The Tobiano Gene in Horses

Tobiano was the first type of white body spotting in horses recognized as being genetically distinct. Like other white markings, it varies widely in extent, with tobiano horses ranging from white with a colored head to normally colored with white hooves and lower legs, and perhaps a white area in the mane or tail. A few tobianos have blue eyes which are apparently produced by the tobiano gene.

The tobiano pattern has relatively crisp-edged white spots that cross the topline. The arrangement tends to be vertical, though not to the extent of a striped pattern. The head normally remains dark, though the white markings seen on non-spotted horses may be present. At times the dark skin extends under the edges of the white patches, giving a “halo” effect. Portions of the mane and tail growing from white areas are normally white, and in fact this may be the only obvious expression of tobiano in a minimally marked horse.

The pattern is due to a dominant allele, tobiano, at the tobiano locus, To. This locus is near but not at the KIT locus on chromosome 3, and a marker test is available. A horse with two copies of the tobiano allele is perfectly viable and not usually whiter than one with one tobiano and one wild-type allele. It is, however, more likely to show “paw prints” or “bear paws”–roan or spotted areas within the white patches.

Tobiano can occur on any base color: intense, dilute, or with interspersed white hairs. It does occasionally have an odd effect in the presence of one copy of the cream gene. The colored part of the coat “breaks up” into patches of dilute and non-dilute hair. This variation of the pattern is called calico. Calico is thought to be due to a dominant gene at a third locus which can only be detected if both tobiano and cream alleles are present. Theoretically, smoky calico should occur with areas of smoky, black, and white, but I cannot find any reference to this color in Sponenberg.

Although tobiano is dominant, tobiano foals are now and then produced by parents that appear non-spotted. On close examination one of these parents is generally a minimally marked tobiano, with extensive leg white and vary little face white.

The tobiano in the video is a good example of the pattern. Note the way the white markings on the neck are carried into the mane, and the way the white patches cross the topline.

White Body Markings on Horses

Any color horse, full color, dilute, or with intermixed white hairs, can have white body markings. These have long been recognized as falling into two categories: leopard (Appaloosa in North America) and pinto (or paint, piebald, skewbald, or parti-colored.) I’ll leave the leopard complex for later, beyond noting that the horses in Tourist Trap have leopard complex markings. For today, I’ll just give a brief overview of the paint/pinto nomenclature.

Tobiano

In British usage, a piebald was a black and white horse, and a skewbald was red and white. This distinction is rarely made today. Rather, the color of the horse—bay, black, palomino, red dun roan silver, or whatever—is followed by the pattern of marking. And there are a lot more patterns recognized today, often due to quite distinct genes, than was the case when I first became interested in horse genetics!

Paint and pinto are in fact synonyms when they are used as descriptive terms, though they have separate breed registries. In North America the word pinto may be more common in the east and the word paint in the west, but either may include any of the patterns of white body spotting.

Probably frame, based on the wide blaze and generally dark legs.

The first breakdown came when tobiano was recognized as being genetically distinct from overo. Then it turned out that there were several genetically distinct patterns being lumped together as overo—just about everything that wasn’t tobiano, in fact. The latest version of Sponenberg gives no less than seven patterns of white body markings, not including the leopard complex or the dark-eyed solid white of the American Albino. I’ll give a very short summary of the seven here, and cover specific patterns and what is known of their genes in later posts.

Tobiano is a relatively clean, crisp spotting with white legs but generally dark heads. White markings tend to be vertical and generally cross the back in all but minimally marked animals.

The frame pattern was once considered typical overo. It is horizontal, tends to affect the head first and the legs last, and white rarely crosses the spine. Frame to frame breeding can produce white foals that die shortly after birth.

Sabino, showing both the ragged outlines and the roaning typical of this pattern.

Sabino-1 horses normally have both face and leg markings, and often have roaned areas as well. They are usually not as crisply marked as tobianos, but they vary widely and confusion with almost any of the other patterns is possible. Roaning often occurs and is an expected part of the pattern.

