Recently, it seems that the is undergoing a strong movement toward naturally coloured horses, and while I am a supporter of such a movement, I continue to see common mistakes and slip-ups when dealing with genetics and heredity. There are a great deal of fantastic tutorials on the web (I'm going to suggest this one: [link] if you've never seen it), but these mistakes are continuously made, and I believe it's because people tend not to entirely understand the basic concept behind the function.

So, as a Life Science major with an interest in this sort of thing, I'm going to try and give a concise and understandable explanation for equine coat colours, what makes them work and how they're coded for.

Of course, we're dealing with genetics here, so "concise" may not exactly mean "short."


Base Pigments

Pigments are specialized molecules (sometimes called secondary metabolites) which absorb or reflect light photons of varying wavelengths. In plain English, they're responsible for visible colour. Chlorophyll A and B are green pigments found in leaves, for example. Brown and red seaweeds, as well as domestic carrots, are rich in carotenoid pigments, which vary from red and orange to purple in colour. But horses, and indeed a great many animals, have only two pigments available to them: eumelanin and phaeomelanin.

Eumelanin is the black pigment, and phaeomelanin in its purest and most concetrated form is a brilliant orange-red. Remember these terms; they're important.


Brush-up on Genetics

Horses reproduce sexually. That may seem like a pretty DUH statement, but when considering genetics, it's extremely important. You are as you are because you received half of your genetic material from your mother and half from your father, and when the egg and the sperm fused to form Zygote-You, the two halves merged and combined to create your DNA. It's the same with horses.

A German priest called Gregor Mendel was the first to discover exactly how genes are inherited and "combined." He did so during a rather famous experiment using pea plants; by crossing plants of different heights, with different coloured flowers, and with peas with differently textured skins, he dreamed up the concept of dominance and recessiveness of genes.

Check out this diagram from the Wiki Commons: [link]

Every animal, people and horses included, has two copies of the "alleles" responsible for each and every gene. This diagram deals with the colour of flowers on Mendel's pea plants. The flower on the left has what's called "homozygous" white (ww) genotype. The genotype for a specific gene or trait is said to be homozygous when both alleles are the same. On the right is a homozygous red flower (RR). Mendel crossbred a white-flowering plant with a red-flowering plant and produced 100% red flowers, each (though he didn't know it at the time) with the genetic code "wR." This is called a heterozygous genotype.

However, of course you'll notice that despite the fact that each of these offspring has one of the "white" alleles, they're all red. This is because the red allele displays something called "complete dominance," which I'll discuss in more detail later.

Next, he crossbred the heterozygous plants. The square at the bottom is called a Punnett Square, and if you understand how it works and know how to use it, you can solve just about any problem of Mendelian Inheritance you ever see. It works by putting the genotype of the two parents along the top and down the side, as shown, and writing the resulting offspring genotypes in the corresponding squares, as shown.

You'll notice that there is a 25% chance of homozygous red offspring, 50% chance of heterozygous red offspring, and 25% white offspring. But, 75% of the offspring are going to be red.

Before I go on, I need to explain the concepts of genotype and phenotype, and how they interact. A genotype is, simply, the genetic code (in these cases RR, wR or ww). A phenotype is the physical manifestation of the genotype - in other words, what the genotype looks like on the scale you can see (usually).

Phenotypes are always determined by a responsible genotype, but exactly how the genotype is expressed depends on the nature of the individual gene and alleles. Now, we come to the idea of dominance and recessiveness.

Usually, in a heterozygous phenotype, one allele will dominate the other. This is called "complete dominance," and in this case the dominant allele will be expressed in the phenotype while the recessive allele will remain dormant. For example, in Mendel's pea plants, red (R) is dominant to white (w) and a wR plant appears the same as an RR plant. It is only when the plant is homozygous recessive (ww) that the recessive allele is expressed.

In select few cases, however, the two alleles will compete with each other for expression. This is called incomplete dominance. There is one particular case of this in horses with the cream gene, but for now lets stick to the pea plants. Let's say that R was incompletely dominant to w, just for the hell of it. If that was the case, then a wR plant would not appear red; it would be pink. Only a RR plant would be red, and only a ww plant would be white.

And that's basic Mendelian inheritance. Yes, basic.

Quick glossary of terms:

Allele: Half of a gene. For simplicity's sake, geneticists use letters to correspond to specific alleles, i.e. R or w

Genotype: Genetic makeup on the level of DNA
Phenotype: Physical manifestation of the genotype

Homozygous: Alleles in a gene are identical, i.e. RR or ww
Heterozygous: Alleles in a gene are different, i.e. wR

Complete dominance: One allele overpowering the other in the heterozygous genotype; the allele which is not dominant is called recessive.
Incomplete dominance: Both alleles being expressed to some extent in the heterozygous genotype.


