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The Science of Colour
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The Science of Colour

Horse genetics is something I take a huge interest in, and I hope that my blog here will maybe help others to understand even the basics.

Horse genetics and colouring:

Does it impact your ability to look after a horse if you can’t tell me what colour it is? Of course not, not at all. You could be the world’s most amazing horse person, yet barely know the basics, or on the other hand, you could tell me which allele the splash gene resides on, but be an awful rider or owner. The reason I am writing this is just some basic stuff that can be useful to know if you are breeding and want certain colours etc Colour isn’t the only thing worth breeding for but this might help if it's a secondary goal!

BASE COATS

There are three base coats: Red (chestnut/sorrel, whatever you want, it’s red) Black, and Bay. Every single colour that a horse comes in is based around these base coats.

At one point in time, every single horse was bay, and the genes mutated over time, creating chestnuts, blacks, and everything else in between.

But what about grey?

Grey is not a colour believe it or not. Grey is a pigment disease that causes the hair shaft to over-produce pigment, kind of like using the whole tub of paint at the start of a painting instead of touching it up over time - you soon run out of paint! So basically the hair then burns itself out and stops making pigment, so the horse slowly loses colour. This is why horses become more ‘white’ as they age, whilst younger horses are often a dark, iron grey, though eventually, all grey horses end up white.

That’s not all though. Some horses get what is called ‘flea bites’ this is when the hair shaft fires up the colour producers again and the grey horse ends up with little flecks of colour, sometimes they aren’t the same colour as the original base coat, so you have a black that has greyed out, but has chestnut flea bites!

For a horse to be grey, it must have a grey parent. If that parent has one grey gene, then there’s a 50% chance of passing it on, if it has two grey genes (homozygous for grey) then every foal the horse produces will also grey.

Grey is also one of those funny genes that does not hide. If a horse has even one copy, they WILL grey though it may take many years and fun coloured sheds before they do.

Now, where are these genetics!

This is where it gets a little bit more complicated if you know very little, much like me. Horse genetics can get a little complicated, but they never lie, so unlike humans where you occasionally get anomalies, if you breed two red horses, you will never get a black or a bay, and here’s why.

The two main genes on a horse that give base coats are extension and agouti.

EXTENSION

Extension comes in two forms, dominant extension (E) and recessive extension (e)

Dominant extension, or the big E, gives the hair the ability to have red and black pigment. So this means you will have a black or bay coat (Depending on agouti, but we’ll come to that in a minute) but since black is dominant over red, you won’t see the red!

Recessive extension, or little e, only lets the hair have red pigment, thus producing a red horse.

So a horse that is EE will have a black/bay coat, and will not be able to produce red based foals.

An Ee will still have a black/bay coat but will be able to produce red foals with horses who also carry the recessive extension (e) when bred to another Ee or an ee horse.

An ee will have a red coat, and with another ee will produce only red foals. However, with an Ee or EE they can produce black/bay too.

Remember that big E is dominant, so it beats little e as such and will display on the coat. Some people call EE homozygous black or “true black” which isn’t entirely correct, as an Ee horse is still black, just with the ability to produce red foals with the right mate!

AGOUTI

Agouti works in much the same way. All horses have agouti and extension, either in homozygous (two the same) or heterozygous (two different) forms.

Agouti is the gene that makes sure the black pigment is nice and evenly spread all over the coat, so a horse which is aa (just like extension, this would be recessive agouti) has a nice even spread of black, all across the body, so this gives you a black horse.

Aa, bringing a dominant agouti gene into play makes the bay base coat. So Dominant A restricts the black colour to the points, being the legs, ear tips, mane, and tail, giving that lovely red colour across the body, with the black on the points.

AA can further restrict points, but it is still a bay horse!

Please note that because agouti only works on black pigment, it doesn’t matter what the agouti status of a red horse is, because it will never show on the coat because there’s no black to restrict!

So wait, what?

In simple terms, as was once explained to me, think of a horse as a canvas.

So your first coat of paint, no matter what, will be red. Then afterward, you look at the genes. If the horse is ‘ee’ the red is enough, and you don’t need to worry.

