Basics and coat colors

Since there was a request (Hi, Dom!), I'm going to work my way through the other horse color genetics, a few at a time.

Caveat here: I learned all of this a few years ago.  If I get energetic, I might go look up some of the newer stuff, but that's going to depend on how curious I get. It's also going to be the as-layman's-terms-as-I-can-get version of horse color genetics; I am by no means a biologist and I honestly check out when you get into things like "these genes share the same locus."  (Which I think means they're on the same piece of the gene?  Maybe?)  So a) bear with me, and b) bear in mind that I could be wrong in the details.

Let's tackle the basics first.  Every gene we talk about will have an off state and one or more on states.  Every horse has two copies of the gene, one that came from mom and one that came from dad.  And every horse has... well, pretty much all of the genes they've discovered; what's turned on and what's turned off is what determines what color they are.  All the genes together kind of build a chain of information, and if you know how to read the genetic results, you can generally guess what color the horse is without seeing it.

Some genes are dominant.  That means that if one copy is turned on, you see the effects.

Some genes are incompletely dominant.  That means that if one copy is turned on, you see the effects... but if both copies of the gene are turned on, you see a different effect.  (LP is a good example of this.)

Some genes are recessive.  That means to see any effect, you have to have both of them.  I actually don't know that they've spotted any of the color genes that are recessive for sure?  Most of them seem to be dominant or incompletely dominant.  That said - there are genetic diseases that affect horses (HERDA, I'm looking at you) that are recessive, so it's good to know what it does.

When you write down the genetics, you write them in pairs.  So, for instance, Ee means a certain color.  Generally, uppercase means the gene is turned on; lowercase means it's turned off.  And a question mark, which you'd see as E? or e?, means that half the genetic pair is known, but the other half either is unknown or - as will be the case when I use it as I'm explaining - unimportant.

And now... because we have to start somewhere, let's start with chestnut!

From a local show

Chestnut happens when a gene called extension is turned off and nothing else that would affect the red coat is turned on.  (Some genes affect chestnuts only, some affect black-based horses only, and some affect both - so as long as those are off, you've got chestnut.)

Now, if extension is turned on - one or both copies, as it's a dominant gene - you get black.

Gorgeous Morgan at the same local show

Again, as with chestnut, this assumes that nothing else is turned on that would affect the color.  Interesting side note: there was some discussion about whether there were two types of black - either separate genes or Ee vs EE - one of which fades in the sun and one of which doesn't.  I'm not sure where that debate stands at this point, but it is an interesting point that some black horses fade and some don't.

So what affects the color?  Agouti, grey, cream, pearl, silver, dun, and champagne.  With the exception of agouti and grey, they're generally referred to as dilute genes, and considering how freaking long this post is getting, I'll save the dilutes for another day.

Agouti is kind of special.  Why?  It's what gives us bays and browns, the third "basic horse color" everybody learns.

Who, me?

To get a bay horse, you have to have extension turned on and agouti turned on.  So the horse has to be E?A?.  Now, they could be EEAA; they could be EeAa.  They could be some combination of the two.

Brown is... brown depends on who you listen to.  Some people say brown happens when you've got a horse who is E?AA.  Some people say that brown is actually a different version of bay, generally notated as At - and there was a test for that for a while, but it seems to be unavailable these days.  Some people say that brown is actually bay plus some darkening genes (generally referred to as sooty) and a gene that lightens the muzzle and flanks (generally referred to as pangare). 

Theory at the time I was really researching all of this leaned towards the At gene for brown.  It furthermore suggested that there was an additional gene in there called A+ that produced wild bay (a bay where the black only goes up to the pasterns or so).  I haven't seen any recent, reliable research on the subject, though.

And last but not least for today is grey.  (Or gray, if you prefer that spelling.)  Grey is special because grey ruins everything.

One of the BO's mares, sadly deceased.

Well, okay, it doesn't actually ruin anything except color.  :)

Grey basically takes whatever else you've got going on, color-wise, and just... hides it.  And it's dominant - one copy turned on means you've got a grey horse.  There's some theory back and forth about whether two copies mean you grey faster or not, and there's some fascinating discussion among breeders about whether you can tell if a foal will turn grey before their coats start to turn (answer: sometimes, there are certain characteristics that tend to point that way - but not always)... but in the end?  Grey is grey, and it only really matters what's underneath if you're breeding.

Now, I say grey ruins everything... that's not entirely true.  Grey on a horse with LPlp and a PATN gene does something funky.

Like this mare.  Born so dark a brown she was thought to be black, greyed out to this.

The color basically concentrates in the spots, which either don't ever go grey or go grey so slowly that it's hardly noticeable.  The rest of the horse greys out just like any other horse would.  If you google the Friesian/App cross Mystic Warrior, he's another great example of this.  I'm not sure what would happen if you've got LPLP and grey, but I'm going to go out on a limb here and say you'd have a white horse!