Tag Archives | pigment-type switching

Starting at the beginning – the process


So if we started at the beginning, with the horse before he was domesticated, we would be looking at an animal with a coloration much like the Fjord pictured above. The similarity between this particular type of bay dun and the coloring of wild equids is obvious, and was noted before the founding of the science of genetics. In his book The Variation of Animals and Plants Under Domestication, Darwin noted the primitive nature of this color.

[the similarity of color] in duns, of leg-stripes and of double or triple shoulder stripes… indicate the probability of the descent of all the existing races from a single, dun-coloured, more or less striped, primitive stock, to which our horses occasionally revert. — Charles Darwin (1896)

With the rediscovery of Mendel and his laws of inheritance, color variations came to be spoken of as “factors”, and then later as “genes”. Understanding physical reality behind these “factors”—the discovery of DNA—was still the better part of a half-century away. So a horse like this Fjord would have been said to have the “bay gene” and the “dun gene”. Much of how non-scientists talk about animal color still sounds like this. But within the scientific community, where advances in technology have given incredible insight into the mechanisms controlling development, color is spoken of as a process. A very complex and (at the moment) only partially understood process.

Let me try to give a simplified explanation of this developmental process and how it applies to bay dun.

Step 1 – Setting up for production

The precursors to pigment cells originate in the neural crest of the embryo. From there they migrate outward from the dorsal line, and multiply across the rest of the body. Once at home in the skin and hair follicles, these become the “factories” where pigment will be produced.

If you break something in this part of the system, you get spotted* phenotypes. The reason white patterns tend to trump all the other color traits—why, for instance, a dorsal stripe does not continue on through and bisect the white area of a tobiano—is that this is the start of the process. What happens within those cells after they start making pigment doesn’t matter if the cells never make it to a given location. Although horsemen, and certainly artists, tend to think of white as something added over the top of the basic color, understanding that color-producing cells have to migrate across the body makes it more obvious that white markings and patterns are actually the areas that those cells did not reach.

When pigment cells fail to migrate to the end of the limb, the result is a white marking on that leg.

Step 2 – Make the “factories”

Those pigment cells, once in place, are where melanin is produced. This process, which involves numerous steps, is known as melanogenesis. If you break something in this part of the process, the body may have viable pigment cells, but their ability to make pigment is compromised. Dilutions like cream, champagne and silver are mutations to (well-known) genes that control some aspect of melanogenesis, and the fact that different genes govern different parts of the process is why the phenotypes are different.

Step 3 – Regulate the product

Pigment cells also regulate the chemical composition of the melanin, which determines whether black (eumelanin) or red (pheomelanin) is produced. This is what was discussed in the series of posts on pigment-type switching, which is the proper term for this part of the process. If you break something in that part of the system, you change the proportion of red and black hair.

Step 4 – Maintain production

Because hair and skin are routinely replaced, pigment cells must continue to function to maintain coloration. If something in this part of the process is broken, there is a progressive loss of color. Greying is probably the most familiar example of an alteration that occurs in this step.

How this makes bay dun

So back to our domestic horse ancestor, who was bay dun. That first part, his bay “base” color, is determined in the process explained in Step 3. Back when colors were still “factors”, two major controls were theorized: Extension and Agouti. In modern terms, the theorized “Extension” is a gene known as MC1R and “Agouti” is a gene known as ASIP.  Together those two sites form the primary control of pigment-type switching in horses. In their original, unmutated form, they work together to give a pheomelanic (red) body and eumelanic (black) points. That is what is meant by the statement that “bay is the ancestral (base) color of horses”.

Because the pigment-type switches were formally identified first, it was possible to confirm that bay was the original wild color for horses. The assumption was that the ancestors of the domestic horse were also dun, but dun proved more elusive to identify at the molecular level. Part of the reason for that was that it was not in an expected place. In fact, it was not found in the expected part of the process. Because dun is thought of as a dilution—indeed the phenotype is diluted in appearance—the assumption was that the cause would be found in one of the sites known to be involved in melanogenesis (Step 2). In the paper I linked to in the previous post, the MLPH gene was examined and ruled out. That gene is involved in Dilute (d) coloration in dogs (often called “blue”), but had not yet been linked to any of the diluted phenotypes in equines, so it was a logical candidate.