Splashed white gives the appearance of the horse being splashed with white paint from below. The legs are normally white, and so is the belly area. In addition, white is normally present on the head, often to such an extent that the head is entirely white.

Polygenetic sabino and the form of dominant white that sometimes produces colored areas are not well characterized genetically. but are apparently distinct from the other forms of white spotting.

The final pattern, which is very rare, is called manchado, and has been seen in several breeds in Argentina. In this pattern, white first appears along the top line, and can produce a white mane on an otherwise colored horse. The head and legs tend to stay dark as the white areas grow larger, and there are often dark spots in the white, giving a superficial similarity to some leopard patterns.

All of these patterns vary widely in the amount of white, and all have pink skin under the white portions of the coat. I’ll take them one at a time in later posts.

Other Patterns of White Hairs in Horses

Rabicano under saddle

This week will be a bit of a catch-all, covering a variety of patterns of white hairs that are neither grey, classic roan, face and leg markings, or associated with white spotting. (Varnish roan, for instance, is a leopard gene pattern, and sabino and dominant white may also produce roaning as part of the pattern.) The genetics of none are well understood. Following Sponenberg, I will list and describe them here. Sorry for the lack of photos, but I haven’t even seen all of these patterns myself.

The first, frosty, may be a variant of classic roan, as it is found in the same breeds. In this pattern, the roaning is most pronounced over bony areas such as the hips, and roaning may affect the mane, tail and head as well as the body. “Squaw manes” and “squaw tails” with white hair mixed in often indicate the frosty pattern. Although there is little doubt that the pattern is genetic, it is not well understood.

“Roaned” is used to refer to horses with a scattering of white hairs not due to the roan or grey genes. It is not always possible to distinguish them from minimal classic roans, but they do occur in breeds where roan does not occur.

Rabicano horse, showing the white at the tail base.

White ticking is a much more specific pattern, involving the base of the tail and the flank. It is not progressive and may occur on any base color. Tails with the base white are sometimes referred to as “skunk tails” or “coon tails.” In Spanish the pattern is called rabicano. This pattern is one of the few “roan” patterns to occur in Arabians. Inheritance is thought to be dominant.

Birdcatcher spots are small white spots scattered over a horse’s body. They are named for a Thoroughbred horse, Irish Birdcatcher, who had such spots. They run in families so probably are genetic, but no studies have been carried out.

Rabicano, showing how white hairs are arranged in stripes on the sides.

White striping is very rare in horses. The vertical white stripes may be a form of roan, as seen on the rabicano photos. Or it may simply be an accident of gestation. One striped Thoroughbred in Australia, Catch a Bird, is himself striped but is producing as a classic roan.

Finally, minor white markings may occur as a result of scarring. These are most common with freeze branding or saddle sores, but one pattern, called white lacing, is commonly due to a skin problem called reticulated leuktricia. Most often the growth of white hair in a net-like pattern over the hips and back is preceded by the formation of crusts in the skin, but not always. Both genetic and environmental causes seem to be involved. If you have an Amazon account, you may be able to see Sponenberg’s photos here.

Next week I’ll start discussing the patterns usually called paint or pinto.

This information is an update of an earlier post.

The Roan Gene in Horses

Roan, like grey, is a pattern gene which sprinkles white hair over an otherwise normally pigmented animal. However, the pattern of white hair, the progression with age and the response to scarring are quite different from grey.

It should be pointed out that horsemen use the word “roan” quite loosely. In Thoroughbreds, for instance, it is used as a synonym for grey, particularly rose grey. There are several forms of roan covered by this loose usage, but the one discussed here is classic roan, which is due to the dominant roan gene. Frosty roan, varnish roan, roaned, rabicano and the roaning caused by some white spotting patterns will be discussed separately.

In classic roan the head, legs, mane and tail remain fully pigmented but there is an admixture of white hairs on the body of the horse. Foals are born roan or shed their foal coat to roan, and beyond that point the roan pattern is not progressive with age. In fact, roans may darken with age. They may also change appearance with season, appearing lightest when the coat is shortest and darker in winter coat.

