From the former user Harlequin Raven:

Okay, I suppose I should do my job as genetics guru.

First, let us go over the basic terms and ideas.

Genes and Alleles
People tend to think use the word "gene" incorrectly. For the sake of ease, I started off this guide using it how it is often used. However, it was bothering me, so I am changing it.

A GENE is a particular section of DNA that codes for a protein. Proteins are what give us the actual visual effect such as a change in coat colour. An ALLELE is a version of the gene. For example, the tobiano gene has two different versions, therefore two different alleles. One allele is solid (no white spots) while the other is the allele for tobiano (white spots).

Inheritance
Think of a bully and a kid who gets picked on. Whenever the bully is around, the weaker kid is going to stay hidden. The only time the weaker kid will come out is when the bully is not around. The bully is the "dominant allele" while the weaker kid is the "recessive gene."

Dominant: This is a gene that is "stronger" than another. It can "hide" other genes. There only needs to be ONE copy of this gene in order to show up. Bay is an example of a dominant colour. Bay is dominant to black.

Recessive: This is a gene that is "weaker" as compared to another. It can "hide" behind other genes. A recessive gene will never show up in the presence of a dominant gene. Remember the bully. A completely recessive gene (one that is weaker than all the others that can be paired with it) can ONLY show up if there are TWO of it. Black is an example of a recessive colour. Black is recessive to bay.

Incomplete Dominance: (AKA Codominance). This is where things get a little trickier. With incompletely dominant genes, they "share" their traits. A good example is snapdragon flowers. A red snapdragon crossed to a while snapdragon will produce a snapdragon with pink flowers. The pink flowers are a combination of the two genes. Neither one is stronger or weaker than the other. A perfect example in horses are the cream genetics. Ccr is cream, whereas ccr is non-cream. A chestnut is ccrccr. A cremello is CcrCcr. A palomino is a combination of the two, so is Ccrccr. A palomino is (more or less) halfway between chestnut and cremello in colouring, perfectly showing how incomplete dominance works.


Other Terms and Ideas

Phenotype: This is the observable traits. If you say, "That horse is 16 hh, is black, and is male," you are describing part of the phenotype.

Genotype: This includes are the actual genes involved, whether their effects are observable or not. If you say, "That horse is a bay carrying chestnut," you are describing part of the genotype.

Chromosome: A single, long (relative to scale) piece of coiled DNA that contains many different genes. Normally, chromosomes come in pairs. Horses have 32 pairs of chromosomes, or 64 total chromosomes. Rarely an organism will have an extra chromosome, but it usually results in some sort of genetic defect such as Down's Syndrome in humans or infertility in male calico cats.

Locus: (Plural "Loci"). A locus is a fixed position on the chromosome. This describes what we normally think of as a "set" of colours. For example, Ccr and ccr are both on the "C Locus". There are two "slots" per locus (remember, chromosomes come in pairs, so each one has a "slot" to fill on that fixed position). One slot is filled with a gene inherited from the sire, and the other is filled with a gene inherited from the dam. This is why normal horses can never have more than TWO genes on a particular locus. Generally speaking, you could not have a horse that is Ccrccrccr, for example.

Now I am going to talk about individual colour loci and alleles.

If there is a space left after or before an allele, it means that any of the allele in that particular locus could be in that spot. For example, if you have a bay horse, you might not know if it carries black or not. So you would write it out A_.

Base Colours
A Locus - "Agouti"
The term "agouti" actually refers to a South American rodent. The term is often applied to the main dominant or "wild" colour of a species. Agouti in cats is tabby, agouti in horses is bay.

A - Agouti: Bay
a - Non-Agouti: Black

A is dominant to a. A true black horse (or any 'aa' genotype horse) can never produce a bay when bred to another 'aa' genotype horse. However, a bay (or any 'A_' genotype horse) can produce blacks (or another 'aa' genotype colour).

Examples of agouti colours: Bay, buckskin, perlino, brown, bay roan (sometimes called purple roan), bay dun.

Examples of non-agouti colours: Black, smokey black, smokey creme, blue roan, grullo.


E Locus - "Extension"
The term "extension" actually refers to whether or not the allele allows black to "extend" across the coat.

E - Extension: Black
a - Non-Extension: Red

E is dominant to e. A true chestnut horse (or any 'ee' genotype horse) can never produce a black when bred to another 'ee' genotype horse. However, a black (or any 'E_' genotype horse) can produce chestnuts (or another 'e' genotype colour).

Examples of extension colours: Bay, buckskin, perlino, brown, bay roan (sometimes called purple roan), bay dun, black, smokey black, smokey creme, blue roan, grullo.

