Seal brown (horse)

Seal brown is a hair coat color of horses characterized by a near-black body color; with black points, the mane, tail and legs; but also reddish or tan areas around the eyes, muzzle, behind the elbow and in front of the stifle. The term is not to be confused with "brown", which is used by some breed registries to refer to either a seal brown horse or to a dark bay without the additional characteristics of seal brown genetics.
Like bay, the seal brown color is produced by the Agouti ("A") gene acting upon a genetically black base coat, suppressing the black into point coloration and allowing the underlying reddish or brownish color to appear. The shade variation is polygenetic and affected by a various external factors. However some researchers distinguish seal brown with the qualifier At. The genetic study of seal brown is relatively new. Several theories were advanced in the last century to explain the heredity of the seal brown coat, and while a DNA test said to detect the seal brown (At) allele was developed, the test was never subjected to peer review and due to unreliable results was subsequently pulled from the market, due to the admittance of the creator that mouse DNA was used in the results of the test.
The genetically and visually related dark bay coat color, which also features black points and a dark body, differs from seal brown by the absence of tan markings. Another mimic is the liver chestnut, an all-over dark brown coat including mane and tail, that is sometimes confused with seal brown. However, true seal browns have black points characteristic of all bay horses, while liver chestnuts do not.
Identification.
The research behind the classification of seal brown as distinct from dark bay is quite new, and as a result, opinions vary on what constitutes a true seal brown. In "Equine Color Genetics", Dan Phillip Sponenberg wrote "In general, all dark colors with black points that are lighter than black but darker than bay are called brown." In this text, he classifies black-pointed, clear reddish coats of any shade as bay, and black-pointed coats of any shade with black countershading as brown. These definitions, while precise, are no longer accurate in light of current research.
Seal brown is best described as a black or nearly-black coat with reddish or tan hairs on the "soft parts": the muzzle, eyes, inner ears, underbelly, behind the elbow, and in front of the stifle. Like other coat colors, seal browns can range in shade. The very darkest are just about black except for their tan areas. Lighter examples are easily confused with dark bays. The mane, tail, and legs are always black.
Terminology.
Non-horse people often refer to many horse coat colors as "brown," in particular the bay color. Among horse aficionados, a common assessment is that "...[the term] is only used by people with one horse or with two hundred." The implication is that lay observers will refer to a horse's coat color to be "brown" due to a lack of vocabulary, and those discussing large populations of horses will use "brown" out of a need for a more specific vocabulary. The term "seal brown" is unlikely to be part of a novice's repertoire and is therefore preferable when discussing this specific coat color. This coat color is, illuminatingly, called "black and tan" in some languages.
"Brown" but not seal brown.
In the most simple terms, the vast majority of horses are indeed some shade of brown, but not "seal brown." Such coat colors include:
Seal browns on paper.
Not all breed registries or studbooks recognize seal brown as a distinct coat color. The American Quarter Horse Association and American Paint Horse Association both recognize "brown" as a separate category, while the Arabian Horse Association labels all non-black, black-pointed shades "bay."
Still other registries, such as The Jockey Club which registers Thoroughbreds and Appaloosa Horse Club, offer the designation "dark bay or brown" to cope with the ambiguity in terminology and identification. Among historically German breeds and registries, the term "rappe" indicates a black horse, "braun" is bay, while "dunkelbraun" indicates dark bay and "schwarzbraun" indicates seal brown (literally black-brown). In France, seal brown horses are recognized among the "black coat family".
Related coat colors.
The presence of other coat color genes can modify a seal brown coat. The seal brown family includes:
Genetics of seal brown.
The appearance of a horse's skin, eye, and coat-color is determined by pigment chemicals called melanins. Two types of melanins are used by mammals, such as horses and humans: "eumelanin", which is visually black to brown, and "phaeomelanin", visually red to yellow. Specialized cells in the skin and eyes, melanocytes or pigment cells, produce melanins and deposit them into the skin and hair using complex chemical reactions. The instructions for these chemical reactions are genetically encoded as DNA, and are therefore inherited. To be seal brown, a horse must have at least one copy of the functional "MC1R" gene ("E"/"E" or "E/Ee") and must have one of the following genotypes at the Agouti locus: "A/A" or "A/a".
One protein with an important role in eumelanin production is Melanocortin 1 receptor (MC1R). The gene which encodes a functional MC1R protein occupies the "Extension" locus, or chromosomal position, and is symbolized by the capital "E". A mutation, or change, in the equine MC1R gene, that resulted in a non-functioning MC1R protein, was identified in 1996. This form of the gene is symbolized by the lowercase "e" or sometimes "Ee". Since each horse has two copies of the MC1R gene, one from each parent, horses with one "broken" copy ("e") can still produce eumelanin in the hair. However, if a horse has two copies of the "broken" allele and therefore no copies of the functional "E" allele, the horse is completely incapable of depositing black pigment in the hair. Such horses are chestnut, or at least, are not black, bay, or seal brown.
