Animal GeneticsAnimalsBlogHorses

What is a bay horse?

Bay horses is one of the most common horse colors out there. They have an unmistakable appearance; red body, black mane, tail and legs. However common they may be, and simple in appearance, the color is incredibly disputed on, when it comes to the genetics of it.

In truth, it’s quite simple genetics that make this beautiful, albeit common, color. The leading cause of this genetical havoc is people spreading incorrect information, giving the laymen the completely wrong idea. Equine Tapestry has an excellent article, giving a clear explanation on why bay isn’t a modified version of black. I also would like to add that most of this wrong information has it roots in simplification. People have simplified the more complicated agouti and extension relationship to better explain it to laymen. However, probably by accident, oversimplification has occurred, converting it to misinforming laymen.


The more common notion is that black and red are the two base colors, and that bay is a modified version of black.

Which isn’t the case. Let’s leave the phenotypes alone and go into genotypes. What causes the phenotype of black? If you know anything about the basics of genetics, you’ll know that horses, or any other animal or human, have two chromosomes. Therefore, they have two loci, and therefore, two alleles for each locus.

Horses have one specific locus called the extension locus. The gene that occupies it has two alleles, often referred to as the black factor allele and the red factor allele. They’re abbreviations are ‘E’ and ‘e’, respectively. Personally, the red and black factor names seem inaccurate to me, because, as we’ll see below, the E allele has the power to produce both black and red pigment.

Black is a dominant phenotype, while red is a recessive phenotype, which means that black will mask red. (Also, the general notion is that alleles are dominant and recessive, while actually, it is the phenotypes that are.)

For example, take a horse that is heterozygous at extension, or simply put, ‘Ee’. This horse will appear black (or bay), because while the ‘e’ allele produces a red phenotype, the presence of the ‘E’ allele results in a black. Actually, it could also be a bay, but for this example, I’d like to assume said horse is a black horse.

Now, because he is a black, for want of the allele at the gene causing bay, the E allele produces black pigment all over the body. The ‘e’ allele would produce red pigment, too, but anytime there is a black phenotype, the red won’t display.


This may all seem to you unrelated to the heavily-disputed genotype of bay, but, this is the core of horse color genetics. Without a clear understanding of extension and agouti, understanding any other colors will be arduous.


Agouti in horses

Agouti in horses is a genetic locus, not a color. Because of this, a horse cannot not have agouti. There are two alleles for the gene at agouti. Keep in mind that agouti is different in horses as opposed to the other animals. I know in cat’s that agouti is a gene that causes banded hair, but in horses, agouti is mostly used as a simple term for ASIP, the proper name for the agouti locus.

Okay, back to topic. The two alleles at agouti are often known as “bay” and “non-bay”, but A and a are more common, respectively. Agouti acts as a guide to where black pigment goes and where red pigment goes. This does not affect a horse who is “ee”at extension, meaning that it needs at least a single E allele at extension to have an affect. Therefore, a red-based horse’s agouti status cannot be known without testing, parentage, or progeny. More on this later.

The a allele allows black pigment to be distributed evenly across the entire horse’s body, main, tail, and face. Black is recessive to bay (though dominant to red), so a black horse could be Ee aa, or EE aa. Remember, a single E allele is necessary to produce black pigment.

A bay horse, on the other hand, needs a single A allele, which limits black pigments to the points, namely, tail, mane, forelock, and legs, while red pigment is spread over the rest of the body.

A typical bay horse.

Now, many people get confused if you tell them, “Agouti doesn’t modify the effect of the E allele”. You’ll probably get asked, “Where’d the red come from?”. Remember I said earlier that E can produce two different pigments, so calling it the black-factor allele is inaccurate? Now, let’s return to that.


What pigment goes where?

The E allele produces both red and black pigment, and it’s up to ASIP (agouti) to decide what pigment goes up the hair shaft. The a allele always wants black pigments to go through the hair shaft, but black is recessive to bay, so if there is a single A allele, which wants red pigment to go through the body hair shafts and black only on the points, the phenotype will be bay, not black. Thus, two a alleles are needed to produce a black horse, in combination with a E allele at extension. To produce the phenotype of bay, only one A allele and one E allele are required.


To recap:

A quick recap.

  • Black horses must have at least one E allele and two a alleles. Possible genotypes for a black or black based horse: Ee aa | EE aa
  • Bay horses must have at least one allele and one A allele. Possible genotypes for a bay or bay based horse: Ee Aa | EE Aa | Ee AA | EE AA
  • Red horses must have at least two alleles and any allele at agouti. Possible genotypes for a red or red bases horse: ee aa | ee Aa | ee AA
  • The A allele at agouti needs at least one E allele to have a visible effect, as a lack of it results in no black pigment to limit to the points; thus red horses do not display the effects of A.


That’s it for now.


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