Corn marks (flecks of the base color) are common on roans, and scars often lack roaning. Photographs of wild horses often show this to an extreme, as dominance battles frequently leave extensive scars.

Roan is due to a dominant gene. At one time, the gene was thought to be a lethal when two roan alleles were present at the roan locus, but more recent work has shown this not to be true. The gene itself has not been found, but it is known to be near, if not part of, the KIT locus on equine chromosome 3. There is clear linkage with chestnut at the extension locus, and tobiano is also linked. As an example of this, if a bay roan is bred to a chestnut, most of the foals will be bay roans or chestnuts, with only a few being chestnut roan or bay. Linked genes do not follow the rules of totally independent inheritance. A linkage test for roan is available if you want to know if a roan is homozygous.

Roan is quite variable in its intensity. Now and then a roan foal comes from two parents thought not to be roans, but close examination of the parents generally shows one to be a roan with very little roaning.

Roan may occur on any base color with any combination of diluting genes and marking genes. Black roans are often referred to as blue roans, bay roans as red roans, and chestnut roans as strawberry roans, but there are also references to purple roans, lilac roans, and honey roans. Further, a “red roan” could have either bay or chestnut as the underlying color, while some dark bay roans were called blue roan or purple roan. The modern practice is to put the base color first, followed by “roan.”

Roi (in Homecoming) will someday get a palomino roan mare with leopard (Appaloosa) markings—a horse overlooked by others because of her color but in fact quite a good horse. She is also a good example of the way different color genes can combine.

(The 3 photos on the left were taken at my cousin’s horse farm in Alabama.)

The Grey Gene in Horses

Grey is frequently considered one of the basic colors of horses, but it is more correct to think of it as a pattern of white hairs. Further, it is the only pattern that changes systematically and predictably with age, and one of the few patterns which can hide most other color genes.

The grey locus is well documented, with two alleles. Grey is dominant to wild-type, and is due to a “4.6 kilobase duplication into intron six of the STYX17 (syntaxis 17) locus, on chromosome 25.” The practical meaning of this is that the grey gene can be tested for, and carriers of wild-type identified.

The horse nearer the camera is a grey that has turned pure white, but the dak eyes and muzzle identify it as a grey.

Gray is a pattern of interspersed white hairs that increase in a fairly predictable fashion with age. I say fairly predictable, because there are several patterns of greying, and any genetic controls for which pattern will occur have not yet been found. The speed at which greying occurs is also quite variable, though in most cases a horse is light grey or white by ten years of age. In all cases, however, the greying begins first on the head. This is in sharp contrast to roan, where the horse is born roan and the head remains dark.

Greys can be born almost any color, but when the foal coat is shed, the horse

This photo clearly show the white rear fetlock. With increasing age, this marking will probably remain visible only in the skin color.

can usually be identified as a grey. Other changes are more variable. The foal may be born with red body pigment, and remain red as the white hairs begin to appear, leading to a rose grey—often miscalled a roan. A red foal coat may shed to black, which then greys as the fraction of white hairs steadily increases. Or the foal may be born black, regardless of the genetic color, and then grey from the black.

Some greys develop a white mane and tail early. These horses generally become pure white with age, though their skin normally remains dark.

A famous grey, General Robert E. Lee’s Traveller. Good example of mane and tail remaining dark.

Others retain a dark mane and tail as the body lightens. These individuals may retain some dark shading on the legs and even body for a long time, and some never become entirely white.

Some grays are dappled at the intermediate stages—the body is covered with circular areas of lighter hair surrounded by darker circles. Others are more uniform—iron greys. Many, as they grow older, develop reddish flecks and are called flea-bitten greys. So-called blood marks—larger areas of red coat—may also develop.

Fleabitten grey with blood mark. Note that the fleabitten stage may come after the grey has become pure white.

One down side of grey is that greys are particularly prone to developing melanomas. Usually these are benign, but not in all cases.

