Bay Horse, Non Bay Horse

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The Agouti gene controls the distribution of black pigment. This pigment can be either uniformly distributed or distributed to "points" of the body (ear rims, lower legs, mane, tail, etc.). Agouti has been linked to a deletion of 11 nucleotides in the gene that controls the agouti coloration. The 11 nucleotide deletions of this gene cause the recessive form of the gene. Only when the agouti gene is homozygous recessive for the deletions (aa) is the black pigment evenly distributed.

When a horse is heterozygous (Aa) or homozygous dominant (AA), the horse will then show signs of point distribution of the black pigment rather than even distribution. This is because the horse possesses a copy of the gene that holds the 11 nucleotides. These nucleotides must be absent in order for the black pigment to be evenly distributed.

The agouti gene will have no effect on horses that possess a homozygous positive red factor (ee). These horses lack the ability to produce black pigment. Therefore, if a horse tests positive for red factor (ee), it is impossible for the agouti gene to produce the point distribution or the even distribution, regardless of whether or not the horse is aa, Aa, or AA.

Agouti coloration is not shown physically on red (ee) horses. However, just because the agouti coloration is not visible does not mean that the horse isn’t able to pass a copy of the agouti coloration to its offspring. A red horse can still produce an agouti horse. This is where DNA testing becomes important.

A breeder might want to test a chestnut-base horse to see if it is an Agouti carrier. Testing bay horses to see whether the horse carries one (Aa) or two (AA) copies of the Agouti allele reveals what kind of horse they could potentially produce.

A homozygous agouti (AA) horse will always pass point distribution to its offspring. A heterozygous (Aa) horse will have a 50% chance of passing on the gene. Another reason to test for Agouti might be if there is some doubt whether a black horse is truly black or a very dark bay. The effects of other genes can make it hard to tell if Agouti is present or not.

This test does not determine if a horse is homozygous for black factor. To determine black homozygosity, a breeder should test for red/black Factor. See the Red/Black Factor page for more info.

Possible Results

Genotype Description
A/A Homozygous Agouti: Horse carries two copies (AA) of the Agouti gene and will pass a copy on to every offspring.
A/a Heterozygous: Horse carries one copy (Aa) of the Agouti gene and has a chance to pass it on to all offspring.
a/a Non-Agouti: Horse is homozygous for recessive black (aa) and will pass a copy on to every offspring.


Mamm Genome. 2001 Jun;12(6):450-5. Mutations in the agouti (ASIP), the extension (MC1R), and the brown (TYRP1) loci and their association to coat color phenotypes in horses (Equus caballus). Rieder S1, Taourit S, Mariat D, Langlois B, Guérin G.