindness, which means they are unable to see in low light conditions.
Current genetic tests for white spotting pattern mutations in the horse include:
- Appaloosa Spotting
- Appaloosa Pattern-1
- Camarillo White
- Dominant White
- Lethal White Overo
- Sabino 1
- Splashed White
Some color assignments and also genotypes can be correctly determined based on physical appearance or phenotype alone. However, genetic testing may be necessary to define phenotypes that are visually ambiguous and can help to determine color possibilities for offspring. For example, it is not possible to know by appearance alone if a chestnut horse is able to produce a black horse. Therefore, genotyping for Agouti can assist in these cases. There are many examples where genetic testing for coat color in horses can an assist with predicting breeding outcomes as well as inform clinical management decisions for those coat color phenotypes with pleiotropic effects. Researchers at the Veterinary Genetics Laboratory and around the globe are working towards identifying other variants involved in producing the myriad of beautiful coat color phenotypes that exist in the horse.
For more information on Equine Color Genetics please see
Sponenberg, D.P. and Bellone, R.R. (2017). Equine Color Genetics. 4th Edition Ames, IA: Iowa State University Press. ISBN: 978-1-119-13058-1.
|Gene Name||Variant Allele(s)||Function||
Wild type allele
|Agouti||a||The dominant allele (A) restricts black pigment to the points of the horse (mane, tail, lower legs and ear rims). The recessive allele (a) uniformly distributes black pigment over the entire body.||A|
|Red Factor||e, ea||The recessive alleles e and the rare ea produce red pigment (pheomelanin).||E|
|Cream||Cr||Dilutes red pigment (pheomelanin) to yellow pigment in single dose (e.g. palominos, buckskins, smoky blacks) and to pale cream in double dose (e.g. cremellos, perlinos, smoky cream).||N|
|Champagne||Ch||Dilutes hair pigment from black to brown and red to gold.||N|
|Dun||nd1, nd2||The dominant allele (D) lightens the body color and dilutes both red and black pigment, leaving the head, lower legs, mane, and tail undiluted, and also produces primitive markings. Horses with nd1 (and without D) will not be dun dilute but may have primitive markings. nd2/nd2 horses will not be dun dilute and will not have primitive markings.||D|
|Pearl||Prl||Two doses on a chestnut background produce a pale, uniform apricot color of body hair, mane and tail. Skin is also pale. Interacts with cream dilution to produce pseudo-double cream dilute phenotypes including pale skin and blue/green eyes.||N|
|Silver||Z||Lightens black/brown pigment but has no effect on red/yellow pigment. The mane and tail are typically lightened to flaxen or silver gray color but may darken with age on some horses.||N|
|Mushroom Dilution||Mu||Dilutes red pigment (pheomelanin) and is characterized by a distinctive sepia-toned body hair color, often accompanied by a flaxen mane and tail.||N|
|Leopard Complex||LP||White coat pattern characterized by variable patterning with or without pigmented spots known as leopard spots. Also characterized by mottled skin, stripped hooves, white sclera, and progressive loss of pigment in the coat with age (varnish roaning).||N|
|Appaloosa Pattern-1||PATN1||Modifier of leopard complex spotting (LP), controls the amount white in the coat. Horses with LP and PATN1 are typically born with a 60% or greater white spotting pattern.||N|
|Camarillo White||CW||Causes completely white coat, mane, and tail.||N|
|Dominant White||W5, W10, W20, W22||W5, W10, and W22 cause white patterning. W20 may have a subtler effect on the amount of white expressed unless in combination with other dominant white alleles, in which case it may increase the amount of white patterning.||N|
|Gray||G||Causes a progressive depigmentation of the hair, often resulting in a color that is almost completely white, and can act on any base coat color.||N|
|Lethal White Overo||O||Causes the frame overo pattern in heterozygotes and in homozygotes causes a disease characterized by a completely white coat and improper innervation to the gut, leading to death soon after birth.||N|
|Roan||Rn||Also known as classic roan, causes intermixed white and colored hairs on the body while the head, lower legs, mane, and tail remain colored.||N|
|Sabino 1||SB1||One copy causes white spotting pattern, usually on the legs, belly, and face, often with extensive roaning. Two copies produce horses that are at least 90% white and are referred to as sabino-white.||N|
|Splashed White||SW1, SW2, SW3, SW4, SW5, SW6||SW1-6 cause variable white spotting patterns characterized primarily by a large, broad blaze, extensive white markings on legs, variable white spotting on belly, and often blue eyes.||N|
|Tobiano||TO||Causes a clearly marked white spotting pattern characterized by white across the spine that extends downward between the ears and tail. The tail can be both white and pigmented.||N|
Tests Available at the VGL
Currently, genetic tests for specific pigmentation mutations available for the horse include:
Iris Color Variation:
Coat Color Panels:
- Red Factor & Agouti
- White Pattern 1
- White Pattern 2
- Appaloosa 1
- Appaloosa 2
- Coat Color
- Full Color & Pattern
- Shetland Pony