Base Colours

So now we actually get to talk about how all this nonsense about pea plants has anything to do with pretty ponies.

As you might have guessed, the three base colours (chestnut, bay and black) are caused by interactions between genes responsible for the base pigments.

The first and most important bit of a horse's genotype to know is in what's called the Extension Locus. This decides whether a horse is "red" or "black," i.e. whether phaeomelanin or eumelanin is expressed. The alleles are E and e, where E is the dominant extension allele responsible for black pigment. A horse with the genotypes EE or Ee will have a black base, then, while only ee will produce the red base.

The only other "base" locus is the Agouti Locus. Agouti is a dilution of eumelanin which essentially shoves black out to a horse's points, leaving phaeomelanin expression where eumelanin is pushed away. Still, there is usually still some black pigment produced, which causes a body darker than a chestnut. Yep, this is bay. Agouti expression is dominant, so either AA or Aa will result in bay from a black base. aa leaves the black untouched.

Also note that agouti has no effect on phaeomelanin, so even if a chestnut (ee) horse is homozygous dominant agouti (AA), it will still be chestnut.

So this is what we've got so far:

E is black, e is red, E is dominant.
A is agouti, a is no agouti, A is dominant.

Black: EE/aa or Ee/aa
Bay: EE/AA, EE/Aa, Ee/AA or Ee/Aa
Chestnut: ee/AA, ee/Aa or ee/aa

It makes sense. Really.

Black horse|Bay horse|Chestnut Horse


Brown

Brown, the colour characterized by a black body with tan at the muzzle and other soft points, is a variation of bay caused by an agouti modifier (A^t). It is only expressed on a bay base because it is a modifier of agouti.

Brown - EE/A^tA^t, EE/A^ta, Ee/A^tA^t or Ee/A^ta

Also keep in mind that the brown modifier is dominant to regular agouti, so the above aren't even all of the possible brown genotypes. You could potentially get A^tA, for example, on any of the other bases.

Brown horse


Greys

Grey is not a base colour. Kindly get this through your noggin if you hadn't already. Greying is a process that can occur to any horse of any colour, making it a "modifier."

And believe it or not, every one of the endless variety of greys out there is caused by one single completely dominant gene which causes a horse to gradually stop producing pigment. The grey gene (G/g) affects both eumelanin and phaeomelanin, and a grey horse will get lighter as it ages as a result.

G is grey, g is not grey, G is dominant.

Grey: Any base colour with either GG or Gg.

Grey horse|Another grey|And one more


Champagne

Champagne (Ch/n) is a dilution of both eumelanin and phaeomelanin. It also causes freckled pink skin. Champagne foals are born with blue eyes that gradually darken to a greenish (often called "hazel") colour at maturity.

There are four recognized champagne colours: Gold, Amber, Sable and Classic, which are the champagne-modified versions of chestnut, bay, brown and black respectively.

Classic Champagne: E-/aa/ChCh or E-/aa/nCh
Amber Champagne: E-/A-/ChCh or E-/A-/nCh
Sable Champagne: E-/A^t-/ChCh or E-/A^t-/nCh
Gold Champagne: ee/A-/ChCh, ee/aa/ChCh, ee/A-/nCh or ee/aa/nCh

(A dash "-" represents a choice between either dominant or recessive allele. When I write that, it just means it doesn't matter what the other allele is, the phenotype will be the same.)

Classic|Amber|Sable|Gold|Freckled skin


Roans

The roan gene (R/r) causes a scattering of white hairs on the body, but not at the points. It affects both eumelanin and phaeomelanin production, so you can have roan on just about anything. The roans with specific names are red roan (or strawberry roan) and blue roan. Everything else is written "(colour) roan." Sable Champagne Roan, for example.

Red roan: ee/A-/R- or ee/aa/R-
Bay roan: E-/A-/R-
Blue roan: E-/aa/R-
Sable champagne roan: E-/A^t-/Ch-/R-
et cetera

Red Roan|Bay Roan|Blue Roan


The Dun Factor

Which, yes, sounds like it should be an action movie or something. You know, The Bourne Supremacy, The Dun Factor...

Shaddup, I have my own humour.

The dun factor (D/d) is one of the most widely misunderstood genes, even though it's one of the simplest. Usually, that's because it's confused with the cream dilute, which we'll get to in a moment, but first I'm going to actually define what the dun factor is and what it does:

Primitive markings. C'est tout. That's it. Dorsal stripe, leg barring, shoulder shading, sooty face. If the horse has at least the dorsal stripe and the beginnings of leg barring, it's got the dun factor. Dun on chestnut makes red dun (or claybank dun), which is basically a chestnut with primitive markings. Dun on bay makes the classic yellowy dun that so many people mistake for buckskin. Dun on black makes grullo/grulla, which is a dark mousy brown-grey with *ta-da* primitive markings. You can have a dun dilute on anything.

