Bay horses are commonly seen representing many breeds, although only in one breed, the Cleveland Bay, are the horses exclusively of this color. Ranging in shade from golden brown, to reddish brown to almost a deep purpely brown, bays always have dark points, which are black in standard bays but may be a bit lighter in light bays. Along with dun, bay, especially light bay, was probably one of the colors common among ancestral horses.

the genetics of bay horses

Bay horses must have at least one E⁺ allele at the extension locus (i.e. bay horses are of genotype E⁺E⁺, E⁺e or E⁺e^a at this locus). This allele causes the production of the black eumelanin pigment that occurs in black, bay and brown horses, and the colors derived from them (e.g. buckskin). The A or agouti locus controls the distribution of black pigment in horses with at least one E⁺ allele: whether it occurs evenly throughout the body, as in true black horses, or only in certain parts, as in brown and bay horses.

The agouti gene controls a switch from normal eumelanin production to a reddish (or sometimes yellowish) form of phaeomelanin in the body of the horse, but not in the mane, tail and points (lower legs and ear rims).

The recessive alleles are A^a and, A^t. Horses of genotype A^aA^a have a base color of black, while horses of genotypes A^tA^t or A^tA^a have a base color of brown. Brown, including seal brown, is genetically and phenotypically distinct from both black and bay, as explained by Gowers agouti model.

Again according to Gower, bay horses have allele A^A, or the wild-type allele A⁺. It is now the case that (in 2009) 3 alleles have been identified at the molecular level, where previously only 2 were known (the four allele model is certainly a possibility).

If Gower is correct the following explains bay: allele A^A is dominant over both A^t and A^a, but recessive to the wild-type allele A⁺. A⁺ is therefore dominant to all other alleles in the series.

Bay horses with allele A^A but not A⁺ are bay, with a black mane, tail and points. Their bodies may be reddish-brown (as in standard, blood and mahogany bays), orange-red (as in copper bays) or yellowish (as in golden bays) and may have a black cast.

Horses with allele A⁺ are light or wild-type bay. Their points (particularly the lower legs), along with the mane, may be less strongly marked than for other bays (they may be “off-black”). The black on the points may also be more limited than for other bays (e.g. restricted to the fetlocks of the legs). There may be red hairs mixed in with the black portions of the cannon and lower leg, rather than them being solid black.

Light bay is believed to be the original "wild-type" coloring that was commonly found in the horse prior to its domestication. It is still fairly common in wild horses, but is not restricted to them. The muzzle, underside, flanks, and girth area may be lightened in light bay horses. This may be caused by a seperate gene called Pangare (mealy), or it may be another affect of the A⁺ allele.

A summary of the effects of the A series on black is shown below. Some genotypes are shown using an underscore, e.g. A^A_. This represents where an allele can either be the same as the allele shown (i.e. A^A in the example) or any other allele recessive to it (i.e. either A^t or A^a in the example, but not A+ which is dominant to A^A).

The agouti locus reduces eumelanin production in certain parts of bay and brown horses, probably due to the gene only being operative (“switched-on”) in these parts. Different alleles of the agouti locus are responsible for different forms of phaeomelanin.

breeding bay horses
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