It is worth pointing out that all “white” horses with dark skin are actually grey. All other genetic mechanisms for a white coat in horses also produce pink skin.

Greys can have any of the dilution or white marking patterns in addition to the grey pattern. I had a grey and white frame (paint) myself at one point, and while he looked white with slightly darker mane

Grey aged to white

and tail, the frame markings stood out sharply when I bathed him—the skin under the grey areas was black, while that under all of his white markings was pink. He eventually developed a flea-bitten pattern only over the dark skin.

Two greys are mentioned in Homecoming. The first is Derik’s grey, probably a dappled grey. Coryn took the paralyzed Roi for a ride on the second, Cotton, a horse aged to pure white. The novel I’m currently working on, Rescue Operation, will have two greys, an iron grey called Shadow and a dappled grey called Silver. Both are descended from Arabian stock allowed to run wild on a plateau for a couple of hundred years.

Silver Dapple—Another Dilution Gene in Horses

Silver on brown. Without silver, this horse would be mostly black, with black mane and tail.

Silver is another dilution gene in horses, quite distinct from cream/pearl, dun, or champagne. The silver dapple color is quite common in ponies, especially Shetlands. Body color on these ponies ranges from chocolate to blue, often with quite pronounced dappling and light mane and tail. But the gene occurs as well in many other types of horses, especially the gaited breeds in America and a number of breeds in Europe.

Different breeds and areas have different nomenclatures for horses with the silver gene. In Australia, silver is called taffy. In the Rocky Mountain Horse, it is referred to as chocolate.

Typical color for silver on black. Note the light eyelashes.

In all cases the gene occurs at the silver (Z) locus, and the alleles are silver (Z^Z) which is dominant, and wild-type (Z⁺) which is recessive. It is possible to test for the presence of the silver allele, which is at the PMEL17 locus.

The dilution genes we have discussed so far all have the same effect on black and red pigment, or somewhat more effect on red. Silver appears to have no effect on red pigment, and a highly variable effect on black. Interestingly, the coarsest hairs, whiskers and eyelashes, are most affected, often appearing nearly white. Manes and tails, also coarse, are generally affected more than the body coat.

Silver Dapple; Rocky Mountain Horse.

A genetically black horse may have the body color lightened so little it still looks black. On the other hand, the body may appear blue, chocolate or dead-grass color, but without the reddish cast typical of a chestnut. The mane and tail are generally lighter than the body, and the lower legs may be a little paler near the hoof. The contrast between mane and body color may vary—at one extreme the horse may have a mane only a little lighter than the body; at the other a black horse with a white mane and tail is quite possible. A chocolate silver with light mane and tail may be mistaken for a flaxen-maned liver chestnut.

Silver dapple on a bay background.

A genetically bay horse may show little effect of the silver gene aside from the light eyelashes and whiskers, or may have a variable amount of white hair in the mane and tail and a lightening of the black lower legs toward the hoof. The body color stays red, being unaffected by the silver gene. At the light extreme, a silver bay (called a red silver) may be very difficult to distinguish from a flaxen-maned chestnut. Usually the lower legs darken to near-black before lightening again near the hoof, but it may take a gene test to be sure.

Although I have not seen a red silver in person, I have seen what I suspect to be a buckskin silver. Such a horse could easily be the result of at least two types of breeding expected to produce palomino: a red silver misidentified as a chestnut to a palomino, or a chestnut carrying silver invisibly to a buckskin.

The owner identified this horse as a palomino, but I strongly suspect it is buckskin (cream on bay) with the silver dapple gene. Palominos not uncommonly have black hair in the mane and tail, but very rarely on the lower legs. This illustrates the difficulty of identifying horses with multiple dilution genes.

Clear chestnut completely hides the presence of the silver gene, though in theory a chestnut with a large amount of interspersed black hair or black eyelashes or whiskers would have that black replaced by interspersed blue or chocolate an the body and white eyelashes and whiskers. Without a magnifying glass and a very careful, hair-by-hair examination, however, this would likely go undetected. Since skin color is mostly due to black pigment, that also could be affected, though the silver dapples I have seen have normal skin color.