However, if there's a ‘E’ at play, then you give the coat a nice brush over with black. The red is still there, but because there’s a big dominant gene muscling its way in, you can’t see the little recessive one.

Hold on though! Now you need to check agouti! If there's ‘aa’ that's fine, you can leave your nice black painting somewhere to dry. But if there’s an ‘A’ anywhere, then you need to scrape the black paint off the middle. This will give you that nice red showing through, but there will still be black around the edges, like a bay!

Dilution genes

Now we move onto to my favourite, where I could rant for hours.

Dilution genes do exactly what’s in the name, they dilute, so much like added water to your paint, it messes with the colours. I’m no expert, so I’ll have a little section on dun, cream and silver dilution genes. There is other genes such as champagne and pearl, but I’m not informed enough to teach other people about it in case I mess up! So it’s up to yourself to look that up.

DUN

Okay, so first things first, let me get this off my chest…. DUN IS NOT THE SAME AS BUCKSKIN. Phew, now that’s out the way, let’s get on with things.

Dun is a modifier which causes the base coat, so bay, black or red (or palomino, or buckskin or… or.. Just any colour) to be diluted to a lighter colour. Bay turns to a kind of light biscuit colour, black turns out greyish mousey and red becomes well, a lighter, orangey red.

But it’s not that easy, in order for a horse to be dun they must have this dilution, as well as the dorsal stripe (The line down the back) that also must run down through the tail, along with primitive markings such as leg and neck barring.

Now to throw a spanner in the works, there is also a gene called Nd-1, this is non-dun, and it will give much the same effects, but without actually being dun! To the untrained eye, it can be difficult to spot the difference, however, a Nd-1 horse won’t have the same dilution, and the dorsal stripe will not run through the tail either.

FUN FACT, whilst a bay dun is called bay dun, and red dun is red dun, black dun is often called ‘Grulla’ (not grullo) as it is the colour of the Spanish Crane bird that the colour is named after!

CREAM

Cream is my personal favourite gene. Just because of the absolutely beautiful colours it can create. Cream dilutes the coat, as again, it’s a dilution gene, it’s what it does. Although cream is what is called an ‘Incomplete dominant’ as when you only have one copy of cream, so Crcr, it affects the horse very differently from when you have two dominant genes, CrCr.

The easiest way to do this is a simple little table like so.

Red + 1 Cream = Palomino

Red + 2 Cream = Cremello

---

Bay + 1 Cream = Buckskin (not the same as dun)

Bay +  2 Cream = Perlino

---

Black + 1 Cream = Smoky Black (A single cream doesn’t affect black pigment!)

Black + 2 Cream = Smoky Cream

And it’s as easy as that. When a horse has 2 cream genes it is known as a DOUBLE DILUTE, because it has two dilute genes! These double dilutes will be a pale milky colour and it’s impossible to tell them apart without actually testing because of the way they look can overlap between the three.

But you said cream doesn’t affect black pigment!

I said one single cream didn’t! This is why a buckskin, which is bay with cream, will still have its black points, whilst the brown coloured body is diluted to a lovely shiny golden colour.

In the case of a black coat, it is physically impossible to tell if a black horse has the cream gene without either knowing the parents or testing because it will look like any other normal black! Unless… Its paired with silver, which is explained below. A black horse with silver and cream will be diluted to a colour like “a brown paper bag.”

I’ve heard about dilutes! They’re the albino horses, aren’t they? No, stop right there.

Believe it or not, there is absolutely no such thing as an albino horse.

There is an actual factual reason behind this and I can explain it as well as I can except that I’ve forgotten the name of the gene, I know it starts with T so we’ll roll from there.

So in animals such as humans (we are animals) dogs, and a lot of other mammals, our coding for pigmentation is linked to the T gene. Albinism is basically a break in that gene.

In horses, the T gene has absolutely nothing to do with colouring, so a break in the T gene wouldn’t affect a horses colour at all.

On top of this, when most animals have albinism and the pigment is removed from the eyes, it creates the red-eyed look. Whereas on horses, there isn’t the right pigment to turn red, so a horse without pigment around the eyes, actually has blue eyes, which is quite common and does not affect the eyesight at all unlike what the old tales say.

