Category: Genetics

Dapple grey, trotting

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Last week we reviewed the base color and dilution loci. Today we will do a final review of the interspersed white hair and white marking genes, along with the darkening genes. Although the blog series will end today, links will be put in the index to all  posts in this series.

There are two main loci responsible for interspersed white hair. These are Grey (born dark with white hairs becoming more numerous with age) and Roan (born roan with white hairs constant or decreasing with age.)

The Grey locus is the syntaxin-17 (STYX17) locus on equine chromosome 25. It causes an initial increase in melanocytes  followed by their depletion. There are two alleles at this locus: grey and wild-type, with gray being incompletely dominant. (Horses with two copies of the grey allele lighten faster than horses with one grey and one wild-type allele, are less likely to develop a fleabitten appearance, and are more likely to develop melanomas with age.) At this time the progression of graying (dark vs. light mane and tail) and the color of dark hair (usually black, but some individuals become rose grey, with the dark hair remaining red) are not known to be subject to genetic control. In any case the final result is a mostly white horse.

The Roan locus is close enough to the Extension locus that there is significant linkage. It is considered part of the KIT linkage group on equine chromosome 3. There are two alleles: roan (dominant) and wild-type. At one time possession of two roan alleles was thought to be lethal, but this has now been shown not to be true. Classic roan causes interspersed white hairs on the body, but the legs, mane and tail normally remain dark. The frosty pattern, in which the mane and tail are also affected, may be a variant of roan, but the genetic mechanism is at present unknown. Scars commonly lack white hair, causing dark corn marks.

Spotting loci are far more numerous, and some produce roaning as well as white areas.

Blazed face on chestnut

Blazed face on chestnut

Minor spotting genes may be responsible for white facial and leg markings. These genes are present in most breeds, and facial and leg white tend to increase in tandem. Animals with wide blazes and no white on the legs, or with high stockings and plain faces are very often minimally marked animals with one of the other spotting genes.

Tobiano horseThe Tobiano locus is closely associated with the KIT locus, and hence on equine chromosome 3. There are two known alleles, tobiano and wild-type, with tobiano being an incomplete dominant. Generally tobianos are crisply marked, with white crossing the topline. Legs are normally white and the face is plain or has minor markings. Minimal tobianos may have high stockings with plain faces; in the maximal pattern only the head may be colored. Roan or colored spots known as paw prints may occur in white areas on animals with two tobiano alleles. There is a dominant modifier which in the presence of both tobiano and cream produces what is called a calico pattern—the yellow of the buckskin or palomino is broken up, with some areas being red.

Black and white frame horseThe Frame locus is on equine chromosome 17, and is at the locus that controls endothelin receptor b (EDNRB.) The alleles are frame and wild-type. The frame allele is lethal in double dose, producing the so-called lethal white foal syndrome, so all frame horses should have one frame and one wild-type allele. The minimal expression of frame is extensive white on the head with colored legs. The maximal extent may have color confined to the topline and legs. The fact that the frame allele still seems sometimes to come out of nowhere need further clarification—a masking gene may also exist.

The sabino pattern is a combination of spotting and roaning, and extremely variable in expression. It may also have more than one genetic explanation. The Sabino-1 locus is part of the KIT complex (equine chromosome 3) and has two alleles, sabino and wild-type. The sabino allele is incompletely dominant over wild-type, as horses with two sabino alleles generally have more white (even to being almost completely white) than horses with one sabino and one wild-type allele. There are other mutations near the KIT locus that cause white spotting, some of which appear to be lethal in double dose.

The Splashed White locus is yet another that seems to be near the KIT locus, though not at it. The locus probably has two alleles, splashed white and wild-type, with splashed white behaving as an incomplete dominant. The minimal effect of splashed white may not be detectable, or the horse may be more extensively marked with white legs, possibly white underbody and generally white on the head, sometimes to the extent that the whole head is white. Think of a horse trotting through a puddle of white paint with its head lowered. Splashed white is also associated with deafness.

Lone Ranger andSilverManchado is a relatively rare type of spotting found in several breeds in Argentina, though that may be because of the Argentine fascination with coat color. Parts of the body, often including the top of the neck (and mane) are white, often with round colored spots. The genetic basis is unknown.

White with pink skin and dark eyes may be a separate gene, possibly lethal in horses with two white alleles. At the moment, this is somewhat up in the air.