But dun was found in a gene known as TBX3, which was not previously known to be involved in pigmentation at all, and the part of the process was not in the production of pigment but in the placement of pigment cells when hair follicles are formed. That’s back in Step 1. Hairs from the diluted areas of a Dun (D) horse have pigment asymmetrically distributed, so that the sides (viewed in cross-section) are unpigmented. It is that placement of the pigment on the hair shaft that gives the impression of paler hairs. In her dissertation on the topic, the lead author Freya Imsland describes the situation with Dun this way (emphasis is mine):

The precise nature of the reduced pigment intensity in Dun is highly unusual; it can in essence be described as a microscopic spotting pattern, whereby the pigment distribution within each hair is radially asymmetric.

She reiterates this explanation in the abstract for the dissertation:

This results in a microscopic spotting phenotype on the level of the individual hair, giving the impression of pigment dilution.

The timing of the mechanism behind Dun explains why, unlike cream or silver dilutes, dun horses have diluted bodies regardless of their base color. It is the placement of the pigment cells in the hair follicle, and not impaired production of pigment, that make the coat lighter in those areas. And that happens before pigment is made or pigment-type determined. That may also explain why Dun characteristics (like the dorsal stripe) persist even when the color is paired with subsequent dilutions.

The discovery of a new role for an established gene is an important scientific discovery. As people interested in horse color, we tend to think of discoveries like Dun in terms of tests (or more accurate versions of existing tests). But the investigation into Dun is a good reminder that when it comes to the process by which animals acquire their color, there are is still much that is left to discover, and that some of it may be surprising. Another interesting aspect of this discovery is that the idea that dun hairs were different at the microscopic level is not entirely new; this idea was suggested in older books on horses color (Geurts, 1973 and Green, 1974). This also has intriguing implications for the type of color-shifting seen in some of the traditional (large-scale, as opposed to “microscopic”) spotting patterns. But that is all jumping ahead, and a topic for another day!

How we got to here from there


So the original wild horses probably looked a bit like this Fjord, with pigment distribution causing a body color that was visually quite pale while the primitive markings were more intensely pigmented. But the color of the modern domestic horse is more typically pigmented at full intensity across the entire body, like the warmblood to the left. What changed? And why? The other big finding of the recent dun research was that this was a gradual process, and that it began long before—close to 40,000 years before—horses were domesticated. That will be the subject of the next post.

*Although it has been used by some horsemen for specific patterns, “spotted/spotting” is also the generic scientific term for any form of white marking or pattern.

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Translating horses to dogs


Before I return to basic dog colors, here is a short guide for translating horse color and dog color. I have posted about this a few times before, but since there is going to be a lot of new material in the next few posts, I thought a refresher on this might eliminate at least some of the potential for confusion.

Yellow = Red

In horses, we talk about two types of melanin pigment: black and red. The latter type, known as pheomelanin, is sometimes referred to as red, yellow or even orange, depending on the species. In horses, we use red. In mice, which are the most common model for research on pigmentation, it is referred to as yellow. This is also true in dogs. Because pheomelanin in horses ranges into the deeper tones—and perhaps because “yellow” was once used in some regions to mean palomino or buckskin—red is the traditional term. These are just different names for the same thing.

Red ≠ Liver or Chocolate

Which brings us to the other area of potential confusion. When horsemen talk about red, they mean pheomelanic pigment. When some dog people speak of red, what they mean is a dog like the one at the top of this post, otherwise known as liver or chocolate. On this blog, this type of coloration in dogs, which is not thought to occur in horses, is referred to by its traditional name of brown while red is reserved for pheomelanin.

Seal brown ≠ Brown (b)

Brown is the other confusing term, because it means something very different in horses than in almost any other species. In other animals, brown is an alternate form of black (eumelanin). The dog at the top of this post is the brown version of tricolor (black, tan and white). In posts on this blog, brown usually means the seal brown coloring of the sort seen on the tobiano mare below.


To avoid confusion, when speaking of the non-equine brown I follow the term with the genetic notation “(b)”. When speaking about both, I either use the genetic notations (b and At) or the more specific equine term “seal brown”. (Dogs also have a different color called seal brown, but I will leave that for another day!)

Agouti vs. agouti

In horses, as in other mammals, Agouti is a locus (a specific location on a chromosome) that is involved in pigment-type switching. In other animals, agouti is also the name given to a specific coloration that involves black and red banded hairs. Horses do not appear to have banded (agouti) hairs, but dogs do. The general convention used by this blog is that when referring to a specific locus, the name is capitalized and italicized (or underlined when in a block quote). When used to mean a pattern of banded hairs, agouti appears in regular lowercase letters. This will be an important distinction later in this conversation, because in dogs some of the alleles at Extension and Agouti produce patterns that have both agouti and non-agouti areas. So Agouti is the locus where a number of the alleles for basic coloring reside, and agouti is a specific type of coloring involving banded hairs.

