Bay (horse)

Bay is a hair coat color of horses, characterized by a reddish-brown or brown body color with a black point coloration of the mane, tail, ear edges, and lower legs. Bay is one of the most common coat colors in many horse breeds.
The black areas of a bay horse's hair coat are called "black points", and without them, a horse is not a bay horse. Black points may sometimes be covered by white markings; however such markings do not alter a horse's classification as "bay". Bay horses have dark skin — except under white markings, where the skin is pink. Genetically, bay occurs when a horse carries both the Agouti gene and a black base coat. The addition of other genes creates many additional coat colors. While the basic concepts behind bay coloring are fairly simple, the genes themselves and the mechanisms that cause shade variations within the bay family are quite complex and, at times, disputed. The genetics of dark shades of bay are still under study. A DNA test said to detect the seal brown (At) allele was developed, but subsequently pulled from the market. Sooty genetics also appear to darken some horses' bay coats, and that genetic mechanism is yet to be fully understood.
Color variations and terminology.
Bay horses range in color from a light copper red, to a rich red "blood bay" (the best-known variety of bay horse) to a very dark red or brown called "dark bay," "mahogany bay," "black-bay," or "brown" (occasionally "seal brown"). The dark, brown shades of bay are referred to in other languages by words meaning "black-and-tan." Dark bays/browns may be so dark as to have nearly black coats, with brownish-red hairs visible only under the eyes, around the muzzle, behind the elbow, and in front of the stifle. Dark bay should not be confused with "Liver" chestnut, which is also a very dark brown color, but a liver chestnut has a brown mane, tail and legs, and no black points.
The pigment in a bay horse's coat, regardless of shade, is rich and fully saturated. This makes bays particularly lustrous in the sun if properly cared for. Some bay horses exhibit "dappling," which is caused by textured, concentric rings within the coat. Dapples on a bay horse suggest good condition and care, though many well-cared for horses never dapple. The tendency to dapple may also be, to some extent, genetic.
Bays often have a two-toned hair shaft, which, if shaved too closely (such as when body-clipping for a horse show), may cause the horse to appear several shades lighter, a somewhat dull orange-gold, almost like a dun. However, as the hair grows out, it will darken again to the proper shade. This phenomenon is part of bay color genetics, but usually not seen in darker shades of bay because there is less red in the hair shaft.
There are many terms that are used to describe particular shades and qualities of a bay coat. Some shade variations can be related to nutrition and grooming, but most appear to be caused by inherited factors not yet fully understood.
The palest shades, which lack specific English terminology found in other languages, are called "wild bays." Wild bays are true bays with fully pigmented reddish coat color and black manes and tails, but the black points only extend up to the pastern or fetlock. Wild bay is often found in conjunction with a trait called "pangare" that produces pale color on the underbelly and soft areas, such as near the stifle and around the muzzle. 
Bay horses have black skin and dark eyes, except for the skin under markings, which is pink. Skin color can help an observer distinguish between a bay horse with white markings and a horse which resembles bay but is not.
Ambiguity of "brown".
Some breed registries (including the Jockey Club Thoroughbred registry) use the term "brown" to describe dark bays. However, "liver" chestnuts, horses with a red or brown mane and tail as well as a dark brownish body coat, are also sometimes called "brown" in some colloquial contexts. Therefore, "brown" can be an ambiguous term for describing horse coat color. It is clearer to refer to dark-colored horses as dark bays or liver chestnuts.
However, to further complicate matters, the genetics that lead to darker coat colors are also under study, and there exists more than one genetic mechanism that darkens the coat color. One is a theorized sooty gene which produces dark shading on any coat color. The other is a specific allele of Agouti linked to a certain type of dark bay, called seal brown. The seal brown horse has dark brown body and lighter areas around the eyes, the muzzle, and flanks. A DNA test said to detect the seal brown (At) allele was developed, but the test was never subjected to peer review and due to unreliable results was subsequently pulled from the market.
Effect of gray gene.
Some foals are born bay, but carry the dominant gene for graying, and thus will turn gray as they mature until eventually their hair coat is completely white. Foals that are going to become gray must have one parent that is gray. Some foals may be born with a few white hairs already visible around the eyes, muzzle, and other fine-haired, thin-skinned areas, but others may not show signs of graying until they are several months old.
Bay-family colors.
