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.