The Agouti Locus –  A, At, & a
This is the gene locus that controls the distribution of black pigmented hair across the body and points of the horse when in combination with ‘E/E’ or ‘E/e’ at the Extension Locus , BUT in ‘e/e’ horses there is no black pigment produced so although the Agouti alleles are still present in the horse their effect cannot be seen.
This Locus in horses has 3 Alleles (Dogs have 4 or 5 Agouti alleles, and mice have around 14 Agouti alleles)
‘A’ – Bay coat colour
‘At’ – Seal Brown (known as ‘Black & Tan’ in most other mammals eg Rottweiler dogs)
‘a’ – Black – solid black all over the horse

The dominant allele ‘A’ confines the black hair to the points (ear rims, lower legs, mane and tail) to produce a coat colour called Bay (Castaña/o in Spanish). There are many shades of Bay ranging from an almost black looking dark bay through mahogany bay (looks very like a mahogany table), blood bay, cherry bay, flame bay, orange bay, golden bay, to light bay. The genetics of these variations has not been identified though there are some likely candidates for some of the shades. The very dark Bays are generally believed to be due to an unidentified gene which is known as ‘Sooty’ because it often makes horses look like they have had a load of black soot thrown over their necks and backline (Sooty will have its own page as soon as possible because it does some interesting things).  Sooty gives a pronounced darkening effect along the dorsal aspect of Bay coats and tends to spread its darkness further with the passing years until most of the horse, from the head front-profile, neck, body to its backside are almost black, leaving just the underside of the horse showing the red hair typical of a Bay. So adult dark mahogany bays can be very hard to distinguish from Seal-Brown (Black & Tan) see below reference ‘At’. All BAY horses will include ‘A’ and ‘E’ in its genetic formula.

Red Bay ‘A/a E/e’ with slight Sooty shading – PRE Stallion

The main alternative Agouti Locus allele ‘a‘ is completely recessive to the other Agouti alleles and it is completely recessive to ‘A‘ and. The ‘a’ allele has lost the ability to switch between produce red pigment in the majority of the horse coat with black pigment on the points, instead in the presence of the allele ‘E’ of the Extension locus ‘a/a’ will produce a uniformly black horse. The mutation from the original wild Agouti allele ‘A‘ to ‘a‘ pre-dates the domestication of horses as it has been detected in wild horse remains from the late Pleistocene period. But today in most breeds of horses, the ‘a’ allele is rare, so black horses are infrequently seen. Many black horses will sun-fade, especially around the sides and flanks, and this is known as fading black.

A possible third allele, ‘At’ has been recognised to explain the colour Seal Brown – a black horse with red/tan muzzle, flankfolds, breast, underarms, and inner-ears, which is also referred to as ‘Black & Tan’ due to similarities to that colour in dogs (Dobermans, Rottweilers etc). Seal-Brown horses are born with this coat colour pattern fully established, quite unlike Sooty Bay horses who are born with red foal coats and darkish legs but rapidly darken along the backline after 15 months old. Seal-Brown slots inbetween ‘A’ & ‘a’ in dominance, and a laboratory in Arizona (Pet DNA Services) has spent many years working on proving the existence of this third Agouti allele for seal brown with some success, developing a genetic test for it. Other Genetics Laboratories lump Seal-Brown in with the various shades of Bay.

Seal-Brown ‘At/a’ – PRE Mare

Neither ‘A’ nor ‘a’ affects the shade of red pigment or the distribution of red hair in ‘e/e’ horses, so it is not possible to determine by examination of coat colour which alleles of the Agouti Locus are present in a Chestnut horse without either test-breeding it or DNA testing it.

GENETIC TEST:- The Non-agouti or Black ‘a’ allele can now be genetically tested for, allowing you to determine whether a horse has no copy, one copy, or 2 copies, see information at bottom of the article. Thus allowing one to prove that a fading black is actually a black not a bay !! The other Agouti alleles ‘A’ and ‘At’ are treated as one and the same thing ie. as Bay ‘A’ , because ‘At’ can only be tested for by one laboratory, Pet DNA Services, Arizona, USA who discovered the mutation and patented that test. The most recent news is that Pet DNA Services has closed in February 2016, and at the moment the fate of the Seal Brown DNA test is unknown.

Genetic Laboratories that provide Coat Colour DNA analysis (NB:-other Laboratories are available around the world)

1.The ANCCE-LGPRE Genetics Laboratory (NBT, Seville) will test for the Extension Locus alleles at the same time as they test for 6 other colour genes if you apply to the BAPSH Registry Office for LGPRE Service 243 using the ANCCE International Service Application form. Find the current Fee for this Service on the Registry Service Fees page.

2. Animal Genetics UK, based in Cornwall, UK and Florida, USA – www.animalgenetics.eu/equine

3. UC Davis Veterinary Genetics Laboratory, California, USA – www.vgl.ucdavis.edu/services/horse