Silver dapple has been a rare color in North American horses other than ponies, but this is changing as breeders select for rare and unusual colors.

Some silver dapples, especially those with two copies of the silver allele, do have an ocular abnormality, though it is rare that vision is actually affected. This may be due to a linked gene, rather than the silver allele itself, but it is probably safest to have the eyes of silver animals intended for breeding checked.

Upper photos courtesy of Safyre Sporthorses.

Dun: a Wild-type Dilution Gene in Horses

Red Dun. Notice how flat the color looks compared with chestnut.

The colors of all wild animals are a tradeoff between camouflage, which hides the animal from its predators or hides the predator from its prey, and display, which involves making the animal more attractive to members of the opposite sex or more threatening to rivals of the same sex. In equines, camouflage may involve blending into the herd (as in zebras) or blending with the background (often dry grass.) Bay, black and chestnut are not very good camouflage colors, but flatter, duller shades of these colors are.

Dorsal stripe on the same red dun as the first picture.

The dun gene flattens and dulls the coat color over most of the body, sometimes leaving head, lower legs, and manes and tails darker than the body. Both red and black pigments are affected. It also produces a highly variable degree of striping of the coat. In general a dun horse will have a dark stripe running from the mane to the base of the tail, which in some cases continues down the center of the mane (dark mane center with light edges as in the Fjord horse) and tail. (Dorsal stripes do occur on other colors, but they are rarely unbroken from mane to tail.) In addition duns often have zebra-like stripes on the legs (especially near the knees and hocks.)

Dun Fjord horse. Note that the dorsal stripe continues up the middle of the mane. This horse also has tiger striping (faint) on the hocks.

Less commonly, they will have spiderweb-like markings on the forehead, or a cross stripe over the wither area—a marking common in donkeys. All of these markings are grouped as primitive marks.

One early study of dun suggested that the dulling is due to a crowding of the pigment granules to one side of the hair. My own observations tentatively support this, but I am aware of no published studies—looking at individual hairs under a microscope doesn’t seem to be popular today.

Dun is thought to be the wild-type gene for horses, and it is definitely dominant to non-dun. Why do we think it is the wild-type gene?

Dun Fjord horse. Note that the dorsal stripe runs into the tail, and the faint zebra markings on the hocks.

First, cave paintings.  Almost all show the darker head typical of dun, and some also show other primitive marks. Cave artists were limited by the available pigments, but their renditions are certainly compatible with the various types of dun.

Second, the wild horses that survived long enough to have their color recorded. These include the living Przewalski’s horse of Asia and the now extinct Tarpan of Europe, both duns.

Dun, though a dominant gene, is not that common in most horse breeds today. Why? During domestication, an occasional mutation to non-dun must have occurred. Human beings are attracted to what is different, and the earliest domesticators of the horse probably prized these intensely colored variants—to such a degree that in many horse breeds of today dun is either non-existent or very rare.

A darker shade of dun on bay. This horse had the dorsal stripe (clearer in another photo) and a clear shoulder stripe.

The words dun and buckskin are rather loosely used, and often treated as synonyms. Genetically, however, it is better to reserve buckskin for a bay with one cream gene at the cream locus, and dun for the whole suite of colors produced by one or two doses of the dun gene. The colors include red dun (dun on a chestnut background) various shades of tan with black mane, tail and lower legs known as  zebra dun, (dun on a bay background) and various shades of dark slate gray to tan to silver with dark points known as grullo (dun on a black background.)

In my  science fiction book, Tourist Trap, I have both wild horses assumed to be descended from some transplanted from Earth during the Pleistocene, described as striped duns, and a domestic mare, Raindrop, whose base color is grulla (feminine form of grullo.) Those striped duns are assumed to be duns of various base colors with very strong primitive marks. I might add that Raindrop’s color and markings correspond almost exactly with those of the foal in the last picture.