Please note, this does not mean that horses with blue eyes are albino, as I said above, albinism just doesn’t exist, there has never been an albino horse recorded in history.

SILVER

Silver is a beautiful gene, and the opposite of cream, but only because silver only affects black pigment! So whilst cream will dilute a chestnut into a pretty palomino, silver won’t touch it at all.

A black horse with silver is often called a silver black, or silver dapple, and is the envy of horse owners everywhere, the body becomes a deep chocolate colour with a mane varying from yellow blonde, to outright silver.

Bay is also affected by silver, and can sometimes even be mistaken for a flaxen chestnut because of how it dilutes the coat to a much lighter brown, and just like a silver black, the mane and tail will be a blonde kind of colour.

But my friend has a chocolate palomino…

Nope, that’s a forbidden term right there. Chocolate is a food, not a genetic term. I understand that it’s widely used, just like ‘buttermilk buckskin’ and ‘biscuit dun’ and ‘golden palomino’ but I won’t use them here because they cause a lot of confusion and wrong information.

Use of the term ‘chocolate palomino’ has been used for, but is not limited to:

Silver dapples

Sooty Palominos

Sooty flaxen chestnut

Liver flaxen chestnut

Silver bays

Even just dark palominos.

So what happens if you have a buckskin with dun and silver?

Honestly? I don’t know, although I can tell you about the actual genes themselves, I’m not too clued up on how they mingle, though I know cream and silver together do weird things to coat colour. Although just beyond that, I don’t want to say too much and provide wrong information. I can point you in the right direction if you would like to learn more!

SPOTS AND STUFF

So I’m sure a lot of us love a coloured horse, but what really is a coloured horse?

Well, first of all, there’s a huge list of colour patterns, such as tobiano, frame overo, splash, sabino, rabicano, there’s the white genes, all 1 to twenty-something of them, as well as multiple genes that haven’t actually been marked yet! This is a confusing topic for some, myself included, but I’ll do my best to give as much information for as many as I can!

Roan

Lots of horse breeds have roan, it’s that lovely spray-painted look where the horse has white hairs spread evenly through the coat though it tends to leave the head and legs, as well as the mane and tail alone. I’ve seen some pretty odd looking roans, where the body is nearly entirely white, whilst the mane, tail, head and legs are still pitch black! Roan is a dominant gene, meaning that if a horse has the roan gene, they will have roaning on the coat.

Tobiano

Tobiano is everybody’s favourite word to fling around when there are white patches on a horse, and a lot of the time, it’s right. Tobiano is a widespread gene that occurs in a lot of different breeds, it creates big white patches on the base coat. This does not make the horse bi or tri-coloured like people seem to think, but it’s still the base, coat, just interrupted with big white spots.

Tobiano is characterised by a lot of things, however, a lot of these things are also shared by the other genes that cause white on the coat, one of the things I’ll always remember is about tobiano horses having a garter belt. So the white legs running up and creating a ‘belt’ over the rump that connects on the other side, but this isn’t always true, its common to see tobianos with the white stripe over the rump, sometimes without the white legs, but like everything, take it with a pinch of salt.

Frame Overo

Frame is a gene that is found mostly (I said mostly, not always) found in stock breeds such as the Quarter horse and Paints. The scary part about this gene is that it kills. Don’t be alarmed, a single copy of this gene is harmless and can cause some very pretty patterns, but I’ll explain its lethality in a paragraph by itself below.

Frame is usually shown by big patches of white on the sides of the horse, surrounded by colour, so that when you look at a horse side on, the white looks ‘framed’ by the colour, although, as I’ve said multiple times through the article, this isn’t always true. I have seen horses tested positive for frame that don’t have a single white hair on their body, not one, zero, zilch. Not even a sock or a star. This is partly why it makes it so dangerous.

But you said frame was deadly! It is.

However, as I’ve also said, it’s pretty much harmless in a single copy, however, if a horse is homozygous for frame, has two copies, it results in either a miscarriage in the womb or the foal does not live for more than 1-2 days after suffering. This is because two copies of frame causes issues with the intestinal tract, and the foal is born without part of its tract, or part is sealed etc. There is absolutely no cure for this, try as we might, and the kindest option is to put the foal down.

