Archive | September, 2014

Why Extension?


A friend of mine pointed out that one of the reasons the term “black-based” is so popular is that the name of the gene is not particularly illuminating. She had a good point. Just why is it called Extension?

The other pigment-type switch in horses, Agouti, is a little more obvious. That locus takes its name from a South American rodent that is a close relative of the Guinea Pig. Because his early studies of coat color used Guinea Pigs, W. E. Castle gave the name to the color typical of wild rodents and to the factor he believed controlled the banding pattern that characterized it. It was usually called “A” or the “A Factor”. (The term “gene” had not yet been coined.) The piggies in the top image are examples of the agouti color.

Early in the course of these studies, it became clear that some other factor was responsible for the color in the lower picture, which is a self-colored red. The scientists noted that, unlike the albino Guinea Pigs, the red ones had black pigment in the skin and the eyes, but it was no longer present in the coat. Black pigment was Restricted to the skin, whereas in the agoutis, it Extended into the coat. You can still find the term Restricted (R) in some older writings on the subject, but the convention became that the “factor” (gene) took its name from the dominant (not the recessive) form. Extended was dominant to Restricted, so the factor (gene) became Extension.

So Extension was about whether black could extend from the skin into the coat. It never really was thought of as a “red or black” option so much as an “enabling black” option. Recessive reds (ee) were animals where black in the hair was not enabled, while those with the dominant allele (E) could have black pigment in the coat.

This is quite different from the way Extension tends to be seen in horses, which is as the choice between red and black. That explanation will work because horses haveat least at this pointonly two options at Extension. That was not the case with the Guinea Pigs, and it is not the case with other species, some of which not only have other options at Extension, but more than just the two pigment-type switches. In the next few posts, I am going to veer off into some of those other pigment-type controls, so if you found the last few posts confusing, you might want to skip reading for a few days. But for those that have found the topic of pigment-type switching helpful, this will probably clarify why these are really a group of genes that all work together to give the final color. I’ll also try to tie this back to horses, and why I believe it is a good idea to lay this foundation now.

See the little guy to the right, with patches of red and agouti? He is a sneak preview for the next few posts, which will explore some of the alleles for Extension in other species, as well as other pigment-type switches.

And finally I want to thank everyone for the feedback they have given on these last few posts. I used to believe that the ideas behind horse color, if presented in just the right way, could give an immediate “aha!” response. That was how I judged whether or not an explanation was successful. As this subject has become increasingly complex in light of new discoveries, I have had to (quite reluctantly!) scale back my expectations and count it a success if an idea was clear to someone after a couple of readings. I really do appreciate the faith readers have that if they read a post a few times, I will eventually make sense. At a time when all of us are so very busy, the willingness to spend that kind of time on anyone’s written words is a profound compliment. I really will try not to make things any more confusing than necessary!

I will close with a quote from one of the earliest books about coat color inheritance. As far back as 1909, people looking at animal coloration noticed that any color was easier to understand than the original wild color of a species!

[the original coat] pigmentation, common to wild rabbits, is complex in its nature, and all other color varieties are relatively simpler. The [wild color] coat results from the joint action of several independent color factors; all other types of types of pigmentation result from a weakening or entire loss of one or other of the factors concerned in producing the [wild color]. — Studies of Inheritance in Rabbits, W. E. Castle

(Photo of the agouti Guinea Pigs by Tim Strater and courtesy of Wikimedia Commons, photo of the red Guinea Pig courtesy of Love-To-Share Stock Photography, photo of the agouti/red Guinea Pig by Carlosar and courtesy of Wikimedia Commons)

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Where the wild things are


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.

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.

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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Bay is not a modifier


When talking about a topic as complex as equine coat color, simplifying concepts is essential. This is particularly true when speaking to a non-technical audience. The trick is to avoid more detail than is necessary without reducing the topic to the point where the information is misleading or inaccurate. Ideally any simplified explanation is compatible with a more nuanced understanding, since it needs to provide a solid foundation for those listeners who want a more in-depth understanding of the subject.