Appaloosa horse

The Leopard locus is the Transient Receptor Potential Cation Channel, Subfamily M, Member 1(TRPM1) locus. It has two alleles, leopard and wild-type, but an enormous array of patterns. Leopard is incompletely dominant over wild-type—horses with two leopard alleles generally have fewer leopard spots than those with one leopard and one wild-type gene, and have a high incidence of night-blindness.

chestnutFinally, darkening due to black hair in the coat may occur in at least three forms. Black hair may be scattered throughout the otherwise red parts of the coat, producing a sooty effect. Black tipping on otherwise red hairs appears to be associated with the agouti locus, and produces shaded effects where the back appears darker than the rest of the horse. Actual black striping of the coat, brindle, is rare but documented. Some types of roan, especially sabino, may produce a type of brindle with white stripes. The genetics are unclear in all of these cases.

Horse head

Look at the ear tips on this bay.

This article was originally posted April 24, 2011. It is being repeated here with new photos and some revision.

Horse colors are due to the interaction of a large number of genes, many of which we’ve discussed. These may be divided into base color genes, diluting genes, genes that cause interspersed white hairs and marking genes. One type we have not discussed, because the genetics are not really understood, is interspersed black hairs.

I’d like to point out one thing that Sponenberg does not cover: there are two distinct types of darkening due to the presence of black. It takes a magnifying glass and a great deal of patience to tell the difference, but darkening can be due either to interspersed black hairs (called sooty and it can occur on any base color) or to hairs that are red/yellow at the base and black at the tip (producing a shaded appearance and I think occurring only on bay, wild bay and some seal brown horses.)

For the rest of this discussion I will assume the horse is of one of the base colors, but sooty and shading can occur with any dilution or marking genes, or together with roaning or grey. You just have to remember what the other genes do to red and black pigment, or if they have different effects on coarse and fine hair.


Chestnut with sooty gene. The dark mane and tail almost look bay, but the lower legs clearly identify this horse as a chestnut.

Liver chestnuts are often sooty. It takes careful examination to tell if a chestnut has interspersed black hair, but when I was examining them with a magnifying glass, this was true of every liver chestnut I examined. Even red chestnuts often have a few black hairs mixed into the coat and the mane and tail. Bays can also be sooty, but this may be confused by the presence of shading.

In order to understand black shading, it is necessary to go back and look at how the agouti locus affects mammals in general. The locus got its name from a middle and South American rodent, the agouti. This animal has fur in which the individual hairs are banded in black and yellow. As it happens this is very common in mammals, and a number have banded hair. Unless the hair is very coarse this is not obvious—wild gray mice and rabbits, for instance, really have hair banded in black and light yellow.

The banding may vary from multiple bands on a hair to hair with red/yellow/cream bases and black tips. The banding may also vary with type of hair, with some hairs (often the coarsest) being solid black and others (often the finest) being predominantly yellow.


This guy is a mule, but he shows an interesting combination of shading due to the depth of black tipping and the variation of red/yellow pigment.

Remember bay and wild bay are due to genes at the agouti locus. Most bay horses have at least some banded hair on the body, usually with a red base and black tip. This is easiest to see around the edges of the ears, and the banded hairs tend to be most numerous along the spine and spreading down to cover the hips, shoulders and upper barrel. It’s been a long time since I actually looked at individual hairs with a magnifying glass or under a microscope—I was doing this in the late 60’s and early 70’s. But as I recall, just about every bay or buckskin horse I looked at had at least a few black-tipped hairs. In some, the black tipping produced a shaded effect on the body of the horse.

A few horses look black or seal brown in summer coat and quite different in winter. I recall two of these. Duchess was a typical seal brown in the summer—black with tan shading on her flanks, muzzle and under her tail. In winter she looked dark bay. Careful examination of her winter coat showed red near the skin with deep black tips. In her short summer coat, apparently only the tips showed.

The other was even more striking. I first saw him in winter coat, and thought at first he was a blue roan. Careful examination of his coat showed yellow bases with black tips rather than interspersed white hair—a buckskin with deep black tipping. In summer, I knew he was the same horse only because the stable owner identified him—he was a typical seal brown.

Note that this shaded effect due to black tipping is quite different from the counter-shading often seen in red/yellow pigment, which leads to the undersides being lighter than the back. This is very common in mammals, and tends to offset the fact that light comes from above, making the animal less visible to predators. The shading in a bay may be due to the same selection pressure, but the effect on the individual hairs is quite different.

This is an area that needs much more research. Unfortunately with the prominence of DNA in genetic research, researchers seem not to be paying as much attention to the distribution of pigment in the hair.