Examples of non-extension colours: Chestnut, palomino, cremello, strawberry roan, strawberry dun.



Dilute Colours
Dilute alleles are alleles that reduce the amount of pigmentation that is allowed to show.

Ccr Locus - "Cream"
As was mentioned before, this locus shows incomplete dominance.

Ccr - Creme
C - Non-cream

Ccr and C are incompletely dominant or codominant. They "share" their traits. A horse that is CcrCcr will be a double dilute and will be very pale with blue eyes. A horse that is CC will be normal and will not be diluted at all. A horse that is CcrC will be approximately halfway in between.

Examples of double cream: Cremello, perlino, smokey cream.

Examples of single cream: Palomino, buckskin, smokey black.

Examples of non-cream: Chestnut, bay, black.



Ch Locus - "Champagne"
I have no idea why they refer to it as "champagne," other than maybe because champagne is a light colour.

You will have to bear with me a little on how I "show" the alleles, as different places refer to them differently. I will use the fairly standard upper case means dominant, lower case means recessive.

Ch - Champagne
ch - Non-Champagne

Ch is dominant to ch. A non champagne horse (chch) can never produce a champagne when bred to another non-champagne horse. However, a champagne can produce non-champagnes.

Examples of non-champagne colours: Everything BUT champagnes.

Examples of champagne colours: Classic champagne (black + champagne), sable champagne (seal brown + champagne), amber champagne (bay + champagne), gold champagne (chestnut + champagne).



D Locus - "Dun"
Dun horses almost always have a dorsal (back) stripe. Sometimes (especially in dilutes), the dorsal stripe can be very hard to see. They often have zebra-like stripes on the legs, but this is not always the case.

D - Dun
d - Non-dun

D is dominant to d. A true non-dun horse (dd) can never produce a dun when bred to another non-dun horse. However, a dun can produce non-duns.

Examples of dun colours: Dun (AKA bay dun or zebra dun), red dun, grullo/grulla

Examples of non-dun colours: Everything else! Be careful, in real life, bay-based horses sometimes have countershading on the back that can resemble a dorsal stripe!



Prl Locus - "Pearl"
Pearl practically needs an entire explanation by itself. It is the first allele I will be discussing that has to be in combination with another allele or set of alleles to show up. First things first...

Prl - Non-pearl
prl - Pearl

Pearl will ONLY show up in combination with either 'ee' (non-extension) or creme alleles. Examples:

Apricot: Chestnut with two pearl alleles (ee prlprl)
Apricot Dun: Strawberry dun with two pearl alleles (ee prlprl D_)
Apricot Roan: Strawberry roan with two pearl alleles (ee prlprl R_)

Pearl can also show up in a heterozygous form (one pearl allele) IF it is in combination with a creme allele. CcrC Prlprl is what that would look like. There is speculation that the pearl allele is actually on the creme locus with Ccr and C because of the way it works with it. For example, if you have a buckskin with one pearl allele, it will highly resemble a perlino. A palomino with one pearl allele will look like a cremello, etc. For the sake of the game, we will just assume that it is NOT on the same locus, so you could have a horse that is both ccrccr and prlprl.




Other Colours
ZLocus - "Silver"
Silver is another allele that must be in combination with a different allele to show up. Silver can only show up on full extension colours (black colours 'EE' or 'Ee'). Silver works on the black pigment in the coat, so if there is no black pigment to work on (as in chestnuts), it simply can have no effect.

Z - Silver
z - Non-Silver

Z is dominant to z. A non-silver horse (zz) can never produce a silver when bred to another non-silver horse. However, a slver can produce non-silvers.

Finally, I will get in deep and dirty with the more technical aspects of genetics! This is for people who just want to learn more than just what to pair to get what. It is not at all necessary for breeding in Horse Eden, but I figured some people would love to learn it, anyway!

Vocab:

Melanin: Pigment found in higher life forms (plants and animals) as well as protists. So basically things in the Domain Eukarya. It is formed from tyrosine (an amino acid).

Eumelanin: Black/brown pigment. e.g. The black points on the face, ears, legs, tail, and muzzle of a bay are caused by eumelanin bunching up in that area.

Phaeomelanin: Red/yellow pigment. e.g. The red body colour of a bay is caused by phaeomelanin bunching up in that area.

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Concepts

Some genes affect both eumelanin and phaeomelanin, while others only affect one or the other.

A: Agouti - Splits the eumelanin up onto different hairs, so eumelanin is in the points and phaeomelanin is on the body. In other animals, it causes the pigments to form bands, causing a ticked appearance. Here is a picture (no laughing at me as a kid!) of the effect in rabbits. The layer closest to the skin is formed of eumelanin so it is a blue-black colour, the middle band is phaeomelanin so it is a red-orange colour, and the top band (just at the very tip, allowing some of the orange from below to peak through) is eumelanin again so it is blackish.

