Appaloosa coloration is controlled by 2 things. First the Leopard Complex gene, or LP is what we call the "on switch". With out at least one copy of this gene the horse will appear solid - regardless of the other genes the horse carries for appaloosa color. The second thing is a gene complex we cal "PATN" or pattern. In other words, there are multiple genes that do almost the same thing, so get grouped together in their purpose. Because we have not yet mapped out these genes specifically, but we know they exist because of studying inheritance (phenotype studies) we can only talk about these genes as a group. So, when we say a horse has PATN, we mean it has at least one of a possible 30someodd genes that cause pattern. One of the pattern genes has been shown to be independantly inherited, and that is the leopard pattern. We call this gene PATN-1, and we know that it is a specific gene on its own, and not a combination of multiple genes working together.
Head hurt a little now? It's ok, I'll explain that as we go!
First, we need to understand what is and what is not pattern. Appaloosas change color over time, most of us who deal with these colors know and love this about them. Here's one example:
Now, compare that to this:
Varnish Roan is caused by the LP gene ONLY. This effect is what classifies LP as a "pattern" gene (like tobiano, roan, frame, splash, etc) and not just a color gene. The LP gene has a few specific functions: it coagulates pigment, and that can be seen in the striped hooves, mottled skin, and it also causes white sclera (human eyes) in LP carrying horses. Most of those traits are a simple result of the pigment coagulation thing it does. If you clump the pigment in the hoof, then it will grow out in stripes, in the skin the clumps result in pink areas of skin showing through, and in the hair it causes white areas to be unpigmented and pigment to fade as the horse ages. Only the white sclera is not a direct effect of coagulation. In actuality, that white sclera is a sign of the gene's main function (formation of eye cells).
Now, Varnishing comes in MANY forms. While only the style of roaning that leaves bars on the face and bony areas is thought of as varnish roan, all LP roaning is the same thing. Here are some different examples of roaning in LP colored horses:
This is your common "varnish" type of roaning. Note the heavy dark areas on the face.
And this mare is actually the oldest of the bunch, but has the least roaning. All of those little white dots technically count as "snowflakes" but you can see that they are a very different style of roaning from the other 2. Again, genetically, it's all the same thing.
Now, the question most people have, is "how do I know what my horse is going to do?" Well, sadly, you really don't know. Oh I can tell you that a horse showing characteristics WILL roan, but I can't tell you what style, nor how drastically. ALL appaloosa colored horses roan. If you check out Rico (the bay blanket colt above) you can see that he does have some roaning progression, but not much at all. It has nothing to do with his pattern though, but rather the same reason why the black mare has so little and such small snowflakes.
It's all about suppression and enhancement.
Chestnuts always roan more then bays. Bays more then blacks. High white horses more then those with no face and leg markings. Now these things we can see (the base colors and markings) but there are other genes that we can't see. One example is in my draft crosses. The same gene that allows a Clydesdale to have high white with minimal roaning and sharp edges also affects Rico's lack of roaning progression. What is it? No idea! But with his high white, he should be roaning more then he is. His full brother Scorch is still almost solid black as a 4 year old, yes has high white markings.
Now, keep in mind that most color genes (maybe all) actually do something more important first. The appaloosa gene controls eye cell formation. This is why homozygous appaloosas are night blind. Frame controls the nerve production of the gut, hence the homozygous form of lethal white results in malformed intestines that fail to function and lead to death. Most of our "unique" colors are in reality a mutation of a "normal" or wild type gene. Now some of those alterations are so minor as to only cause color changes in the hair, such as creme.
But Varnish Roan is just an effect of the LP gene. Why do the bony areas stay dark more then the fleshy areas? Notice on Katy (above) that her cannons, hip, shoulder, and face are still mostly dark. This has to do with temperature and its effect on pigment production. The warmer it is, the better the pigment can spread and show up.
Now, here I'm going to postulate a theory of my own. There is NO science to back this up...yet. I am doing some studies in my own herd though, but it's a long process, and I'm probably too lazy to ever bother publishing it. But, living in Texas, I often has severe winters, and other times I have super mild winters. Scorch was born after a very mild winter. Warm temps all winter long with almost no freezing at all. He also "cooked" for 364 days! All that nice warm time for him in utero resulted in a horse with minimal white pattern showing up. On the flip side, his full brother Rico was born after a disgustingly cold winter. Rico also inherited more pattern genes, but they showed to "full strength" in him. His siblings with the same pattern (all inherited from the same sire who carries 3 obvious pattern levels) had less "wow" in their pattern, but were born after warmer winters.
Compare these foals:
It's my theory then, that while in utero, if the cold temperatures alter the foal's environment by even a fraction of a degree, this might be allowing the base color pigment to flow more across the embryo. If that's the case, then it might be possible that the increased coverage by pigment is something that stays with them for life, thus making those minimal snowflakes and frosty roans. For appaloosa color breeders, this is probably not good news, as we do not want to freeze our horses in order to get loud colors! I only have 4 years in on this study, with a handful of horses to compare to. (Full disclosure:) To get better and more solid scientific facts I will need many more years, so for now, it's nothing more then my personal theory and take it for what you paid for it.
So basically, Varnish Roan is nothing more then an effect of the LP or "on switch" of appaloosa color. The type and amount of changes overtime are not yet understood well enough to be predicted or bred for. With the current leaps in understanding of LP color, we all hope that this will be one of the next things they study. Personally, I love a striking varnish horse. That stallion (first picture) and his face bars is lovely to me, while others find it ugly and distasteful. But that's the beauty of horses! We all have things we like, and it doesn't have to be the same.
As more science comes out about it, you can believe that I will be talking about it here. So lets give the Appaloosa Project a hand. I believe they are still offering color testing at the U of KY as a fund raiser for these studies. Get your horse's color genes tested, AND help support the science that will be creating the DNA tests for all of our crazy appaloosa pattern genes.