Agouti is one of the most complex set of genes in horses, the reason for this is because it is the cause for 4 different colours all based on the same locus. These colours result from 4 different alleles; a (Black), At (Seal Brown), A (Bay) and A+ (Wild Bay). As all horses have 2 alleles at the Extension locus, all horses also have two alleles at the Agouti locus in their genome. Although, with 4 different alleles to pick from at the Agouti locus it is more complicated then the Extension, which only has two. Only a small amount of genetic research has gone into the Agouti genes and although some colours have genetic testing available there is still some things theorized.
The Agouti genes only affects black pigment therefore a red horse can carry an Agouti gene but not visually show that they do. What the Agouti genes do is limits the amount of black pigment on the horse. This means that horses with the Black Extension with an Agouti gene of At, A and/or A+ will have both black and red pigments being produced on different parts of the body, the Agouti genes decides what pigment is produced where. If you think of the Black Extension being dominant to the Red Extension think of Agouti being dominant to the Black Extension. Only one copy of the Seal Brown, Bay and/or Wild Bay alleles will dominate over Black limiting the black pigment to specific areas on the body.
As each allele restricts a different amount of black pigment, it is theorized that there is a dominance factor within the 4 alleles within the Agouti locus. Listed is the believed order of dominance from most recessive to most dominant: a (Black), At (Seal Brown), A (Bay), A+ (Wild Bay). According to this theory a Black horse will only be Black if it has two Black alleles at the Agouti locus (E-aa) where as if you have a Black Extension horse with one Black allele and one Bay allele the horse will be Bay (E-Aa) (this is proven fact and what the theory is then based off). Therefore, the theory goes, a horse with a Black Extension with the Bay allele and Wild Bay allele it will be a Wild Bay (E-A+A). As Seal Brown and Wild Bay are so rare compared to Bay some argue that Bay is truly the most dominant Agouti allele, time will tell which theory is correct.
Black, the a Allele
As briefly touched on in the Extension section a Black horse can only be Black under the circumstances when two different loci work together; the Extension and the Agouti. A Black horse must have two copies of the Black Agouti allele for it to be Black (E-aa). A Black horse with no other genes will have black skin and dark brown eyes. Genetic testing is available to the public for the Black allele on the Agouti gene.
Check out the album to see pictures of Black horses:
Seal Brown, the At Allele
Seal Brown is a relatively new discovery genetic wise. Seal Brown (or called Brown by some people, however Brown is also used as a term to sum up a group of colours which is why I specifically refer to this as Seal Brown) are often confused for Dark Bays (and vice versa) which had lead to a debate on whether Seal Brown really did exist before it was genetically discovered. The Seal Brown allele doesn’t limit a lot of black pigment in the heterozygous state however does limit enough in different areas that can lead you to tell the difference between a Seal Brown and Black horse. Seal Brown horses have the red pigmented hairs on it’s under belly, stifle fold and on it’s face around the muzzle and eyes. Horses that are homozygous for Seal Brown are lighter in colour, and have more black pigmented restricted then heterozygous horses looking more similar to a Bay. The big tell between a Seal Brown in both heterozyous and homozygous states is the lighter hair around the muzzle. A Seal Brown horse with no other genes will have black skin and dark brown eyes. Genetic testing is available to the public for the Seal Brown allele, however only a 1 lab that I know offers the Seal Brown test which is PetDNA.
Check out this album to see pictures of Seal Brown horses!
Bay, the A Allele
Arguably Bay is one of the most common horse colours in the world, only a few rare breeds do not carry the Bay allele (Friesian, Haflinger, etc) and it is considered one of the oldest horse colours on record. A Bay horse is a Black based horse with one or two Bay Agouti alleles (E-A-). With the black pigment limited by the Bay allele the only Black on the average Bay horse is found on the legs (stretching from hoof to hock/knee area, sometimes going a good deal farther up depending on the individual) and mane and tail. These are called Black Points. You will likely also see some Black on the horse’s ear rims and muzzle. Black Points can take a few years to fully develop making some youngsters appear to be Wild Bay horses when they are really Bay with Black Points still waiting to ‘fill in’. With the red pigment on the Bay’s body it can largely range in shades from yellows to reds to coppers to dark browns. People seem to love to name shades, however you will find that one shade tends to run into the next so without a clear line I’m not one to name shades most of the time. A Bay horse with no other genes will have black skin and dark brown eyes. Genetic testing is available to the public for the Bay Agouti allele.
Check out the album to see Bay horses:
Wild Bay, the A+ Allele… Maybe..
Wild Bay is the rarest of the Agouti alleles. Having a horse with the Wild Bay Agouti can be a hard find, it can be found in breeds such as the Arabian and Quarter Horse. Wild Bay has not been genetically discovered yet, it is only a theory that it is even part of the Agouti group; some have theorized that it is actually part of the Extension. This blog/website follows the most accepted theory of the Wild Bay Agouti allele. On a Wild Bay the Black Points are limited on the legs stretching up from the hoof to reaching the fetlock. Sometimes the Black Points will reach farther up the legs however they will be incomplete and not cover the entire leg front and back. This is a large difference compared to the Bay’s Black Points on the legs. Due to the rarity of Wild Bay it seems that it will be a bit of a wait to have more genetically studies done. A Wild Bay horse with no other genes will have black skin and dark brown eyes.
Check out this album to see pictures of Wild Bay horses:
Chestnut with Agouti Alleles
As stated earlier the Agouti alleles only affect the black pigment on a horse, therefore a Chestnut with any combination of Agouti is always a Chestnut. Jeanette Gower, in her book Horse Color Explained, expresses a theory that the Agouti alleles present on a Chestnut horse will depict what shade the Chestnut horse would be. According to her theory, the alleles that limit the most black pigment on black based horses gives you the lightest shades of Chestnut based horses and therefore horses with alleles that don’t limit a lot of black pigment on black based horses will be dark shades of Chestnut based horses.