Horse Color Genetics: KIT Genes and Why KIT Matters

As I've researched genetics, I have heard several references to KIT* genes being in the same locus. I had no idea what that meant, and not really any wish to because I didn't know how it applied to what I already knew. The scenario was similar to when I first started genetics and not understanding homozygous and heterozygous: there was no good basic explanation anywhere.

Until, on the genetics forum, someone referred to KIT genes as sharing bunkbeds. And then my mind clicked, and I understood. Now I can pass this brilliant example on to you, and how it applies.

Roan, tobiano, sabino, and dominant white (which I haven't talked much about because the topic confuses me greatly; it's confusing because there are 20 different mutations) are all labeled as KIT genes. KIT genes share the same locus. Locus meaning where the genes are located.

What in the world does this mean, and why is that important?

To use the bunkbed example, each locus is it's own bunkbed. Extension, agouti, gray, dun, etc. are all their own bunkbeds. Each bunk has either one gene that is dominant or recessive. Now, to apply this, the bunkbed for KIT genes can only have carry, well, two. Generally, bunkbeds are for only two people. That means that one horse can only have up to two KIT genes; three is impossible. The reason being that, if a third one tried to sleep in the top bunk, someone's gonna get shoved off the bunkbed.

I have read a little about a couple horses that somehow inherited three KIT genes. Technically, tobiano isn't exactly a KIT gene precisely, but it is so closely linked with KIT that it works in just about the same way. So the horses with three KIT genes are probably homozygous for tobiano and heterozygous for one of the other genes. I read that there are some general health problems with horses with three KIT genes. Sort of like someone trying to squeeze a third person on the bunk; it can work, in a pinch, but usually it causes problems.

Generally, when showing a color genome sequence, the KIT genes are abbreviated the same way as all the others. Sort of like this: Ee, aa, RNrn, Tt. But it almost would make more sense to combine the KIT genes in the same area. More like this (same example): Ee, aa, RnT. See how I combined the roan and tobiano? Since they are in the same locus, it sort of makes sense. Alas, others don't share my feelings.


How this affects breeding is that the parent in question can only pass on one of those KIT genes. So with the horse above (Ee, aa, RNrn, Tt), it can only pass on roan OR tobiano. But it will pass on at least one.
That is one of the reasons roan with tobiano is rather rare. Tobiano with sabino is more common because generally paint breeders breed paint to paint, if that makes sense, and a lot of paints carry sabino.

Another interesting fact about KIT is that Extension (black/red) is closely linked to KIT. Why this matters is that each individual extension allelle is linked to one of the KIT genes. In the example, the horse is blue roan tobiano, Ee, aa, RNrn, Tt. Those two kit genes are each linked to one of the extension genes. Like, the dominant extension linked to the roan and the recessive to the tobiano, or vice versa. All this meaning that, should you choose to breed, those genes will stay linked together. The resulting foal, if the genes were like my example, would be either blue roan or red tobiano, but couldn't be red roan. See what I'm saying? It is simply a matter of determining which gene is linked to which. If there was one other previous foal, then you could surely predict which one was which because that foal would have been one or the other.

This whole linked-gene concept only matters if the horse is heterozygous black; if it is homozygous, it doesn't matter all the much because the horse will always be black based.

*I can't find anywhere what KIT means! If you know, please comment. I'm also not sure it matters because I probably wouldn't understand it anyway.

Horse Color Genetics: Differentiating Shade and Actual Color Difference

On a genetics forum on Facebook, a lot of people often times get mixed up with the 'shade' of the color, and would like to call it something else, when genetically it is the same. But a lot of stumping happens when one horse is so dark or light it is easy to think they are a different color than they actually are.

For instance, one person posted a picture of a horse that was so dark red that it looked black. In fact, at first glance I thought the horse was black. Upon second glance, I had no idea. It looked a lot like the horse below.

Here are some options this horse could be; faded black, smoky black, or dark red. My vote is red on the horse above. That's pretty weird, right?

Same for the horse's below. They could almost be palomino, but they are actually red.

So now, I guess the question is, when does it matter? How do you know when it is one thing, but it looks another? Why do genetics matter if the horse doesn't actually look like what it's genetics are? 

To say the truth, most horses look like what their genetics are. There will always be slight exceptions, especially in the coat pattern tobiano. 

For tobiano, there are certain characteristics that they normally would have. They main one is white crossing over the back, but strangely, in minimal tobiano, it is the rule that is broken the most. Like the horse below looks tobiano to me, but the white does not cross over his back.

Back to the main question of shades; when do shades matter, and when should they be ignored?