One of the common conventions used to explain horse color is that of basic colors and modifiers. By structuring the explanation this way, it is easier to make sense of the wide variety of colors and patterns. When each color is understood to have three (or four) versions—chestnut, bay/brown, and black—it is easier to see the relationships between colors that are not visually similar. The other advantage to this system is that, because the basic colors are a given, you get to skip (or at least gloss over) the mechanics of basic coloration in horses. That is useful because the basic colors require a more complicated explanation than most of the dilutions and white patterns.

In an attempt to simplify basic colors, one approach that has become increasingly common in internet discussions is to move bay into the “modifier” category, and assert that horses are basically red and black. Bay, by this convention, becomes a modifier of black. In the “absence of agouti”, the explanation goes, a horse is black. This approach is problematic on a number of levels, not the least of which is that it obscures the fact that “agouti” (as it is used in horses) is a genetic locus. It is a place in the genetic code, and not the name of a specific color. (The term is used for specific colors in other species.) There is no “absence”, because all horses have Agouti (ASIP). Some of them have the allele at Agouti for bay (A).

A study of ancient remains showed that bay was the original color of horses. At the time it was not possible to test for dun, but based on the pervasiveness of dun in wild equids—like this Przewalski’s Horse—it is assumed that they were likely bay dun.

It also takes a concept that is really about pigment, and applies it to the horse. Pigment in mammals is understood to be basically red (or yellow) and black. At the animal level, though, animals are understood to have a wild color that is typically some combination of those two pigments. In horses, that wild color is not red (chestnut) or black, but bay. Bay—or more likely bay dun—was the original color for the species. Animals that are all-red, or all-black, are usually the result of mutations to (modifications of) the species’ original color. Presenting bay, the wild color for horses, as a modification of black gets this backwards. Black is not the default color, but a mutation to the Agouti (ASIP) locus that could have occurred as early as 5200 BCE. Samples from 9210 BCE and earlier were uniformly bay.

It requires more explanation than the “all horses are red or black” approach, but the basic colors are governed by a category of genes that control pigment-type switching. That is because pigment cells have the ability to produce both types of pigment (red or black), and these genes are what control the switch between the two possibilities. One of the clearest explanations of pigment-type switching can be found in The Colors of Mice: A Model Genetic Network:

Pigment-type switching describes the ability of pigment cells to switch between the production of eumelanin [black] and pheomelanin [red], under the control of the Agouti and Extension loci and modifying genes.

In horses, Extension is sometimes called “the black gene” because its dominant allele (E) is responsible for the colors often referred to as “black-based” (bay, brown and black). That term is somewhat misleading, however, because it does not mean the horses with that allele are “basically black”, but rather than the resulting colors have some portion of black in the coat. It is a category based on the presence of black, not on modification from an all-over black color. Despite its popular name, the dominant form of Extension (E) does not just produce black pigment, but rather black and red pigment. (Remember that pigment cells already have the ability to produce either type.)

For those horses that can have both red and black pigment (E), the alleles at Agouti control which parts of the horse will be black. Agouti does not “add red” or “dilute black to red”, which are the two common assumptions made when Extension is presented as giving either a black (E) or a red (e) horse. There is a recessive mutation to Agouti (a) that distributes black over the entire horse, effectively eliminating the red pigment, but Extension itself does not limit cells to producing only black pigment.

I understand the appeal of simplifying the situation with black and red pigment, but I do think that the distinction between basic pigment colors and basic horse colors is an important one. Because there are some unknowns in this area of color genetics, and because there have been surprises in other species, it is probably helpful to lay the foundation for pigment-type switches as a general category. That means being clear about the situation with Extension and Agouti, even if it takes a little more effort to explain.

This variant of bay, known as wild bay, involves a reduction of black pigment at the points, particularly the legs. It is presently assumed to be an allele at Agouti, but that has not yet been proven.

Note: I would like to talk about some of the pigment-type switching “surprises”, because there have been some fun discoveries in that area in recent years, but that will require wandering a little further afield so I’ll save that for a future post.

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