Horse Color Genetics: Re-Explaining Heredity and Basics

To go back to the basics, as I've learned more about genetics I have thought of better ways to explain how it all works. My first post about heredity was fine, but I thought I would re-write it with a different example.

Let's start with a genome sequence: Ee, AA, Cc, LPlp

If you've tried to understand genetics, then you may have seen something like this. This is a way to abbreviate the horse's color, but being able to read it is what takes practice.

For each individual gene, there are two alelles together that make up the gene. Each alelle individually has the chance to be either 'turned on' or 'turned off'. The 'on' genes are capitolized. The 'on' genes are called dominant, and 'off' genes are recessive. If I ever refer to dominant and recessive, always think of a light switch. If they are reccesive, the light switch is turned off.

When any creatures breed, each parent must give only one alelle from each gene to it's offspring. That means when they breed, the gene will split, and the depending on the parent, they will get either two on genes, one of each, or two off genes.

Using the example above, the gene AA was both turned on. When both genes are turned on, or both turned off, this is called homozygous. 'Homo' means the same; both allelles are the same, and you know what the baby will inherit.

The rest of the genes, Ee, Cc, LPlp, are one of each. That is called heterozygous, 'hetero' meaning different. If this horse were to breed, we can only make a not very good guess as to what color the baby will be, because it is 50/50 whether they get the 'on' gene or the 'off' gene.

If you are still confused, let's use flowers for a simple example. If you breed a red flower and blue flower together, the baby will be purple. One red gene from the red flower and one blue gene from the blue flower. However, the genes inside the baby will still be red and blue. If that baby were to breed with a red flower, then those genes would split. THAT baby would get one red gene from the red parent, and either a red gene OR a blue gene from the purple flower. So that baby would either be red or purple.

So if I were to say that the horse in the example is heterozygous E, that means that there is one dominant gene and one recessive gene. If I said that the horse was homozygous dominant A, that means that both A genes are turned on. It is important to know that when I refer to homozygous, I usually mean homozygous dominant, meaning both genes turned on, versus homozygous recessive, both genes turned off. When a breeder advertizes their stallion for a certain homozygous gene, they are referring to homozygous dominant.

I'll use a different post to go back and re-teach you about the basic colors, and how all this applies.

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.