To me, shades don't generally matter, unless they cause you to question the 'genetical' color. Like the first horse, who some might call black, but is actually red. There are certain colors in which the shade does matter. Like bay dun or dunskin (buckskin plus dun), the difference being that one carries the creme gene, the other does not. Their offspring could be totally different, but the only way to tell without testing is by the shade of tan.

Genetically, these two horses are different. Kind of weird, huh? The first one is bay dun (some might call it just dun), the second is dunskin. How do I know? The first one is more tan, the second is much more gold. The creme gene sort of enhances the dun color and makes it a lot more bright or metallic. The difference in offspring is that the first one can pass on dun, while the second could pass on creme, dun, or both.

One case that constantly gets on my nerves is when people ask whether their horse is sorrel or chestnut or red. That is one case in which it doesn't matter, unless it is extreme, like the first horse. Or another one: what shade of bay is my bay? Cherry, mahogany, or blood bay? Honestly, that is one of the most insignificant questions ever, when they almost look the same. The only time that one would matter was if the horse was dark bay, or seal bay or brown. Even then, there is only a slight genetic difference.

All that to say, there will always be a couple horses who break the rules, especially with paint, and some horses that continue to stump people. I have heard of paints who the owners tested for every single paint coat pattern there is, and each one came back negative. In those cases, they are unknown mutations of paint no one knows how to test for.

Horse Color Genetics: Identifying Crop-Out Paints

Review: TO=tobiano, O=frame overo, SB1=sabino

One thing that confuses and frustrates a lot of non-geneticists is when they breed two paints together and the resulting baby is completely solid, no interesting pattern at all. But the one combination that totally doesn't make sense to a lot of people is when they breed two non-paints and the baby is paint. How do you explain this, and why does it happen?

As a side note, before I begin, I use paint and pinto interchangeably. In genetics, there is no difference, it is a patterned horse with pattern genes. Some people get into crazy arguements about which is correct, but there is no difference. If you are speaking about which is a breed, then generally Paint is a breed, whereas pinto is a color.

It's important to understand that pinto-patterned horses come in a lot of different varieties. Some are crazily patterned....

Some have only a minimal pattern, but are still obviously paint (well, the one below isn't super obvious, but you get the idea)....

And some don't look paint at all!

I know, you may be gasping, but I'm guessing both of the above horses carry some sort of paint gene. How do I know? And why aren't they as flashy as other paints?

Similar to other markings, all various genes are inherited from the parents. Paints don't just happen, they had to get them from somewhere. 

The horses above are what you might call a 'crop-out' paint. Crop-outs are born from a pinto-patterned horse, but to the disappointment of the owners, they turned out solid. But the difference between a crop-out paint and a solid horse is that a crop-out paint actually DOES have a paint gene in there, the owner just may or may not know it. It takes a little knowledge and practice to be able to identify a crop-out.

In pinto patterns, all paints carry a certain amount of expressing or suppressing gene. Because all horses start out as a base color (chestnut, bay, black), white is added in. Fully expressed pinto horses have more white; some are so white they almost don't look pinto, like the foal below (notice his ears).

While most paints have a more even balance of both, like the horse below

It does seem like there are a lot of paint horses out there, I personally think there are a lot more crop-out paints than most people would think. The horse below is what some people may or may not recognize as a crop-out paint.

So now, the big question: how do I tell a crop-out pinto from a horse who simply didn't didn't inherit any paint genes? 

A minimally-marked pinto will look, well, like the horse above. Tall white stockings are an indicator of pinto, and also the marking sometimes called, 'bald face', where the face is quite white.

Besides double-dilute horses (cremello, perlino, and smoky white), blue eyes are ALWAYS an indicator of pinto. The horse below has no white markings on her legs, but her face marking is rather large. Even though it doesn't cross over her eyes, it is large enough to mark her as a paint. Plus the blue eyes.

The horses below are very unusual; they doesn't have any particular face marking, but their eyes are blue. It's in there somewhere!

Going back to the stockings, some crop-out paints don't have particularly tall stockings. This is one of the horses I posted earlier:

He is super cool. While I can't be positive about his pinto status, what makes me guess that he is a pinto is because of the way that back left stocking has that jagged edge. Very jagged edges on leg markings, whether tall or short, can give you a clue. I don't know whether this is a hard and fast rule or not. And like I said, I'm not very sure on the above horse.

So, back to the very first question: how does a paint produce a solid horse, and a solid horse produce a paint?

They are actually very different questions. The first question, how does a paint produce a solid horse, is not too hard to answer. Just like other genes, unless more is known about the horse, it is safe to assume that there is a 50% chance of the foal inheriting it. If the foal is born solid, then you need to ask yourself whether they are crop-outs, or whether they actually didn't inherit any pinto gene at all. 