The basic rule for duns is that the primitive markings will be expressed in eumelanin. That rule is bent slightly with red-based duns, which have darker, but not black, markings. But if you have an amber champagne dun, for example, the primitive markings will appear the same colour as the points.

Grullo/grulla: E-/aa/D-
Classic (bay) dun: E-/A-/D-
Red (claybank) dun: ee/A-/D- or ee/aa/D-
Amber champagne dun: E-/A-/Ch-/D-
AND SO FORTH.

Grulla|Classic|Red Dun


The Cream Dilute

Cream (Cr/n) is one of those rare instances of incomplete dominance. That is to say that homozygous dominant and heterozygous dominant genotypes have different phenotypes. In this case, one cream allele in two affects only phaeomelanin, leaving eumelanin untouched, while two cream alleles completely wash out phaeomelanin and dilute eumelanin as well. So, you end up with this mishmash of possibilities:

Palomino: ee/A-/nCr or ee/aa/nCr (one cream on chestnut)
Buckskin: E-/A-/nCr (one cream on bay)
Smoky black: E-/aa/nCr (one cream on black)
Cremello: ee/A-/CrCr or ee/aa/CrCr (two creams on chestnut)
Perlino: E-/A-/CrCr (two creams on bay)
Smoky cream: E-/aa/CrCr (two creams on black)

Palominos appear yellow or golden in colour, with pale cream or white manes and tails. Buckskins look just like bays, except lighter and yellower. Smoky blacks are almost identical to regular blacks, except that they may be slightly browner on the body and might bleach in the sun.

Cremellos, perlinos and smoky creams, because they've had all of their pigments diluted, will have pink skin and pale blue eyes and may be completely indistinguishible from one another. Sometimes perlinos will have slightly darker manes and tails, and smoky creams can have that slightly darker, redder tint all over their bodies.

Palomino|Buckskin|Smoky Black|Cremello|Perlino|Smoky Cream


Silver Dapple

One of my favourite dilutes, and one of the least well understood.

The silver gene (Z/n), let me say this right now, affects EUMELANIN and ONLY EUMELANIN. The black pigment in silvers is diluted. Not the red pigment. The name might be slightly confusing, but silver dapple doesn't magically turn your horse silvery-coloured. It blocks the production and expression of eumelanin. That means that a silver bay will look just like a regular bay, except that his points will be diluted nearly white (with black roots). A silver dapple black will have similarly diluted manes and tails, but because the body hair is so short and the silver dilute leaves roots dark, the body will be slightly lighter and browner than black.

Silver chestnuts don't exist because Z only affects eumelanin. A chestnut can be a carrier of a silver gene, but it won't show in the phenotype.

Silver Dapple (Black) - E-/aa/Z-
Silver Bay - E-/A-/Z-
Silver Buckskin - E-/A-/nCr/Z-
And so on, and so forth.

Silver Dapple|Silver Bay|Silver Buckskin


KIT mutations

OH YAY, COMPLICATED GENETICS. You know, because the rest was just so darn easy and simple.

Every paint pattern, as well as rabicano and dominant white (which exists, yes it does, there are eleven separate mutations, but more on that later) are caused by mutations in the same gene called the KIT locus. It's not important to know exactly what KIT does, but it is kinda cool to know that it causes every paint patter in existence.

ANYWAY.

Up until recently, the only widely recognized paint patterns were Tobiano and Overo. Now what was Overo has been split into Frame, Splash and Sabino. Rabicano and Dominant White will be put in separate sections.

Tobiano

Tobiano (To/n) is characterized by smooth-edged white markings, stockings, white over the topline and a two-toned tail. Tobiano also tends to keep white away from the eyes and face.

Tobiano

Frame

Frame (Fr/n) is characterized by jagged-edged markings restricted to the body and neck (no white over the topline). There may be white on the legs, but not always. There may be extensive white on the face, but not typically over the eyes, which are most often brown.

Lethal White Syndrome (sometimes called lethal white overo or LWO) is often associated with Frame, but it is actually caused by a separate gene which is common in a few populations of Frame horses. LWO is recessive, which means that a horse can carry the syndrome without having any ill effect if it is heterozygous, and only homozygous recessive individuals die of the syndrome. Responsible breeders should always have their studs or broods tested genetically for LWO if the syndrome has appeared at all in their pedigrees.

Frame Overo

Splash

Splash (Spl/n) was initially lumped into overo because the white never crosses the topline, but as a pattern it is actually one of the easiest to spot. Extensive white on the legs is typical, often extending up to the belly toward the topline, but never crossing it. However, the most visually impressive trait in splashes is the white face; it is the only paint pattern that has extensive white over the eyes, and often turns the eyes blue. Lip spots, patches of colour at the muzzle, are common.

