This post first appeared on August 29, 2011
The conversation over the last few days regarding pintaloosas reminded me that it might be helpful to talk about epistasis.

Most people are familiar with the idea of dominance. Dominance describes the relationship between versions (alleles) of the same gene. The gene responsible for greying (G), for instance, is dominant to the one for not greying (g). Dominance is often misunderstood to mean prevalent, as in “the dominant color in Morgans is chestnut.” In those cases it is probably a lot less confusing to say a color is predominant in a breed, rather than dominant. All the chestnut Morgans in the world cannot make chestnut a dominant gene!

The term dominance is also misused to describe how genes interact with unrelated genes. Grey is again a good example, because it is probably the most common gene spoken of in this way. It is not unusual to hear “grey is dominant to all the other colors.” It is not; grey is only dominant to not-grey. The relationship grey has to the other colors is what is known as epistasis.

Epistasis describes the situation where the actions of one gene hide the actions of another unrelated gene. Grey is not dominant to the other colors, but it is epistatic. It eventually hides the colors and patterns the horse has. Chestnut is the very bottom in terms of dominance, because it is recessive to the black-based colors. But it is also epistatic, because the gene that controls where the black goes (ie., whether the horse is bay or black) cannot be seen on a chestnut horse. There is no black to show which version a chestnut horse has, so those instructions are hidden. They are, however, still there. That’s why the right chestnut horse, bred to a black horse (recessive to bay), can produce a bay foal. It was carrying the dominant bay gene, hidden by the actions of its recessive red gene.

The mare pictured above is another example of how epistasis can work. She is the chestnut Morgan, Amanda’s Suzie Q. She was one of the earliest identified silver carriers in Morgans. The color doesn’t show on her because silver dilutes black pigment. Since Suzie doesn’t have black pigment, the effects of the silver gene cannot be seen. Silver is a dominant gene, but it just doesn’t have anything to work with on Suzie. It was visible on her bay foals, though, which is how she came to be identified. (Suzie was also instrumental in disproving the idea that silver at least lightened the manes and tails of a chestnut, since she has a self-colored mane and tail.)

A very similar situation exists with the cream dilution. Just as silver only dilutes black pigment, cream only dilutes red pigment. Here the epistatic color is black, because there is no red pigment to dilute. This horse is a black Foxtrotter named Quick Trigger. He carries the cream gene hidden by his black coat. Cream is not hidden because it is recessive, but because the genes that made Trigger black set up a situation where the cream could not be seen.

Or perhaps a better statement would be “could not easily be seen”. In many cases epistatic relationships, while they hide the actions of a gene, don’t necessarily make it impossible to see the effects. Sometimes they just make it pretty difficult, or difficult to be sure. Some blacks with the cream gene look more faded than those without it, for instance. Unfortunately for people wanting to identify them visually, though, quite a few blacks without cream fade pretty badly.

That is what was happening with the pintaloosas and the grey appaloosas. Generally the more white the horse has, the harder the individual patterns are to identify. We can guess, based on what is found in a given breed, and what traits are most typical of this or that pattern, but without tests it can be hard to be sure.

Here are some shots of the horse used in the post to illustrate the difference between cremello and truly white skin.

Those were his colored areas, while the rest of him was white. (I was never in a position to get a good shot of his whole body, unfortunately.) He was also a rescue horse, so nothing much was known of his background.

You could overlay a typical tobiano pattern on a horse like this and not see it. Does that mean he is a tobiano? Not necessarily, since you can layer mutiple overo patterns and get that much white. There isn’t any way to know without testing. Whenever people breed a lot of different color genes together, things tend to get muddied like this. It often makes for very cool looking horses, like the ones in the last few posts, but it sure can make it hard to be sure what genes they carry.