Where the wild things are

NotTob

In response to the previous post about the Agouti locus, a reader questioned the importance of the fact that bay was the original color of wild horses—that it “came first”, before black or chestnut. Why should that matter?

This question touches on the reason why I have come believe that the way color gets explained matters so much. I have mentioned in previous posts that equine coat color has become far more complex since I first began writing about it. (At the risk of revealing my age, that was around 1990.) There was a time when everything could be explained in terms of the colors themselves, while the technical aspects of genetics could be skipped or at least minimized. In hindsight, while some of these explanations made certain concepts easier to grasp, they could also be misleading. Let me give an example of a common misunderstanding from fifteen years ago, the explanation that was used to clarify the situation, and how that same concept—so useful then!—is somewhat problematic now.

At the time in question, the concept of dominance was difficult for a lot of people. It was not uncommon to get questions like, “Which is more dominant, grey or bay?” Or, “I know bay is dominant to chestnut, so shouldn’t palomino be recessive to bay?” These questions arose because it was not clear that a color could not be dominant or recessive to an unrelated color. My approach was to point out that colors could only have this kind of relationship with their opposites. Tobiano, for example, could not be dominant or recessive to buckskin; tobiano could only be dominant or recessive to “not-tobiano”. The opposite of a color was not a different color, but the absence of the color. This was a very clear way to get the idea across that the genes for different colors were separate things, and that each presented an independent chance for inheritance.

BuckTobi
Fifteen years ago, many did not understand that each aspect of this horse’s color—bay, cream and tobiano—involved a separate, unrelated gene.

It was a simple explanation, but behind it lurked some puzzling questions for anyone who cared to look a little closer. If tobiano was dominant to “not-tobiano”, what exactly was this “not-tobiano”? If tobiano was believed to have arisen after domestication, how on earth were those wild ancestors carrying around a gene for the absence of something that did not yet exist? The idea of “not-tobiano” worked when it came to predicting breeding outcomes, but looked at in this light it made no sense.

That is why something like the situation with bay as an ancestral color matters, because the key to understanding what is really going on with “not-tobiano” can be found there. As I mentioned in the previous post, bay (or bay dun) is the most likely ancestral, or wild, color for horses. The other two basic colors, chestnut and black, were later mutations to the two genes responsible for bay. Another word for those alleles that were already there is wild-type. The wild-type is the allele that is typical for a given population. Wild-type is the “normal” setting—the default—for a gene. “Not-tobiano” and all those other “not-colors” were really just that: the wild-type for their particular gene. In the case of things like dilutions and white patterns, the wild-type is usually just the instructions for normal pigmentation.

Shifting from a color-based approach to a gene-based approach

Looking at colors in terms of the wild-type eliminates the misunderstandings that come from thinking of the color itself as a gene. Because we often refer to colors this way—as the “tobiano gene” or the “cream gene”—it is easy to get the idea that something like the cream dilution is an additional gene that palomino, buckskins, and smoky creams have; one which non-diluted horses do not have. The cream dilution is actually a mutation that occurred to a gene, known as MATP, that all horses have. In the absence of the cream dilution, MATP is involved in the normal formation of pigment. So the wild-type for that gene gives a fully-pigmented horse.

Not knowing there is a wild-type makes it seem that the color (Cream) is the gene itself and therefor the starting point. That is why there is a tendency to assume later discoveries are “mutations of the color” rather than alleles for the same (non-mutated, wild-type) gene. So pearl, which is found in the same genetic location as cream, becomes a “mutation of cream” rather than a second, unrelated mutation of the MATP gene. But the starting point is not cream, but the wild-type at MATP. The cream mutation did not have to be present for pearl to occur; it is a mutation like cream, not necessarily a mutation to cream.

But perhaps more importantly, many colors were named before their relationships to other colors were understood. Things that once were assumed to be separate later proved to be alleles of the same gene. At one time we thought, and taught, that the opposite of tobiano was the absence of tobiano. But the “tobiano gene” is not a separate gene. Tobiano is a mutation to the KIT gene, which again is a gene that all horses have regardless of their color. Tobiano shares the KIT gene with a host of other alleles (like Sabino1, Roan and the White Spotting patterns) that have historically been thought of as unrelated. That complex situation is very difficult to explain, especially if someone’s basic understanding of the subject is color-based rather than gene-based, because the relationship between that group of colors is not visually obvious.

Unicorn
Tobiano and roan are both alleles of the KIT gene, which is why the combination does not breed true. The offspring can only get one or the other from the parent.

I know for many who have learned about horse color exclusively in terms of basic colors and their modifiers, focusing on the actual genes is a very different approach. It may seem like it adds a lot of unnecessary complexity to the subject. I certainly can appreciate that point of view, but genes and the importance of using their wild-type as a starting point is the missing piece of the puzzle for a lot of people. When that piece falls into place, color genetics—especially as it is currently understood—begins to make a lot more sense.

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8 Responses to Where the wild things are

  1. Alexandra Dees September 25, 2014 at 2:26 pm #

    Well stated explanation , thank you. If Dun was part of the wild color package – where has it gone? It is not common in most breeds now. Is it a more fragile gene that has fractured in to all the ” dun like” marks we see that don’t show an associated dilution?

    • equinetapestry September 26, 2014 at 7:02 pm #

      I think the relative rarity of dun in the modern population is really puzzling, and it is one reason I would love to see the new test used on those same ancient samples. Of course dilutions were often purged from the earliest stud books, particularly in Europe, but even so I have always thought the distribution seemed odd for something that was once pervasive. So, yes, I have wondered if the “dun” of the ancestral horse was the same mutation as the modern version.

      • Caitlin September 29, 2014 at 5:41 pm #

        I think we can thank our love of novelty and shininess for that.

      • Elaine September 29, 2014 at 8:02 pm #

        It could be as simple as association with the lower classes/unrefined “peasant stock.”

  2. Elaine September 25, 2014 at 4:26 pm #

    Wait! So I didn’t realize that roan and tobiano were at the same locus. Does that mean that your roan tobiano there is heterozygous, that if you have a copy of each they can both be expressed?

    • equinetapestry September 25, 2014 at 7:48 pm #

      Yes, she would be expected to be heterozygous for tobiano, and heterozygous for roan. She can have a copy of each, since animals have one from each parent. Theoretically, she could only give one of those – either tobiano or roan – to each of her offspring.

  3. Caitlin September 25, 2014 at 5:19 pm #

    Thanks for another coherent, concise piece. I appreciate that you break topics down into these little bite-sized chunks. One thing that I especially like about this discussion is that we get a window into the relationship between early domesticated horses and their owners. I can imagine an early horse-culture, in which all the horses were bay dun, how eye-catching the first red dun, grullo, or non-dun horse would have been. There would have been a period in which most peoples horses were these faded, natural beige tones, but every once in a while, a super-glossy, technicolor bay would have been born. It would’ve been especially striking in a world which was much more green, brown, and gray than our current world.

  4. Kay October 22, 2014 at 12:32 am #

    The roan pictured seems to have some roaning on its face and mane, does that mean that it isn’t classic dark headed roan? I’ve heard of several different roans and I am wondering if they are all KIT alleles or if only a certain one is. With the exception of Varnish roan of course, we all know were that goes.