Equine Coat Color Genetics

Base Coat Color

The base 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). The genotypes for both genes are necessary to determine the base coat color of a horse.

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 e^a. The e and e^aalleles are recessive to E and are considered to be loss of function mutations in MC1R. Only red pigment is produced in homozygous individuals (e/e or e^a/e^a), 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. To have black pigment uniformly distributed all over the body, a horse must have 2 recessive a alleles (a/a)

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

The figures below show images of Punnett Squares displaying the possible outcomes of a breeding in terms of the foal's base coat color. Figure 1 shows the possible outcomes for a foal produced by breeding two bay horses that are E/E for Red Factor and A/a for Agouti. There is a 25% chance of producing a black foal and a 75% chance of producing a bay foal from this breeding. A chestnut foal is not possible from this breeding.

Diagram illustrating a Punnett Square used to predict the possible outcomes of a breeding pair in terms of horse base coat color. — Figure 1: Punnett Square showing the possible outcomes of breeding two bay horses that are heterozygous for Agouti (A/a). There is a 25% chance of producing a black foal and a 75% chance of producing a bay foal from this breeding. Please note the above outcomes are assuming that the horses are homozygous dominant for Red factor.

Figure 2 shows the possible outcomes for a foal produced by breeding two bay horses that are A/A for Agouti and E/e for Red Factor. In this breeding, there is a 25% chance of producing a chestnut foal and a 75% chance of producing a bay foal. A black foal is not possible from this breeding.

Punnett Square showing the possible outcomes of breeding two bay horses that are homozygous dominant for Agouti and heterozygous for Red Factor. — Figure 2: Punnett Square showing the possible outcomes of breeding two bay horses heterozygous for Red Factor (Ee). There is a 25% chance of producing a chestnut foal and a 75% chance of producing a bay foal from this breeding. Please note this mating assumes horses are homozygous dominant at the Agouti locus.

When both parents have heterozygous genotypes for both Agouti (A/a) and Red Factor (E/e), their foal can inherit any of the three base coat colors. However, the probability of each color occurring is not the same. Figure 3 shows the possible outcomes for a foal produced by breeding two bay horses that are A/a for Agouti and E/e for Red Factor. In this case, there is a 56.25% (9/16) chance of producing a bay foal, 25% (4/16) chance of producing a chestnut foal, and 18.75% (3/16) chance of producing a black foal.

Genetic diagram showing Agouti and Red Factor inheritance in horses. — Figure 3: Punnett Square showing the possible outcomes of breeding two bay horses that are heterozygous for both Agouti (A/a) and Red Factor (E/e). There is a 25% chance of producing a chestnut foal, an 18.75% chance of producing a black foal, and a 56.25% chance of producing a bay foal when this cross is made.

Base Color - Shades

Variability exists among the three base coat colors. This variability has been described as shade. For example, some horses are a very dark chestnut and referred to as liver chestnut, while others are a much lighter yellow shade. Although more than 300 genes have been identified as contributors to mammalian pigmentation, the specific roles many of these genes play in equine color variation are still not fully understood. The genetics behind the variability of shade in horses is something we still have a lot to learn about.

Dilution Genes

There are several genes that have been shown to reduce the amount of pigment produced and/or reduce the amount of pigment 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 genes 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 (Figure 4). 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 (Figure 5).

Chart depicting horse coat colors: chestnut, bay, black, and their respective dilutions — Figure 4: Illustration showing the resulting dilution of each base coat color depending on whether the horse has 1 or 2 copies of the Cream allele (Ccr). The wildtype (normal) allele is represented by N.

Color genetics chart for horses with visual examples of coat colors and dilutions. — Figure 5: Illustration showing the resulting dilution of the base coat color of a horse by the pearl allele (CPr). The pearl allele is recessive, so no change is seen when a single copy of pearl is present. Dilutions of the coat color are seen when the horse has 1 copy of the cream allele and 1 copy of the pearl allele, or when 2 copies of the pearl allele are present.

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:

Conclusions

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.

Summary Table

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, e^a	The recessive alleles e and the rare e^a 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, W13, W20, W22	W5, W10, W13, 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. Horses with W5/W5, W10/W10, W13/W13, W22/W22 are thought to be embryonic lethal.	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:

Tiger Eye

Veterinary Genetics Laboratory

Equine Coat Color Genetics