This is a repeat with some updating and additional photos of an article originally posted April 10, 2011

Lace blanketNot all horses with white markings produced by the Leopard gene are leopards. The white markings are generally symmetrical and present at birth, but they vary a great deal from horse to horse and may even be absent entirely. The minimal expression is white over the top of the rump, and the broad term for the pattern is blanket. Note that I am speaking only of white produced by the leopard gene. Leg and face white are generally independent of the leopard gene.

Edges of the white blanket may be crisp, flecked or roaned.

Appaloosaa horseSponenberger divides the white patterns by percent of white at birth. The modification I am using in Tourist Trap is:

10% or less white spots over hips
10% to 20% lace blanket
20% to 40% hip blanket
40% to 60% body blanket
60% to 80% near leopard
90% to 100% leopard

Note that “leopard” in this table includes both leopard and few-spot leopard, and that the size of the blanket has nothing to do with whether spots are present. If one copy of the leopard allele and one of the wild-type allele are present, whatever white areas are on the horse will normally have spots of the base color. If two copies of the leopard allele are present, the white markings will have few or no spots, and the pattern is often called snowcap or few-spot.

Lace blanketThe Pattern-1 gene is heavily implicated in the amount of white, but it is almost certainly not the only modifier.

Spots will normally be of the base color, but may show a concentration or dilution of color. Thus they may appear darker or lighter than the base color. The horse on the book cover on the right sidebar shows spots on the neck, suggesting that at least some of the spots are darker than the body color. (That horse, by the way, is a stand-in for Raindrop’s granddaughter.)

The description of Roi’s horse, Raindrop, in Tourist Trap is that of a body-blanketed grulla approaching a near-leopard. She has white coronets and spots significantly darker than most of her body, which is already dark and somewhat bluish for a grulla. Roi’s first sight of her gives the following description:

Grulla appaloosa foal

If this foal’s blanket enlarges with maturity, she could grow up looking like Raindrop. Photo credit Gail Lord.

“One of the two led horses had a black-spotted white body, but its neck, legs and chest were a dark mouse gray, set off by a black head and mane and a black and white tail.” Raindrop is later referred to as having a sparse mane (black) and being the color of polished slate. The dark dorsal stripe typical of duns would have been in the white-blanketed area, and hence invisible.

Genetically, she would have had two recessive black alleles at the Agouti locus, at least one wild-type allele at the Extension locus, at least one dun allele at the Dun locus, and one leopard and one wild-type allele at the TRPM1 locus.

Next week I’ll talk about the roan, flecked and snowflake patterns produced by the Leopard gene. Again, these patterns are often called Appaloosa in the United States, but they occur in horses worldwide.

Chestnut Frame horse

Chestnut paint. This particular horse appears to have the frame allele rather than sabino, judging from the face and lower legs, in spite of the ragged appearance of the spots.

Frame is another type of spotting gene in horses, formerly lumped into overo and sometimes called frame overo. It has nothing to do with the KIT locus, unlike tobiano and sabino-1.

Frame involves patterns of white which do not usually include roaning, though frame may occur in conjunction with other genes that cause roaning. In frame, the white areas tend to be arranged horizontally on the sides of the horse, and almost never cross the back. Frame is also almost the only pinto pattern in which the legs remain pigmented, though normal leg markings may occur.

Like all spotted horses, frame horses may vary from mostly colored to predominantly white. A frame horse will almost always have a wide blaze or bald face, and an apparently unspotted horse with a bald face but no white leg markings is likely to be a minimally marked frame. As the white expands the head may become mostly white and the white areas on the sides may expand to cover most of the horse, with the spine and legs being the last areas to lose color.

Black and white frame horse

Another Frame. Note minimal leg markings with wide blaze and white spots on sides.

Frame is due to a single allele, frame (Fr), at a locus called endothelin receptor b (EDNRB) on equine chromosome 17. The locus has two known alleles, frame (FrFr) and wild-type (Fr+). Frame horses, some of which are so minimally marked as to look solid, have one frame and one wild-type allele.

Breeding two frame horses together may produce lethal white foals, with two frame alleles. Such foals are born white, and the part of their nervous systems that controls the lower intestinal tract does not develop properly. They normally die within 72 hours of birth, though most are euthanized as soon as they are recognized. Most breeders avoid mating two frame horses together in order to avoid the production of such foals.

The frame allele can be tested for. Such testing has demonstrated that some genetically frame horses appear to be solid colored. Whether this is due to a suppressor gene or genes or is simply the extreme end of random variation of amount of white is unknown.