* Interestingly enough, the pigment at the top of the hair shaft was the band that was laid down first! It gets laid down kind of in a chain assembly line. The part closest to popping out of the skin gets pigment first, and as the hair moves up, each section goes into the "pigmenting zone."

a: Self - Keeps the eumelanin and the phaeomelanin all mixed up in all of the hair shafts, giving a singular tone. Black is a perfect example of this. Since black pigment is darker than red pigment, the overall affect is that of a black horse. However, if you removed the red pigment, it would appear like a faded black. In rabbits, this is quite common, but in horses there is no known gene that removes the phaeomelanin.

E: Extension: This gene works entirely on the eumelanin and allows it to extend out into the hair shaft. You can see black pigment have its normal affect.

e: Non-Extension: Eumelanin is partially or totally restricted, leaving only phaeomelanin. In rabbits, you have to breed carefully for full restriction of the colour to allow the bright orange to shine through. Otherwise, it kind of muddies the colour. It makes me wonder if liver chestnuts might be chestnuts that did not fully get the eumelanin restricted, but I am not sure if that theory has already been tested by checking what pigment is in the hair shaft. LOL.

Cr: Cream - Cream works on both pigment types. It reduces the TOTAL amount of pigment in the hair shaft. It does this by limiting the tyrosine, which limits the melanin. Since eumelanin and phaeomelanin are both types of melanin, it limits both!

cr: Non-Cream: No pigment restriction.

Crcr: Since this gene is incompletely dominant, a Crcr horse has more total pigmentation than a CrCr horse. If Cr reduces pigment by 50%, CrCr would reduce THAT by another 50%. So the result would be a horse with only 25% pigment. Now, I am not sure exactly how much it reduces it, but 50% is a nice, easy number to use.

In a double does, it also removes the majourity of the pigment from the eyes, leaving blue eyes. This is an indicator of partial albinism. Many species have a lot more genes that work on the C locus than horses do. Albino animals have a complete lack of tyrosine production, meaning they have no melanin and no pigment anywhere. The red eyes are simply the red from the blood vessels! If you see an animal with bright blue (like sapphires), red eyes, or a reddish cast to the eyes, you can bet that some gene is restricting some level of total tyrosine production!

D: Dun - The dun gene is a very interesting gene. It appears to dilute pigment in only SOME areas of the body, while leaving others at full (or at least nearly full) strength. If you take a standard bay and pop dun on it, the effect of the body colour is remarkably similar to the effect of cream on bay. This is why so many people get buckskin and dun confused. However, dun does NOT dilute (or at least does not fully dilute) the areas where the primitive markings are found. The zebra-like leg bars, the dorsal stripe, etc. are not diluted like the rest of the body.

d: Non-Dun - Nothing is diluted.

R: Roan - Roan is fun! It takes certain hairs and essentially wipes out ALL melanin in them, leaving just white. It leaves other hairs with however much of each type of pigment they would normally have. The result is the salt-and-pepper appearance that we call roan!

r: Non-Roan - Normal pigmentation.

Ch: Champagne: This is another gene that reduces both types of pigment. I am not as familiar with it, so that is all I can really say on the matter. I cannot think of any other species that has a similar gene.

ch: Non-Champagne: No pigment reduction.

Prl: Non-Pearl: No pigment reduction.

prl: Pearl: Like the cream gene, it works on both types of pigment. There is speculation that the prl gene is actually on the same locus as the cream dilution gene, since it interacts with the cream gene to form double dilutes.

Z: Non-Silver: No pigment reduction.

z: Silver: This gene works ONLY on eumelanin. It reduces the amount of eumelanin in the coat, especially in the mane and tail. However, if you take a look at silvers, many will have a more brownish cast (less eumelanin allows more phaeomelanin to show). Many also have dapples where the production of eumelanin is very weak. Because it only works on eumelanin, horses without any eumelanin in the coat (chestnuts, palominos, cremellos, red dun, etc.) are not affected.


Phew! That took a long time, so I will work on the pigment distribution in patterns later!

HOLY CRAP THANK YOU!
If it's alright with you, I copied and pasted all this info onto a Word Document so I could study later!
Thanks again!

o.o Woah,that looks confusing from a glance xD

Thank you. So much clearer now.

I love the lengthy explanation, it's exactly what I'm looking for. Trying to figure out the genetics of my top stallion.

Thank you so much for posting this, Kuewi! I had a quiz on horse genetics the other day, and because of this guide, was able to answer almost every one right!

what geno is best to produce amber dun?