Agouti was first found in mice, and resulted in a color pattern called... are you ready for this.... Agouti! You know the typical field mouse brownish-greyish color? Yeah, that's called agouti, and this gene causes it.
Now, in horses, it doesn't something a little bit different! Agouti is a modifying color gene, that is only seen on black based horses. A red based horse can carry a dominant form (either Aa or AA) and you'd never be able to tell. Baffling right?
Until you realize what this gene DOES. Agouti simply tells the color producing cells to push all black pigment out to the edges. If you look at your typical bay horse, such as Cayenne here:
you can see that she has black legs, black mane and tail, and on her head...........
These are what agouti does to the black pigment. It pushes it to the developing edge of the horses while the horse is forming in utero. You can also see how Cayenne is sun faded, and her tail hair is no longer "pure" black, but instead it is very nicely highlighted. I won't go off on how much I wish I could get MY hair to have highlights like that.
Cayenne is an example of a "typical" bay horse. This is not the ONLY type of bay horse though. Agouti has more then just 2 alleles. When we talked about Extension, I only mentioned the dominant and the recessive form. Well, Agouti has another form. It's the "seal bay gene", like as seen on Dee:
At (Seal bay, Often written simply as At) and a (recessive form, no change). It's common to see the seal bay allele written as At simply because it's such a hassle to get that little superscript up there.
Now, A is dominant to At which is dominant to a. Brain hurt yet? All this means is that AAt will be a red bay, while Ata will be a seal bay. Aa is also red bay, and aa is "no bay" or does not cause the pigment pushing effect.
Even on the seal bay horses, you can see how the pigment is thinned out from black, to a dark brown, and there are tan or red areas in the armpits, on the rump, and around the muzzle and eyes. Kiva shows this well in her winter coat:
When you combine the Extension gene, and the agouti gene, you end up with the horse's base color. So, a black horse would be E? aa (where ? means the second allele is unknown or not important). A bay horse would be E? A?, while a seal bay horse would be E? At?. And a chestnut/sorrel horse would be ee ?? (Question marks used because agouti does not affect red based horses).
Now, that leads me to agouti being able to act as a hidden gene. In order for agouti to show up, it must have black pigment to push around. With out that black pigment, it does nothing. That doesn't mean that the horse doesn't have a dominant copy of the gene, it's more like a slow day at the office. If your boss says "bring me any papers you get" and you don't get any papers... then you do nothing! Agouti is lazy like that too.
Because it doesn't affect the red, there is no "phenotypical change" on a red based horse. In normal people speak, that means you can't look at a red based horse and SEE if the horse has agouti or not. The only way to know for sure is either through progeny (not recommended in this economy) or DNA testing.
Now, the normal DNA test for agouti simply looks for "recessive" and "not recessive". It won't tell you if your horse has A or At. Here's how it works. If you've ever seen a crime show, where they show an image of little lines for DNA, well, that's pretty darned acurate. See, DNA is heavy, and the heavier it is, the harder it is to move through a gel, or similar substance. Because of this, the recessive form has one weight, while the other forms have different weights. A standard marker is used for the recessive form. Because horses only have 2 alleles, there will be either one or two lines on the test. If there's one line, it means that the horse is homozygous (i.e. both lines moved the same amount, so only one can be seen). If there are 2 lines, then the horse is heterozygous. If one of those lines is in the same place as the recessive marker, then the horse has the recessive form "a". These tests are highly controlled so the alleles always move at the same rate, and for the same distance.
Now, I'm trying to keep this simple, or as simple as possible, so forgive me if I over generalize a few things on the testing procedures.
Anyone who knows anything, when talking about the genome (those ugly strings of letters) for their horse will always mention Extension and Agouti. These genes make up the basic coat colors, black, chetnut/sorrel, and bay(s). From here, it's all about adding modifiers. Genes such as creme, grey, dun, or pattern genes such as roan, appaloosa, or pinto genes, all just add on top of this.
For tommorrow, the difference between Dun and Creme.
A Note about Sugarbush Draft Horses
I see it over and over again, and no matter how many times it's said, it's still wrong. "Sugarbush Drafts are just an Appaloosa Draft Cross". Uh.... no. The Sugarbush Draft Horse was a breed created many years ago in Ohio. While the initial cross was made using Percherons to Appaloosas, in the many generations following, the breed has been solidified into a consistent type. Saying these horses are "just" a draft cross makes as much sense as saying that AQHA horses are "just" a Thoroughbred cross, American Cream Drafts are "just" a dilute Belgian, or that Morgans are "just" a grade.