The Basics of Base Colors in Horses

Four young horses facing the camera. From Left to Right: black, red, bay, bay

Horses come in a wide variety of colors, with many different genes at play behind the scenes. Throughout this article, I will highlight the three base colors and provide accurate genetics for each. I will show examples of adult horses and point out the most common misconceptions I’ve encountered.

Key Terms

Genotype - The entire genetic makeup.
Phenotype - Set of observable characteristics that result from the interaction between genotype and environment.
Allele - One of two (or more) versions of a gene that live on a chromosome. Each individual inherits one from their mother and one from their father.
Locus - Location of a gene on a chromosome.
Dominant - When two different alleles of the same gene exist, the one that gets expressed is known as dominant. Dominant alleles are typically written first and in capital letters.
Recessive - This is the allele that doesn’t get expressed or is masked by the dominant allele. Recessive alleles are typically written second as lowercase letters.
Homozygous - Two of the same allele. It’s important to distinguish dominant from recessive when writing this.
Heterozygous - One of each allele. Writing heterozygous implies one dominant copy and one recessive copy.

Base Colors

Starting with the basics. There are three base colors that all horses have: bay, black, and red. Genes known as extension and agouti code for these colors. The proper gene names are equine melanocortin-1 receptor (MC1R) for extension and agouti-signaling-protein (ASIP) for agouti. While many genes affect these colors differently, the base coat remains the same underneath. 

Extension presents with two alleles: E and e.
Dominant extension (E) codes for producing red and black pigment.
Recessive extension (e) codes for the production of red pigment only. This is sometimes referred to as the chestnut allele. 

Agouti presents with two alleles: A and a.
Dominant agouti (A) restricts black pigment to the points of a horse (legs, mane, tail, and tips of the ears). This is sometimes referred to as the nonblack or bay allele. 
Recessive agouti (a) allows black pigment to be distributed over the entire body. This is sometimes referred to as the black allele. 

Just like people, horses with the same base color have wide variations in shade. As of now, it’s not possible to test for what causes these differences. It’s important to remember that phenotype combines genetics and environment rather than one or the other.

Common Misconception

People may refer to homozygous dominant extension as “homozygous black” as those horses can never produce a red based foal. Since dominant extension produces both red and black pigment, this label is not genetically accurate.   

Bay (E_A_)

A research article written by Ludwig et al. (2009) shows that the oldest known horses were bay based. Using that data, we can conclude that bay is the original base and agouti is not a modifier, as some speculate. From there, mutations in dominant extension and agouti led to the recessive alleles that code for the red and black base colors, respectively. 

Modern-day bay horses can be spotted by their red bodies and black points. Their genotype can be any of the following:

EEAA - Homozygous dominant extension, homozygous dominant agouti

EeAA - Heterozygous extension, homozygous dominant agouti

EEAa - Homozygous dominant extension, heterozygous agouti

EeAa - Heterozygous extension, heterozygous agouti

Examples of bay horses: 

Bay horse eating from a bucket
Bay, known through parentage (red dam, black sire)

Light bay horse standing in a field
Light bay

Dark bay horse wearing a bridle and reins
Dark bay (brown)
Note how the body is nearly black, with a cinnamon color on the muzzle signifying bay as the base. 

Dark bay horse standing in a paddock
Dark bay

Bay pony at a show wearing a large red ribbon with a number 8 sticker on flank

Single bay horse tied to a post
Bay, tested

Two grouped photos stacked left to right with a blue arrow in between showing a horse with low black points (first picture) and the backs of the ears to show ear tips (second photo)
Low point bay, tested through UC Davis
Example of a low-point bay where black on the legs and ear tips are very small. 

Common Misconception

People may refer to “brown” as its own genotype - this is incorrect. Brown is genetically the same as bay but presents as the darkest phenotype. The third horse is an example of this. Research has shown brown horses testing as EEAa, but this genotype is not strictly reserved for that phenotype. See Druml et al. (2019) below. 

The easiest way to tell the difference between a brown horse and a black horse is by the muzzle - the color should be brown in color rather than black.  