Pearl: a Palomino Complication

Sorry, I do not have a single photo of a pearl–just haven’t been able to find one. Sponenberg doesn’t, either. You’ll have to go with the descriptions.

Last week we discussed palomino as if there were just two forms of the gene associated with palomino color: cream and non-cream. The whole story is a little more complex, but I’ll have to introduce some genetic terminology to explain it, even though I’ve used the terminology, without explaining it properly, several times already.

The three new words we’ll be using are locus, allele and wild–type.

Locus means place in Latin, and it originally meant a place on a chromosome. Since genes code for proteins and are now known to be a little more complex than just the place on the chromosome, it now means the particular protein coded for.

There can be slightly different forms of a protein having the same function, and the different stretches of DNA (genes) that code for these slightly different forms are called alleles. Using this terminology, every horse has two alleles, one from each parent, at each locus (plural loci.) Last week we discussed two alleles, cream and non-cream, at the cream (C) locus.

The complications come from the fact that there are in fact three rather than just two alleles at the cream locus. Each individual horse can have any two of these three alleles. To avoid confusion, I am also going to introduce the term wild-type for the gene assumed to be the “normal” allele at a locus in the wild ancestor of a domesticated animal. What we called “non-cream” last week is in fact the wild-type gene that gives normal full color.

(Note that the wild ancestor of the horse is not the “wild” horse of the West—these are in fact feral, descended from domesticated stock. The only true wild horse alive today is Przewalski’s horse in Asia. The Tarpan in Europe was also wild, but became extinct in the 19^th century.)

Using our new terminology, the cream locus has three alleles: wild-type, cream, and pearl. Pearl was recognized quite recently, and it has a very low frequency except in a few Spanish and Portugese breeds and their derivatives. It could be considered a weaker allele than cream, as it has less diluting effect on the coat.

A horse with one wild-type allele and one pearl allele will look very much like a wild-type horse—chestnut, bay or black depending on what genes are present at other loci. A very close look will show skin slightly lighter than normal, or with small pale spots.

A horse with two pearl alleles will have the red pigment diluted only slightly more than would be expected for a horse with one cream allele and one wild-type allele. Black pigment, however, will be diluted much more than is the usual case for a horse with one cream and one wild-type allele. Thus a bay with two pearl alleles at the cream locus dilutes to tan or gold on the body with chocolate mane, tail and lower legs. A chestnut becomes virtually identical to a pumpkin-skinned palomino (technically gold champagne.) And a black becomes a grayish tan with chocolate mane, tail and lower legs. All of these colors appear very similar to those produced by a single dose of the champagne gene, which is a completely different gene at a different locus, but give very different breeding results. Luckily there is a DNA test for pearl.

If a horse has one pearl allele and one cream allele, the resulting color will be cream, usually slightly darker than the cream resulting from two cream alleles (cremillo, perlino or smoky cream.) In particular the eyes are generally blue or amber, and darker than those of cream horses with two cream alleles.

As I mentioned before, there are a number of different ways of diluting horse color, and when two or more at different loci are combined some very odd colors can result and it may not even be possible to tell what genes are present—or what colors can be produced—without DNA testing.

Next week I’ll consider linebacked dun—one of the few horse genes where the wild-type allele is rare today in many breeds.

(If anyone has photos I could use to illustrate some of these horse coat colors, I would really appreciate them.)

Palomino (Cream) Genetics

Sometimes scientists get it wrong. With time other scientists generally catch and correct the errors, but the initial efforts to explain the palomino color were wrong on two counts: first, the assignment of palomino dilution to the albino locus C (for color,now known to be the gene that codes for the enzyme tyrosinase) and second, the assumption that all dilute colors were palomino. We now know both are false, but the early investigators did explain why palomino does not and cannot breed true.

Palomino. A bay and another palomino are in the background.

