Brown horses can be various shades from light brown to almost completely black. Their bodies may be shaded black and brown or be mostly black (which is often called seal brown). Their soft parts, such as the muzzle and eyebrows, and around the flanks, quarters and girth, are red or golden brown (sometimes called “mealy”). Seal browns are often mistaken for black horses, but the coloring on the soft parts identifies them as brown. They are also genetically distinct from black horses, as discussed below.

Some aspects of colour are uncertain, this includes the genetics of brown horses. They’re not exactly black, they’re not bay.

Seal browns were,until recently, commonly thought to be black horses with a gene called “mealy”, giving pale red or yellowish areas on the lower belly, flanks, behind the elbows, inside the legs, muzzle and over the eyes. Pangarré was thought to be caused by a dominant gene symbolized as Pa+ (it‘s other name is pangarré). Some thought that the same gene caused sorrel chestnut (the lightest shade of chestnut, Thiruvenkadan et al, 2008). However, McCann (1916) reported that sorrel is recessive to chestnut and mating among sorrel horses gives sorrel offspring only. That is certainly inconsistent with sorrel being caused by a dominant gene. It is now known that, consistent with the theory of Gower, seal brown is due to the A^t allele at the agouti locus. This allele has been sequenced and there is now a test for it.

Some horses are more or less uniformly brown. Some of these are due to the action of dilution alleles, such as champagne, on an otherwise black coat. I’ve seen a beautiful chocolaty brown coloured warm blood that tested black, with non of the dilution genes for which there’s currently a test. This could be black with an unknown dilution gene, or it could be that it has a variant agouti allele.

the genetics of brown horses according to the Gower model

It is now known that seal brown is due to the A^t allele at the agouti locus. This allele has been sequenced and there is now a test for it. This is further evidence that the following theory is correct, certainly it shows that Gower, and others, were correct in anticipating a brown agouti allele.

Brown horses must have at least one E⁺ allele at the extension locus (i.e. they 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, brown and bay 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. Brown horses are of genotypes A^tA^t or A^tA^a at this locus.

The recessive allele A^a has no effect on eumelanin (black pigment) production. Horses of genotype A^aA^a therefore have a base color of black. The allele A^t is dominant over A^a, but recessive to the other alleles of the agouti series. Molecular genetic tests have confirmed that seal browns are not blacks and do not have the A^aA^a genotype. This is contrary to a previous theory that seal brown horses were in fact black horses with the Pangarre (or mealy) trait (which is thought to be caused by a seperate gene, though one wonders about this).

The A^t allele obviously causes less restriction of black pigment than the bay alleles of the agouti locus. However we know that brown is genetically distinct from bay since breeding brown horses together only ever results in brown or black foals, and not bay ones.

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 (black pigment) production in brown horses, probably due to the gene only being operative (“switched-on”) in certain parts. Different alleles of the agouti locus are responsible for different forms of phaeomelanin (red/ brown pigment).

link to information on breeding brown horses