Black (E_aa)

The difference between bay and black horses is the mutation of the dominant agouti gene to recessive agouti. With this base color, there are fewer genotypes. Black based horses have at least one dominant extension and two copies of recessive agouti so that black pigment is free to cover the whole body and is not restricted to the points. 

The genotype of a black horse can look like the following: 

EEaa - Homozygous dominant extension, homozygous recessive agouti.

Eeaa - Heterozygous extension, homozygous recessive agouti.

Examples of black based horses: 

Black horse standing in a pasture with a barn in the background
Black, known through offspring (one red foal)

Black stallion wearing a halter and lead rope in front of a fence
Black with some fading, tested through Animal Genetics

Black with some fading, known through parentage (one red parent)

Black mare and foal standing in a grassy field
Black mare and foal

Two stacked photos with blue arrows in between: on the tops are examples of faded black coats, on the bottoms are pictures of non faded black coats
Horse on the right: EEaa
Examples of faded/sunbleached black horses

As with the two examples above, very sunbleached black horses can appear bay. The best way to tell the difference is by looking at the colors of the muzzle and coronet bands, which should remain black. 

Common Misconception

Like all horses, there are many shade variations among black based horses. Some black horses are prone to fading, while others are not. Black horses with non-fading coats or ones tested EE for extension may be called “true black,” but this term is not science-based. As long as they have the correct genotype, they are black horses. See the example of the horse tested EEaa with a very faded coat compared to the Eeaa horse, which has never faded. 

Red (ee _ _)

The last of the three base colors is red. The difference between bay and red horses is the mutation of dominant extension to recessive extension. As recessive extension only codes for red pigment, the presence of dominant or recessive agouti has no effect. At any rate, agouti should not be dismissed, as it still remains and can impact the colors of offspring. 

You might have heard “red” referred to as chestnut or sorrel; both are registry terms, and the phenotype of each depends on who you ask. Both are correct terms to use. However, when talking about genetics, the best practice is to stick to the term red. 

The genotypes of red horses will look like these: 

eeAA - homozygous recessive extension, homozygous dominant agouti

eeAa - homozygous recessive extension, heterozygous agouti

eeaa - homozygous recessive extension, homozygous recessive agouti

Examples of red horses: 

Red, known through offspring (one black, one bay with a black sire)



Eeaa (foal, black), eeaa (mare), 
Red, mare tested through UC Davis

Dark red
Note the lightness of the fetlocks through the coronet bands.

Red with flaxen causing light mane and tail

Stacked pictures separated by a blue arrow showing seasonal changes of a red horse. Top shows a lighter shade, bottom horse appears black.
Seasonal changes on a very dark red horse that appears black

Like brown for bay horses, liver is a term used to describe the darkest phenotype of red horses. However, there is no found testable difference for this shade. The reason these horses appear so dark is due to a heavy concentration of red pigment. Most of the time, even the darkest red horses still have lighter pigment around their coronet bands. 

I recommend UC Davis and Animal Genetics for color testing horses. Both companies are known for their reliability and accuracy of test results. Quality is very important when testing for genes that can be lethal in homozygous forms.  

In the beginning, horse color genetics can be complicated and confusing. But once you can grasp the basics, the rest comes naturally!

All images used in this post are the property of Hoof and Quill or used with permission from owners. 

Articles discussed

Druml, T., Grilz-Seger, G., Horna, M., & Brem, G. (2018). Discriminant analysis of colour measurements reveals allele dosage effect of ASIP/MC1R in bay horses. Czech Journal of Animal Science, 63(9), 347-355. doi: 10.17221/105/2017-CJAS

Ludwig, A., Pruvost, M., Reissmann, M., Benecke, N., Brockmann, G. A., CastaƱos, P., Cieslak, M., Lippold, S., Llorente, L., Malaspinas, A. S., Slatkin, M., & Hofreiter, M. (2009). Coat color variation at the beginning of horse domestication. Science (New York, N.Y.), 324(5926), 485.