(If you’re here because you like horses, my story, Horse Power, is free today on Kindle. Click on the cover in the sidebar.)

Sabino Spotting in Horses

“Chico”, owned by Charlotte Rowe

For many years two types of “pinto” spotting were recognized—tobiano and overo. Overo has now been broken into a number of distinct spotting genes—frame, splash, sabino-1, other sabinos, polygenic sabino, some types of dominant white, and manchado. Sabino now seems to be as much a grab-bag of genetically different types of white markings as overo once was. Here I will concentrate on Sabino-1, while noting that several other genetic types of sabinos and dominant whites seem to be associated with mutations at nearly the same locus.

Sabino jumper

Sabino with near minimum markings.

The sabino pattern has a wide variety of expressions, and some can be easily confused with other types of spotting, or even with roan. Sabinos not infrequently have areas of roaning as well as white spots, or flecks of color within the white areas. Almost all have white feet and facial markings, and the minimally marked ones can sometimes be detected by narrow extensions of the white up a leg or down the throat. The horse in the photograph to the right, for instance, has extensions of the high stockings in points up the legs as well as small white belly spots.

Sabino head

Sabino head, showing white underside.

In contrast, tobianos tend to have white legs but relatively plain faces, while frame horses have heavily marked faces with generally dark legs. It is unlikely that a sabino would have a completely plain head or completely dark legs, but sabino can certainly mimic any of the other pinto patterns combined with normal face and leg markings.

The sabino-1 allele is due to a single base-pair change in intron 6 of the KIT locus on equine chromosome 3. This means it is very tightly linked with tobiano and roan, both of which are also associated with the KIT locus. There are actually a number of mutations at the KIT locus that can produce sabino-like patterns.


Note the ragged, flecked appearance of the white.

Sabino-1 is incompletely dominant to the wild-type allele. This means that a horse with one sabino-1 allele and one wild-type allele will be a typical sabino. A horse with two sabino-1 alleles may be mostly white, often with a pattern approximating the “War bonnet” pattern—color in a head bonnet, chest patch, flanks and tail base. This pattern, however, can also be produced by combining the tobiano and frame genes. Sabinos sometimes come from two parents that appear to be non-spotted, but as with tobianos, one parent is generally a minimally marked sabino.

Some of the other KIT-related sabino alleles may be lethal when the foal inherits them from both parents, but this is still being investigated. There is also the problem that it may not be possible to determine visually whether a sabino may have more than one spotting gene.

The sabino-1 allele is well known and a genetic test is available.

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.



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.

Black & White Frame

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.

Rabicano under saddle

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 tail

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 horse

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.

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 19th 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.)

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.

Bay horse

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 Aa is the symbol for recessive black, also called non-agouti. At 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. AA 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.

Seal Brown

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 Sheltie

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, Ee, which suppresses the black pigment. Not completely—a horse with two Ee alleles can still have black whiskers and may have black hairs scattered throughout the coat. (In contrast, an EeEe dog has no black in the coat or whiskers, but an EeEe 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 EeEe 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 ED and countershading, EB. (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 ED horse will be black regardless of what alleles are present at the A locus, and an EeEe 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.

With 550 posts as of today, I’ve started to have problems remembering what I’ve already put on here. This is particularly a problem with posting existing content such as poems, short pieces from the Summer Arts Festival, or science explanations originally written for the Alaska Science Forum. I can’t remember which books or DVDs I’ve posted reviews on. It also is starting to be a problem when I want to link to a previous post and can’t remember when it was put up or what the title was. And there are posts on this blog that have permanent information, like the series on planet building and the one on horse color genetics, or the book and DVD reviews. I want to make it easier for my readers as well as myself to find things.

I made a start some time ago by adding an index page, which can be accessed from the menu at the top of any page. Right now, the only links are to index pages on my author site. This takes you out of the site and sometimes back in, which is rather clumsy. The index list is also incomplete.

I’m going to start posting an occasional entry which is strictly an index of past posts on a particular topic. These posts will be linked from the index page, and will link forward to the individual blog posts. As it takes a while to find all the posts that belong together, this will be a slow process—probably extending over the next few months. The first in this series, on DVD reviews, is already queued for January 3. Others will follow, most on Thursdays.

I probably won’t be indexing every post. Some, like those early posts which were simply glossary entries for my books, are on the author site and really belong there. Others, like the regular Monday updates on North Pole weather starting in November 2010, can be found easily enough just by using the calendar on the site. But I hope that by the time I have finished this, older posts of interest will be easier to find.