Now, lets talk about a few color modifiers!
Now, these traits are not "genes". A gene is a sequence of DNA that produces a protein, and that protein has an effect. Head hurt now? Let me make that easier. A "gene" is a single thing that does a single job. Extension is a GENE. It makes black pigment, or when homozygous recessive, it has no effect (red pigment is always produced). A "trait" is a larger concept, and refers to the phenotype (appearance) of the horse. The black TRAIT is caused by a single gene, where the shade of a horse's color is a trait caused by a bunch of genes working together. While both are traits, not both are genes.
An analogy to help make the concept clear: A car is an vehicle, but not all vehicles are cars - some are trucks, some are motorcycles.
So, coat color modifiers come in groups. In most cases we don't have the genetics mapped out yet, but we can follow their phenotypical expressions (horses that look like this, and how they pass it to their offspring).
The first, is Sooty. Sooty is most likely caused by a handful of genes working together. Because of this, we don't have a definitive letter to use to describe it, although some people use "STY" when talking about this group.
Also, the thing to keep in mind, is when you talk about a group of genes that result in a specific trait (a polygenic trait is the technical term) is that there will be variations of expression. With most genes there are 2, or maybe 3 options. The horse is black based, or its not (2 phenotypes as found with simple dominant genes). The horse is chestnut, palomino, or cremello (3 phenotypes as found with incompletely dominant genes). With these polygenic traits, there is a whole range of options.
A horse can be a little sooty, mostly sooty, very sooty, or somewhere in between. So, with that in mind, you have to accept that the level of expression of these traits varies because of genes we haven't located yet, and discussing this is beyond the realm of currently known science! Exciting isn't it?
Ok, I'm a dork. It's true.
So, sooty makes dark counter shading on horses. This would be areas of dark pigment in the body color that starts at the top (spine) and progresses down the horse's side (usually). Here is a good example
In other cases, it starts at the legs, and works its way up, like in this mustang shown below.
Sooty is important, because what ever causes it, in some cases it alters a horse's color drastically, making it appear to have a different genome then it does. Here is a picture of my sooty mare, Hex:
Now, the next coat modifier is Pangare. This trait lightens the under belly, armpits, rump and muzzle of a horse. This horse is a great and extreme example of pangare.
And, all those quarter horse people out there, please forgive me. With most stock horse breeds, it is commonly accepted that sorrel is a light version of chestnut. In draft breeds it is accepted that sorrel is chestnut with pangare, like the horse above. You can have many shades of "sorrel" such as honey sorrel, or blonde sorrel, but with out the light markings, a horse is just a chestnut. When I refer to a sorrel horse, I am most often referring to a horse with pangare.
Through out most of the genes we have discussed, I have references shade quite a bit. Shade affects any horse's color. From dark blacks to light blacks....
Such as Jinx, my homozygous black mare, shown sun faded and in her "dark" state above. She's never a true dark black, but she's still genetically EEaa. Jinx is a perfect example of a "pale black" horse. Her shade is light, but her color is black. All colors are affected by shade, and sometimes we give names to the various shades of the same color.
There are many other traits besides sooty, pangare, and shade. Most have not yet been studied. DNA maping is still a relatively new science, and while progress is being made in leaps and bounds, there is still so much more to do. These coat color modifiers are often the cause for people's confusion on their own horse's color. Just imagine how the owners of the above palominos felt trying to explain their horse's color to people! The genetics I have talked about in the last few days are the basis of a horse's base coat color, in all their magnificence. When you mix and match the genetic options, you can have so many different outcomes.
Now, there's still more! Base color is one thing, but what so many people love, are the patterns. From pinto genes to appaloosa genes, with some other white pattern genes thrown in to make it interesting, I'll start covering pattern type genes. How they work, what they look like, and how they are inherited. I'll be honest, the pinto genes (Tobaino, OLWS, and the sabinos) are not my strong point, so feel free to correct me on those, and share links to good information in the comments.