This is called Lethal Overo

As sad as it may be, it’s perfectly preventable. Make sure your horse is tested, and if they are positive for frame, do not breed to another frame, a 25% chance of a dead foal is too heartbreakingly high. If you don’t know your horse's frame status, don’t breed to an untested horse, or one who has tested positive for frame, again, it’s a dangerous gamble.

I don’t like going on about breeding, as it’s your horse, your decision, however, think twice when doing so.

Splash

This is a fun gene, causing the horse to look like it’s been dipped in paint from the bottom up, often the face is white too. It’s one of my favourites, just because it can look very striking on dark coats. Two copies of splash can often leave the horse deaf unfortunately as the inner ear in unpigmented (you can’t see this from the outside, so just because your horse has white ears, it doesn’t mean panic stations)

White genes

There’s a lot of white genes that haven’t entirely been mapped yet, and some which can be very intriguing. W21, for instance, is supposedly only found (so far) in the Icelandic stallion Ellert, who has foals on the ground as of 2018, and they appear to have their fathers lovely colouration. W20 does nothing by itself, but when paired with other white patterns acts as a booster. Suddenly there’s lots more white! Like shouting through a megaphone compared to just shouting.

Some white genes can cause Max White, this is where basically the horses entire body is one big massive white spot. They still have a base colour underneath, however, their white pattern has swallowed them up entirely! Unfortunately, along with double dilutes, people call them albino, which is totally wrong.

Appaloosa genes - LP and Patn

Here we go. I’m not overly versed in appy genes either but I’ll do my best.

The ‘appaloosa gene’ is known as Lp or leopard complex and technically, it’s a pigmenting problem, just like grey, that bans the colour to certain spots. But in this effect also comes the PATN gene. These genes work together to create the beautiful spotted patterns.

So Lp just by itself without PATN is what makes a varnish, a horse with the characteristics of an Appaloosa, with the mottled sclera (The eye linings) the stripy hooves and the other things that make Lp show up, except without Patn to control it, it causes varnishing - an effect almost similar to grey where the Lp creeps up and steals colour with every coat shed.

However, throw PATN into the mix and this is how you end up with all those spots. Normal PATN only gives Lp certain bits, whilst PATN1 lets Lp play with the whole body of a horse.

Bear in mind here, that a horse could have a million PATN genes, but if it doesn’t have one Lp, then you won’t have an appaloosa.

lplp patn - No appaloosa

lplp PATN - No appy

Lplp PATN1 - Leopard appaloosa

LpLp PATN 1 - few spot appaloosa

Lplp PATN - a ‘blanket’ appaloosa

LpLp PATN - a ‘snow cap’ appaloosa

Lplp/ LpLp without PATN - a varnish appaloosa, with all of the features of an appy, bt without a lot of the patterning.

Wheres overo in your list?

Overo, just like a chocolate palomino, is an incorrect term. People use Overo for basically every single pattern except tobiano. And sometimes still tobiano. So in the magical land of genetics, it isn’t used much, except in the case of saying frame overo, but you’re still specifying that it’s frame you’re on about, so tally ho.

OTHER THINGS WORTH NOTING

I’ve compiled a small list of things here that are worth bearing in mind if you’re getting into genetics, some that have helped me, as well as just a few small fun facts.

- Miniature ponies, Icelandics and Fjords (just most ponies really) don’t really play by the rules of genetics. It’s a pain in the butt to deal with them.

- Speaking of fjords… Most Fjord ponies are homozygous dun, and Fjords have their own names for their colours too!

- Buckskin and dun are not the same things!

- Brown and bay are genetically the exact same thing. They’re just shades of the same genetics

- If you cross a red and a cremello (a tested cremello, not perlino or smoky cream) the only colour you can get is palomino

- Again, although you can pretty much breed for any colour, shade is completely random. You could breed the lightest reds together and a liver chestnut could come out, or vice versa.

- A paint is only a paint if it has papers. A Paint is a breed. If your horse is paperless but has colour, it’s a pinto.

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