Traditionally, bay is considered to be one of the "hard" or "base" coat colors in horses, although genetically the simple base coat colors, based on the presence or absence of the extension gene ("E" or "e", respectively), are chestnut and black. Bay is the result of the agouti gene acting upon a black base coat. The effects of additional equine coat color genes on a bay template alter the basic color into other shades or patterns:
Genetics.
The various shades of bay may be genetically produced by multiple factors, but a simple explanation of bay genetics is that "red" color, seen in the chestnut horse, represented by the recessive "e" allele; and black color, represented by the dominant "E" allele, are the two most basic coat color genes. All other colors are produced by the action of additional alleles acting on these two base colors.
A bay horse carries both the Extension (E) allele and a suppression gene known as the agouti gene (A).The agouti gene, dominant over the black gene, limits or suppresses the black coloring to black points, allowing the underlying red coat color to come through. Unlike other types of "point" coloring, such as that seen in Siamese cats, the black points characteristic of bay coloring are not produced by a dilution or albinism gene. 
Because the extension (E) gene and agouti (A) gene can be either heterozygous or homozygous, the extent to which a bay passes on its color varies widely from one horse to another depending on its genotype and that of its mate. Also, a chestnut may carry the Agouti gene, which will be "masked" or not manifest until the horse is bred to a horse with the E allele and produces offspring with both genes.
Inheritance and expression.
The bay family of coat colors is dependent on two autosomal simple dominant genes: Extension and Agouti. The role of the Extension gene is to produce a protein called Melanocortin 1 receptor or "Mc1r". "Mc1r" allows the black pigment eumelanin to form in hair. Closely tied to this process, the role of the Agouti gene is to produce Agouti signalling peptide "Asip", which disables "Mc1r", effectively allowing the red pigment phaeomelanin to "show through." However, this disabling does not occur throughout the coat; it occurs only in pulses on the body coat and not at all on the extremities or "points".
If a horse does not possess a functional, dominant copy of the wildtype E-allele at the Extension locus, then "Mc1r" cannot be produced. Without this protein, the black pigment eumelanin cannot form in the hair. Such horses, having two copies of the recessive mutation, have eumelanin-free, phaeomelanin-rich coats; they are red, or chestnut. In summary, unless a horse has at least one functional E-allele, it cannot be bay.
Similarly, if a horse does not possess a functional, dominant copy of the A-allele at the Agouti locus, then "Asip" cannot be produced. Without "Asip", eumelanin is unregulated and the coat is wholly black. The regulation of black pigment, though, is dependent on its presence in the first place; a horse with the recessive Agouti genotype aa is indistinguishable from any other genotype in a horse with a eumelanin-free coat. When eumelanin is present, it is restricted in varying degrees by the action of "Asip".
The action of "Asip" can be observed in horses which have their winter coats clipped. When shaved close, the black tip is shorn off leaving the phaeomelanic bottom of the shaft. This produces a dull, orange-gold appearance on the body coat which is lost with the spring shed. This is not usually seen in dark bays, which have little red in the hair shaft.
Agouti.
The cause behind the various shades of bay, particularly the genetic factors responsible for wild bay and seal brown, have been contested for over 50 years. In 1951, zoologist Miguel Odriozola published "A los colores del caballo" in which he suggested four possible alleles for the "A" gene. He described an order of dominance between the alleles and the associated phenotypes:
This was accepted until the 1990s, when a new theory became popular. The new theory suggested that shades of bay were caused by many different genes, some which lightened the coat, some which darkened it. This theory also suggested that seal brown horses were black horses with a trait called "pangare". Pangaré is an ancestral trait also called "mealy", which outlines the soft or communicative parts of the horse in buff tan.
The combination of black and pangaré was dismissed as the cause of brown in 2001, when a French research team published "Mutations in the agouti (ASIP), the extension (MC1R), and the brown (TYRP1) loci and their association to coat color phenotypes in horses (Equus caballus)". This study used a DNA test to identify the recessive "a" allele on the Agouti locus, and found that none of the horses fitting the phenotype of seal brown were homozygous for the "a" allele.
Since 2001, the mechanisms of the variations within the "bay" category remain unclear. Ongoing research suggests that Odriozola's theories may have been correct, evidenced by a parallel condition in mice. Mice have more than six alleles at the Agouti locus, including At which produces black-and-tan.
It is still likely that to some extent, the "shade" of coat color may be regulated by unrelated genes for traits like "sooty", and that the phenotypes of sooty or dark bays/browns may overlap.