[Chronometer]

Hey guys! Are you ready to learn about horse colour genetics?
*awaits yells of enthusiastic agreement*

The Basic Base Colours
If you are, then we'll start simple - with the base colours. Think of painting. You know how sometimes you need a nice base colour that you can work with to layer more colours on top? Well, think of that for a little. That's sort of how horsey base colours work. They are what all the other dilutions, patterns and modifiers are piled on top of to get a final result.

The three equine base colours are:

~Red
aka
Chestnut
Sorrel

~Black

~Bay

I'll go into more detail about these soon! I'll also explain why there are some strange shade variations within the colours themselves. But first, let me confuse you tell you something very important!

Most mammals, including horses produce two pigments; red (or yellow but not in horses) and black.

Now, I can imagine you're asking yourself "but why are there three base colours? Chono this is really crazy!" Of course its crazy. Nature is crazy. What did you expect? Anyways, a gene called Extension controls these two pigments. Its dominant allele is E (a big scary capital letter because its dominant). When a horse has one of these big Es, this means the Extension gene will tell his cells to make lots and lots of black pigment, and a really teeny little bit of red. Yes, there will still be a little bit of red, which you don't see at all, but it will be veeery important when we talk about bay. If the horse has a big E (a dominant Extension allele) and no other funny genes to make the colour different, he will be black.

Okay, so we always must talk about alleles in pairs because they don't like hanging around alone. The dominant Extension allele's friend is the recessive e. This little e is what tries to tell cells to make lots and lots of red pigment. Because it is recessive, when it sits next to a big E like Ee, the dominant allele will be black, and lots of black pigment will be produced. To get lots of red pigment, we need two little es - ee. A horse with ee will have cells that are being told to make loads of red pigment, and will be red (or chestnut or sorrel if you like). Therefore:
EE = Black because of two dominate black alleles
Ee = Black because one dominant allele is 'stronger' than the recessive red one
ee = Red because there are no dominant alleles to tell cells to make black pigment

It's time for the fun stuff - Agouti! Agouti is the name given to the gene that determines where black pigment can go. It controls Extension. the letter that represents a dominant Agouti allele is A. When a dominant Agouti gene is present, it makes cells produce black pigment only on the points of the horse - the lower legs, mane, tail, and ear tips. A horse with this colour is called bay. If both Agouti alleles are recessive, aa, black pigment will be evenly distributed. Remember - the effect of Agouti is only seen on black pigment. If you have a red horse, ee, the agouti zygosity will have nothing to do with the horse's coat colour.
So;

AA = Two dominant Agoiti alleles mean black pigment is restricted to the horse's points only
Aa = Black pigment is restricted to the horse's point again - the effect of the dominant allele is seen
aa = Black pigment is distributed uniformly

Now we can combine these letters into real genetic codes:


EE/AA = This horse is bay. The dominant Extension genes cause the horse's cells to produce lots of black pigment, and the dominant Agouti genes restrict this pigment to the horse's points
EE/Aa = This horse is also bay. The dominant Extension genes cause the horse to produce lots of black pigment, and the dominant Agouti gene restricts this pigment to the horse's points. The effect of the recessive agouti gene is not seen
EE/aa = Not a bay! This horse is black. Extension is dominant, but there are no dominant Agouti genes to tell the black pigment where to go. It is distributed evenly around the horse
Ee/AA = This horse is bay. The dominant Extension gene causes the horse's cells to produce lots of black pigment, and the dominant Agouti genes restrict this pigment to the horse's points
Ee/Aa = Surprise! Another bay. The dominant Extension gene causes the horse's cells to produce lots of black pigment, and the dominant Agouti gene restricts this pigment to the horse's points
Ee/aa = Here we have a black horse. The dominant E allele means black pigment will be produced, but the recessive Agouti alleles mean the pigment is not restricted
ee/AA = This horse is red. Or chestnut. Or sorrel. Technically he is red, since his cells are only producing red pigment. The dominant Agouti alleles can't affect red pigment
ee/Aa = Here's another red horse. Again, the recessive e's mean red pigment is produced, which is unaffected by the dominant Agouti allele
ee/aa = Another red horse. His cells are only producing red pigment due to the recessive Extension alleles. Despite having a recessive Agouti status, those cells can't determine where the black pigment goes because there is none


It's Shade Time!
Shades refer to the strange variations in tint that horse coat colours have. Like how blue is divided into sky blue, phthalo blue, dark blue and others. Up above on my pretty drawing, you can see some shade variations. Here they are, row by row, left to right:

~Red
The first horse in this row is a bog standard chestnut/sorrel. Most chestnuts will be within a couple shades darker/lighter, and vary in tone slightly. There is usually lightening of the hair around the coronet band.

The second horse is known as a Liver Chestnut. Don't ask me why they chose the word liver. This colour is still considered red, and will still have the Extension status of ee, despite being quite dark. Little is known about the inheritance of this shade. Here is a surprisingly dark chestnut horse. Note the lighter fetlocks!

The third horse in this row is known as a Flaxen Chestnut. He has a normal chestnut coloured body, but a light straw mane and tail. This is what the flaxen gene does to chestnut. Its inheritance is confusing, and it may not be a single gene that causes this expression. Flaxen can be visible on liver chestnut horses to make Flaxen Liver Chestnut. The degree of flaxen expression can vary from super light mane and tails to only slightly lighter than the body.

[GhiraWar]

Awesome so far!