The thing about crop-out pinto horses is that they ARE pintos with pass-alongable pinto genes, just not easily recognizable. One problem with the APHA (American Paint Horse Association) is that they don't admit that crop-outs have pinto patterns, and are then labeled as 'solid breeding stock'. But crop-outs can still produce colored babies, unlike true solid-colored horses. While they can still be registered just as any other paint, they are less desirable.

Back to the other question: how can a solid horse produce a paint? Now that you are more informed, you know the answer: that pinto pattern didn't come from nowhere. One of the parents is a crop-out, who is actually not solid.

Going back to the expressed/suppressed pinto genes, that will have to be another post! I'm having a hard time understanding myself how a supressed pinto gene can be hidden for many generations, and then all of a sudden the suppressed gene is turned off and you have a pinto foal.

Horse Color Genetics: Bloody Shoulder Marking

Review: E=black, A=bay, G=gray.

I know a 'bloody shoulder' marking may sound very violent and gory, but trust me. It's not.

A bloody shoulder marking is actually the exact same thing as a somatic mutation, but with a gray horse. In a gray horse's somatic mutation, the gray gene gets switched off in a certain area, leaving it colorful. 

While the name bloody shoulder may seem a bit obvious as to the location of the mutation, bloody shoulder markings can happen anywhere on the body. The horse below has it on his face.

Here is a Bedouin legend about the bloody-shoulder mare: http://www.babsonarabians.com/Readers_Corner/Legend.htm

Horse Color Genetics: Rabicano

To Review: E=black, A=bay, C=cream, Rn=roan

The color rabicano is often confused with the modifier roan, but they are actually very different. Rabicano is a gene that causes roaning in a small area of the body, restricting the roaning section to just around the flanks.

The above horse has minimal rabicano, but the tail sort of gives it away.

Interestingly, rabicano horses usually have very peculiar tails. They are sometimes called 'skunk' or 'coon' tails. The pictures are sort of self-explanatory. The word rabicano is Spanish, 'rabo' meaning tail and 'cano' meaning white. Thus, 'white tail'. 

Horse Color Genetics: Graying Out

Review: E=black, A=bay, G=gray, LP=leopard complex, Rn=roan

I know I've talked a little bit about gray in the past, but I thought I would bring it up again after some interesting Facebook genetics topics. Several people on that forum have asked whether their foal will gray out. If one parent is gray, then there is a 50/50 chance of graying out. The main question is: how do I know if my foal will go gray eventually?

When foals are first born, sometimes there is no way to tell. Here are a couple signs that they will gray out.

Some foals will have 'goggles'. This is a fairly certain way of knowing. The little guys below have goggles.

Some foals are born with little white flecks already in their coat; I don't know if I'll be able to find any good pictures of this.

I just learned that black foals who are born jet black usually gray out, while a black foal who will stay black is sort of a mousy grayish color. Compare the black foal above, who will gray out but is very black, to the sort of dingy color of the black below.

Foal coat colors are often misleading. When they are born, that super-soft coat will often shed out to be a different shade than what they were born with. One lady I knew had a bay tobiano filly that she had really wanted to be black. She shaved her after she was a few weeks old and was disappointed to learn that she wasn't actually black underneath, but a slightly darker shade of bay. I believe most foals shed out to be a richer color than they were born with, but remember! Pinto foal's coat patterns never change, even though the base color will a little.

Here is a stumper:

I knew a mare that looked like this once, and at the time, I had no clue. But now I know better.

The horse above WAS a paint (he still carries that gene), but the color is covered up by gray. You can still see the lines where the markings are. Some will develop flea-bites (the marking, not the actual thing) in the colored areas, like the horse below. 

I don't know why, but of all the grayed-out paints I've seen, all of them seem to have a bit of a bluish tint to the color areas. Especially in the first one.

Horse Color Genetics: Paint Combinations

One thing that has popped into my head recently is how many different combinations of colors can you have without the horse exploding? There isn't a right or wrong answer to this question; most patterns will collide and make a crazy horse, like the one below. 

That is any pinto pattern, + appaloosa. It is fairly rare, not because it's hard to get, but because horse's in the pinto registry aren't allowed to have any appaloosa relatives, and vice versa. It is more common in miniature horses because both colors are allowed. 

Isn't he gorgeous? Black roan + tobiano. 

The above horse is seal bay + roan + tobiano.

This horse is champagne + tobiano.

Obviously, there are many others, but I chose these because I thought they were particularly pretty.