In the last post, I talked about how the varnish roan gene sets the stage for the louder appaloosa patterns, which means that no matter what else an appaloosa may be, they are also a varnish roan. That means that this guy here, while a chestnut blanket appaloosa, is also a varnish roan.

Modifying the Modifier

This is what has made the current theory about appaloosa patterning so different from those in the past. The new theory states that if leopard
complex (varnish roan) modifies the base color, then there are yet another set of genes that then modify the leopard complex gene. These modifiers are collectively called pattern genes, and are given the abbreviation “PATN” followed by a number.

The first of these has been labeled PATN1. This is the gene responsible for the actual leopard pattern. That is, an otherwise white horse that is covered “nose to toes” with distinct dark spots. This is the pattern most past studies have focused on, and it has been central in the work done by the Appaloosa Project. It is believed, however, to be just one of the patterns that interact with the leopard complex gene.

In fact, what has been most interesting about the current research is just how many genes do interact with leopard complex. Researchers expected to find genes for the leopard and blanket patterns. What many did not expect was that many more genes are involved. The picture is actually much more complex. Not only are there major pattern genes like leopard and blanket, but there are probably other genes that alter the final pattern in more subtle ways. It even looks like some genes that add white patterning (like sabino) can function as pattern genes for leopard complex. As Christine mentioned in the comments section of the last post, there is a lot of variation in the appaloosa patterns. All those different modifiers working together is part of the reason that is so.

Why the Varnish Base Pattern Matters

The important thing to remember, though, is that appaloosas are all varnishes. Without a pattern, leopard complex is varnish roan. If the horse also inherits a pattern – say, Pattern 2 (PATN2) – he will be a blanket appaloosa. Genetically he’s still a varnish roan, but the pattern gene he inherited transformed the varnish pattern into a blanket.

And because he is really a varnish, he’ll have the traits that go with that. Just as a bay horse that has begun to turn grey can still show signs of his base coloring, so patterned appaloosas still show signs of their base pattern. They have the striped hooves, visible sclera and the mottled skin. The degree might vary, but they will be there. And where his pattern that leaves large areas of body color, those will eventually lighten just like the body of a unpatterned varnish roan. In a close-up of Comanche, the horse pictured above, the original blanket pattern is still quite visible even though the formerly bay areas of his body have roaned out with age.

This does vary, just as the rate of roaning varies on regular varnish roans. Blanket patterns like the one at the top of this post can be accurately thought of as a temporary phase in the pattern. Most will fade with age, leaving the horse looking like a varnish roan with a blanket.

The varnish pattern does not cause the whole horse to fade, though. The spots on a pattern do not roan out. That is actually the easiest way to determine that grey is present in appaloosas; if the actual spots are fading, then the horse is probably has the grey gene.

That is one of the reasons that true nose-to-toes leopards have always been so popular with breeders. Because their pattern is made up almost completely of spots, they retain their contrast even as they age. Breeders have selected for horses that keep their color longer because contrast is what makes appaloosa patterns attractive. Roaning, like greying, tends to take that away.

It is also true that looking at show pictures is a little misleading because many show horses are young enough that the roaning has either not yet started or has not progressed far. The average group of young halter horses is going to look darker and more contrasted than the average group of aged broodmares, for instance. For artists collecting appaloosa references, though, the first group is what we are more likely to encounter. This also means that artists have to keep in mind age when using references, because varnish roan (and any pattern that shows its effects) is another progressive pattern – just like dapple or fleabitten grey. What is realistic for one age group might not be for another.

There is another important aspect to the leopard complex gene, aside from the characteristics and the fading. That will be the subject of the next post.