A palomino is, ideally, a horse the color of a new-minted gold coin with a white mane and tail. At one time, breeders tried to get them to breed true, and there are still breed registries based on palomino color. But two dark-skinned palominos, mated together, will produce only about half palomino foals, and many of them will not be the pure gold with white manes and tails wanted. Why?

Palomino is an example of what is sometimes called over-dominance or partial dominance. The color is due to a dilution gene, cream or cremillo, acting on a chestnut background. The locus is still called C, with primary alleles C⁺ and C^Cr. A single dose of cream will dilute red pigment to golden yellow, while having very little effect on black pigment—thus the dark skin. A double dose will further dilute the red to a pale cream hard to tell from white, and black to a shade that varies from a slightly dirty white to pale gray.

Palomino with a Bend Or spot on the neck, far more conspicuous on a palomino than it would be on a chestnut.

All horses, in fact all mammals, have two copies of each gene, one from the father and the other from the mother. If the basic color of the horse is chestnut and the horse has a cream gene from one parent and a non-cream gene from the other, the result will be a palomino. If one parent is a cremillo (the result of a double dose of cream acting on chestnut) and the other is chestnut all of their foals will be palomino. But if both parents are palominos, about a quarter of their foals will get the non-cream gene from both parents and will be chestnut, a quarter will get the cream gene from both parents and will be cremillos, and half will get one of each kind of gene and be palominos.

Cremillos are popular with some horse owners today, but at one time they were considered very undesirable by palomino breeders. They have pink skins and blue eyes, and they may be more subject to sunburn than horses with dark skin and eyes. They are not, however, albinos or due to any form of the albino gene. The cream gene has been found and sequenced, and a DNA test for cream is available.

Palominos don’t necessarily have a clear gold body color, or white manes and tails. Remember chestnuts have varying amounts of black hair sprinkled through the coat, and these black hairs will remain and become even more conspicuous if the red of the coat is lightened to gold. Some chestnuts even have what are called Bend Or spots, areas much darker than the body, or even black. These will be much more conspicuous with  the C⁺  C^Cr combination..

Further, chestnuts often have manes that are self-colored or even darker than their bodies. These characteristics will carry over into the dilute animals, and it is not unusual to find palominos with considerable black shading or dappling, and black hair mixed into their manes and tails.

What happens if the cream gene is combined with a base color other than chestnut?

The effect of a single does of cream dilution on a bay, giving buckskin. There is considerable confusion between buckskin and dun, but this horse has the palomino or cream dilution.

One dose of cream on bay gives a buckskin, with a yellow body and black mane, tail, and lower legs. A double dose of cream gives a perlino, a cream horse with mane, tail and lower legs very slightly darker than the body, blue eyes and pink skin.

A single dose of cream on black may be missed entirely, and the horse just called black. Some blacks with a single dose of cream are slightly lighter than normal, and are called smoky. With a double dose of the cream gene, a black becomes a smoky cream, again with blue eyes and pink skin.

Although the darkest variants of cremillo, perlino and smoky cream can be distinguished from each other, the lighter variants are very difficult to tell apart. Often they are just called cream, the distinction becoming important only if they are bred.

A base color of brown or very deeply black-tipped bay? I saw one once in winter coat, and at first glance he looked like a blue roan. Looking closely, however, he did not have a mixture of black and white hairs; rather each hair had a cream base and a black tip. I was able to recognize the same horse in summer coat only because a stable employee pointed him out. In summer coat he was a typical seal brown.

I emphasized palominos with black skin because it turns out that gold horses with lighter skin (sometimes called pumpkin skin) are due to a completely different gene, champagne. I’ll talk about this later.

If you want to read some very basic information about genetics, especially genetics of coat color, have a look at http://bowlingsite.mcf.com/Genetics/Genetics.html

The Agouti and Extension loci in Horses

This was originally posted on November 27, 2010 with different photos and no comparison with other animals. Since I now have far more photographs, I have decided to re-post some of the old horse color genetics posts with better photos.