Splash

Sabino

Sabino (Sb/n) is a wildly jagged paint pattern that is typically expressed through irregular patches gravitating toward the extremities and the face (although not the eyes; sabinos very rarely have blue eyes unless combined with splash). Belly spots are common, and the eges of the white markings can appear roan-like.

It is hypothesized that two doses of the sabino gene (SbSb) causes white or near-white coat colour which can be confused with dominant white, a separate pattern.

Sabino|Another Sabino

(Although, that second one is said to be "believed to be" SbSb, and could in fact have some kind of dominant white mutation.)


Rabicano

Typically thought of as a roan variant, rabicano (Rb/n) is actually closer to sabino than anything. Maximally expressed, It is characterized by dense white hair on the flank and at the dock (base of the tail). A minimal rabicano might only be recognized by sparse white hairs at the dock, which causes "Skunk Tail," or white tail hair sprouting from the base of the tail. Rabicano roaning often spreads with age. True rabicano is a dominant trait, however there are other genetic mutations not fully undertsood which can cause similar white ticking.

Loud Rabicano


Dominant White

I could go on about dominant white all bloody day, and if you're really interested in it, I do suggest reading the very good Wikipedia article on the subject, but the basics go as follows:

Dominant White exists as 11 mutations in the KIT locus, each separately heritable. In general, those which are completely white without any pigmented hair also have pink skin and "glass" (blue) eyes. Those with pigment typically have dark skin under the pigmented areas, and dark eyes. This is because rather than diluting or modifying the "melanocytes," cells that produce eumelanin and phaeomelanin, mutations of KIT such as dominant white completely remove them.

Look at this picture: [link]

On the left, the skin of a normal horse. On the right, a DW. KIT protein is stained blue, and melanocytes are stained brown. Observe the reduced KIT activity and total lack of melanocytes in the unpigmented skin of the white horse.

For descriptions of specific KIT mutation DWs and their expressions, read the Wikipedia article, under the heading "Allelic series.": [link]

Thoroughbred Dominant White families include W2 (From KY Colonel, including the famed Patchen line), W5 (Puchilingui and descendants), W6 (only known to exist in one horse, spontaneously) and W7 (unknown origin).

Dominant White (W2)|Dominant White (W5)|Dominant White (W5)|Dominant White (W1)

(Note that on the page of Puchilingui's babies, many are referred to as sabino. This is false. Puchilingui is a DW mutant, and most of his loud babies are DW as well.)

The Leopard Complex

Incredibly, the Leopard complex (Lp/n) is even less fully understood than the KIT mutations.

The gene can cause various patterns, although the reasons for their doing so is unknown as of today. It is known that in addition to the Leopard complex, another series of genes determines the extent of white patterning (the exception is in LpLp fewspot individuals).

Leopard Spotting

Although the leopard complex is typically completely dominant, leopard spotting patterns almost behave as with incomplete dominance. nLp individuals are more likely to display large, abundant spotting patterns, while LpLp have more white on them and may even be born with barely any pigment at all - these are called "fewspot."

All horses with the leopard complex have white sclera in the eye, mottled skin, striped hooves and (usually) a sparse tail.

Leopard|Fewspot

Other patterns

As I said, the leopard complex is not yet really understood, but the same gene is thought to control other patterns such as blanket, snowflake and varnish roaning.

Blanket horses have a large expanse of roan-edged white on their rumps. The size may vary, and when combined with typical leopard spotting, may have spots on it.

Blanket

Snowflake is characterized by small white spots or flecks all over a solid body. The extent of the white usually increases with age.

Snowflake

Varnish roans are born nearly solid and gradually lighten with age.The lower legs, cheeks, elbows and so forth often keep their base colour or are the last to lighten.

Varnish Roan

There may also be solid horses with the leopard complex. These typically only have one copy of the Lp gene (i.e. are heterozygous, nLp) and are weak in whatever the heck genes that control extent of white. However, they are recognizable by the fact that they have the mottled skin, white sclera, striped hooves and sparse tail of other appaloosa-type horses.

Solid Leopard


Other patterns

There are, of course, all kinds of colours and patterns not yet explained. Brindle, for example, has been found to crop up entirely by random mutation. Sometimes it's even caused by chimera--when two zygotes fuse together and the resulting foal has two whole sets of DNA. Tetrarch, Bend Or and Birdcatcher spots originated in random Thoroughbred mutants and were passed down generations. Research goes on, as research does, and gradually the scientific community is learning more about exactly what causes the wide variety we've come to appreciate today.




Questions? Ask me! Did I make a mistake in coding this ridiculously long journal entry? Tell me! Wanna know possible genotypes for your real/HARPG horse? Ask me! Seriously, I love this stuff.

SCIENCE ARE AWESOME.