I am also going to post a quick comparison of the canine equivalents – from a genetic standpoint – to bay, black and chestnut. With luck using that as a common reference point, this will not be quite as confusing.

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The basic (horse) coat colors

The three basic colors: bay, black and chestnut. Some include seal brown, making it four basic colors.

Since some time has passed since I last posted to the blog, I thought it might be worthwhile to do a quick recap of the basic colors before I ventured back into the more complicated realm of basic colors in dogs. This will also allow me to reframe the discussion of red and black hair in a way that might make the next set of posts a little less confusing.

This series of posts began in response to a common simplification used when explaining horse color, and the misunderstandings that arise from presenting color in this way. That problematic explanation usually goes something like this:

Horses are basically red or black. The genes at Extension determine if the horse is black (“E”) or red (“e”). If a horse is black (“EE” or “Ee”) and ‘has agouti’, then black is modified to bay. If ‘agouti’ is absent, then the horse is just black.

I do understand that the simplicity of this is appealing, but it is not correct. It paints an inaccurate picture of what goes on with color and encourages a number of unnecessary misconceptions. Countering it with an accurate explanation that is still simple is a challenge. The latest series of posts was an attempt to do that, and here is a brief summary. (Note that in these two paragraphs I have boldfaced the distinction between talking about horses and talking about pigments.)

In mammals, there are two types of pigment: red and black. The original coat color of a species, known as the wild color, is typically some combination of both red and black pigment. In horses, the wild color is bay. Cells have the ability to make either of the two pigment types (red or black), and the genes that control them are called “pigment-type switches”.

In horses, like many other mammals, the primary pigment-type switches are Extension and Agouti. The un-mutated (“wild-type”) form of those two genes (“E” and “A”) combine to produce the color we know as bay. The other two basic horse colors, chestnut and black, are the result of mutations to one of those two genes. At Extension, there is a recessive mutation (“e”) that restricts the black pigment to the skin, which means the hair is all-over red. This results in the color we call chestnut. At Agouti, there is a recessive mutation (“a”) that removes all restriction from black pigment, so if the horse can have black hair—that is, if he is not chestnut—he will be all-over black. This is the color we call black. Additionally, it is believed that there may be other variants (alleles) at Agouti that restrict black pigment more or less strongly than either bay (“A”) or black (“a”). These are proposed to be responsible for colors like seal brown and wild bay.

In previous posts in this series I have explained that Extension is the locus that “permits the expression of black pigment” and Agouti is the locus that “determines the location of black pigment, if present.” That is true. All I have done in the paragraph above is turn it around so that the three basic colors are seen, not through what is happening to black pigment, but to what is happening to the normal production of pigment in horses. In this case, that is a mutation (e) that has taken away the ability to make black pigment, and another mutation (a) that has allowed black to express throughout the coat. That is actually what is being identified when you submit a horse for the standard Extension and Agouti tests. The test for Extension is looking for the mutation for chestnut (e) and the test for Agouti is looking for the mutation for black (a). Explaining it in this way makes the tests easier to understand, but it is even more important when we begin to talk about basic dog coloring. That’s because more common black-centric way of explaining the relationship between Extension and Agouti, and the implication that Extension sits at the top of a hierarchy of basic color controls (and that Agouti “modifies” it), does not work as well once you start adding more alleles, or more pigment-type switches.

As the most recent post explained, in dogs (and other animals), the distribution pattern of black and red hair is not solely controlled by the Agouti locus. That is, Agouti is not necessarily “modifying” the outcome at Extension. The Extension locus itself can direct the placement of black pigment, as it does in the Melanistic Mask (EM) allele in dogs. In fact, the relationship between the two loci is even more complex, so that alleles at either (or both) locations can influence the distribution of red and black hair. What’s more, looking at dog color it becomes obvious that a specific “turn on the black” allele is not required in order to have a coat with some portion of black hair. It would be more helpful to think of black hair as being part of the normal coloration that is there unless some mutation occurs that prevents it. For that matter, the same can be said for the presence of red hair. That is because ultimately these variations in basic color are really just mutations to the original wild color—to the original production and distribution of color in the species—which typically has some portion of both colors.

If the construct of “basic color” is understood to be “different distributions of black and red pigment on the animal”, with all-red and all-black simply occupying the extreme ends of that spectrum, and the pigment-type switches as being nothing more than the loci that control the options in that category, that should make some of these dog colors less confusing. That’s important, because after I talk about those, I hope to make a post about the third major pigment-type switch in dogs and what that might tell us about horse color.

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