Blood bay with star

The base colors of horses are bay, black and chestnut, possibly with the addition of wild bay and seal brown (tan-point.) These colors are distinguished by where red and black pigment are found, both where on the whole horse and where on individual hairs. I’m going to go into more detail this time on what determines these base colors.

Red pigment in horses (more correctly, phaeomelanin) can appear brownish red to copper, sometimes approaching gold, in the absence of dilution factors. With dilution factors, it can include white, cream, tan, yellow and gold shades.

Black pigment (more correctly, eumelanin) is black in the absence of modifying genes. In horses, the genes that dilute black to blue-gray or black to chocolate brown are not known to occur, though they do occur in other species. Chocolate Labradors, for instance, have the gene that dilutes black to brown, but this is very rare, if it occurs at all, in horses. Some dilution genes in horses do affect black, changing it to shades from bluish to sepia to dirty white or even nearly pure white.

The Agouti locus is known in almost all mammals. It codes for a protein that affects more than coat color, and is complex to sequence. In general, however, more red pigment is dominant to more black pigment.

The Agouti locus is given the symbol A. Agouti alleles are A with a superscript showing the particular form of the allele. Thus A^a is the symbol for recessive black, also called non-agouti. A^t stands for seal brown (black with tan on the inner legs, flanks and muzzle, very hard to tell from black with the mealy gene) which is also called tan-point in some mammals. A^A is the symbol for bay. A⁺ is the so-called wild bay, where some red pigment appears on the lower legs. Note that + is always the symbol for the “wild-type” allele, that which is believed to be the predominant gene in a truly wild or ancestral population. The wild-type allele can be very rare in a domesticated population if it has been selected against.

Every horse has two alleles at each locus. If one allele is dominant to the other at the agouti locus, that is the allele that determines the color of the horse—if the extension locus allows it to. The order of dominance at the agouti locus is wild bay is dominant to all others, bay is dominant to black and tan-point but recessive to wild bay, tan-point is dominant to black but recessive to both bays, and black is recessive to the other three alleles. This means that two recessive blacks can produce only black foals, while two wild bays can produce any color they carry the genes for.

This horse could be a seal brown or a very darkly shaded bay.

The agouti gene, by the way, was named for a South American rodent, the agouti. It was originally defined as controlling banded hair, seen in many wild animals. In fact, banded hair (black tips on red hairs) can be found on most bay horses, though you’ll need a magnifying glass and very good light to find it. Many of the darker shaded bays actually have rather deep black tips on individual hairs. In a few extreme cases, only the tips are visible in summer coat, and a bay horse may appear to be a seal brown (black with tan shading on muzzle and flanks) in summer and a definite dark bay in winter. The horse in the photograph is probably of this type.

Sable and white Shetland Sheepdog–genetically Agouti.

Agouti in horses is bay. In dogs the same genetic color is sable, and in mice the standard gray color. (The yellow is very light.)

The Extension locus is given the symbol E. Again, this locus is very widespread in mammals. The wild-type allele, E⁺, allows the agouti alleles to be expressed. There is also a recessive allele, E^e, which suppresses the black pigment. Not completely—a horse with two E^e alleles can still have black whiskers and may have black hairs scattered throughout the coat. (In contrast, an E^eE^e dog has no black in the coat or whiskers, but an E^eE^e fox will be a typical “red fox” color.) But it will not have the black mane, tail and lower legs of a bay. In fact, an E^eE^e horse will be a chestnut, regardless of what may be at the Agouti locus.

E may also have two alleles dominant to the wild-type allele. These are dominant black E^D and countershading, E^B. (I have to say I have my doubts about countershading, though countershading on bays is well established.)

At the E locus, alleles with more black are dominant to alleles with more red. Further, the E locus can hide what is present at the A locus. An E^D horse will be black regardless of what alleles are present at the A locus, and an E^eE^e horse will be chestnut regardless of what is present at the A locus. The word epistatic is sometimes used to define this relationship between loci—Extension is epistatic to Agouti.

Note that I am following Sponenberg, Equine Color Genetics Third Edition, plus my own observations on hair color.