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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.

Currently, genetic tests for the three basic coat colors include: Agouti and Red Factor

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.

Dilution Genes

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:


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.

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