The gene with the greatest role in the seal brown coat phenotype is Agouti signalling peptide (ASIP) or simply "Agouti". The functional Agouti signalling peptide (protein) acts as a switch between red-yellow phaeomelanin and black-brown eumelanin. It is ASIP that is responsible for the alternate banding of dark and light on animal hair, although it is also responsible for whole-body effects. ASIP attaches to MC1R molecules to temporarily prevent the latter from continuing the production of eumelanin, and so phaeomelanin is produced in its stead. An individual horse can only have two copies of the Agouti gene, with the following known alleles or options:
Theories of the existence of additional alleles on the Agouti locus have been proposed, but were verified as non existent. These are 
The "A" and "At" alleles cannot be distinguished by DNA testing in horses. A test had been developed, but the underlying studies were not peer-reviewed and the test was pulled from the market due to inconsistent results, this is because mouse DNA was used. Genetic tests exist only for two forms, dominant "A" and recessive "a." The genetic causes of seal brown and wild bay are still thought to be at "Agouti", but it is likely that seal bay is caused by the agouti gene not affecting the black pigment as much as normal, and that wild type bay is the agouti affecting the black pigment more than normal. The effects of shade variation is polygenetic and not yet understood.
Former theories about the genetics of seal brown.
An early version of the currently-accepted equine Agouti gene theory was first presented in 1951 by Miguel Odriozola in "A los colores del caballo", subsequently reviewed by William Ernest Castle in "Genetics". This theory prevailed until the 1990s, when discoveries of similar conditions in other species provided alternate explanations.
Black and pangaré.
For a period, the seal brown phenotype - black or near-black coat with tan or red hairs on the soft areas - was described as a true black coat affected by "pangaré", or mealy-factor. Pangaré is a quality common to the Przewalski's horse and so-called primitive horse breeds such as the Exmoor Pony. The trait is characterized by pale hairs, typically off-white to light tan, around the eyes, muzzle, and underside of the body.
This theory was discarded when the equine Agouti gene (ASIP) was sequenced in 2001, finding all horses fitting the seal brown phenotype did not possess the homozygous recessive "a/a" Agouti genotype.
Tyrosinase-brown.
Tyrosinase-related protein 1 (TYRP1) is a protein involved in melanin synthesis, and is encoded by the "TYRP1" gene, also called the "brown" ("b") locus. In humans, mutations in the "TYRP1" gene account for variations in "normal" skin, hair and eye coloration, as well as types of clinical Albinism. Mutations in the "TYRP1" gene of other mammals result in various reddish-brown coat color phenotypes: Brown in mice, Chocolate in cats, Chocolate in dogs, and Dun in cattle.
The phenotypes associated with "TYRP1" mutations are typically rufous or chocolate rather than the black-dominated coats of seal brown horses, and usually result in pinkish-brown skin and light eyes. This is not the case for seal brown horses, and the role of "TYRP1" in seal brown was ruled out after it was sequenced in 2001.
Extension-brown and dominant black.
The allure of a pure black coat on a horse has struck horse breeders for centuries, resulting in all-black breeds like the Friesian horse. The breeding of pure black horses is attended by two problems: some black coats fade with exposure to light and sweat, and breeding two "black" horses together would sometimes produce non-black horses. In some cases, faded true black horses have lighter coats than the darkest near-black horses.
To account for this, W.E. Castle postulated that there was a third allele at the "Extension" locus: "ED" or "dominant black". Based on the existence of such conditions in other animals, Castle suggested that the dominant black gene ("ED") would override the "points" pattern of dominant "Agouti" ("A") and produce black or near-black horses, which could then go on to have bay offspring. The implication was that the seal brown coat color, which is often quite nearly black, could be produced by this allele.
Similarly, Sponenberg once hypothesized an "Extension-brown" ("EB") allele, dominant over the wildtype "E". He described an allele responsible for black countershading, or sootiness, which would distinguish all shades of brown from all shades of bay.
Both theories were laid to rest after the characterization of the equine "MC1R" or "Extension", which showed no such alleles. However, it remains likely that a genetic control for sootiness does exist.
Dark bay vs. seal brown.
Both Dark Bay horses, which have a black mane, tail, and legs with a dark reddish brown or sooty coat, and seal brown horses, which have very dark brown coats in addition to black "points", with reddish or tan hairs around their muzzle, eyes, elbows, and flanks have one of two genotypes at the Agouti locus: "A/A" or "A/a". Both coat colors exhibit a broad range of potential shades due to a variety of factors including the bleaching or fading of black hair, nutrition, and the presence of sooty or countershading factors.
Many black horses fade, sunbleach, or otherwise undergo a lightening of their coat color with exposure to sunlight and sweat. These horses are often mistaken for seal browns or dark bays. Horses which do not undergo such fading are now usually called “non-fading” black, though other terms were used in the past. However, though hypothesized, there does not appear to be a separate “non-fading” allele for black, either. Mineral and vitamin deficiencies can also contribute to a lighter coat, similar to sunbleaching.
Black-pointed horses that are not uniformly black often exhibit a trait called sootiness. A sooty coat exhibits a mixing of black or darker hairs more concentrated on the dorsal aspect (top) of the animal, and less prevalent on the underparts. Sootiness is thought to be a form of countershading. Horses without any sootiness are termed "clear-coated". Sootiness can be minor or quite extensive, and often includes dappling. Dark bay horses are typically sooty. The difference between the top-down distribution of the sooty trait and the lighter soft areas of a seal brown can also be difficult to distinguish from one another.
The team of French researchers who developed the DNA test for the recessive "a" allele also discussed the possibility that "Extension" might be dosage-dependent. They found a statistically significant tendency for lighter bays to be heterozygous for the dominant, wildtype "Extension" allele ("E/e", also written "E+/Ee") while darker bays were more often homozygous ("E/E"). The authors acknowledged that other factors could play a role, and that the claim needed to be studied on a greater scale. This type of dosage-dependent behavior was not observed with "Agouti".