Equine Coat Color Genetics, Part 1: Black, Chestnut, Bay
If I breed a gray mare to a bay stallion, what color will the foal be? If I bred two palominos, how did I end up with a chestnut foal? Equine coat colors actually follow some fairly straightforward rules – in fact, the same ones discovered by Mendel and his infamous peas that you may have learned about in biology. The first thing to understand is that each horse has two complete pairs of chromosomes – one that came from its sire, and the other from its dam. This means it has two copies of every gene, one from mom, and one from dad. The way the two copies of each gene interact with each other, as well as the interaction between separate genes, is the basis for all things genetic, including color.
We use letters to identify which types of each gene (which allele) the horse has inherited. Capital letters identify the dominant allele, and lower case letters stand for a recessive allele. Most of the time, recessive traits or characteristics are only observed if the horse inherits the recessive allele from both parents.
If for example there was a single gene for speed, (there’s not, but for example), then the letters we might use would be ‘F’ for fast, and ‘f’ for slow. If a horse was ‘FF’ (got ‘fast’ from both parents), it would be fast, and if it was ‘ff’, (got ‘slow’ from both parents) if would be slow. But if it was ‘Ff’ (got ‘fast’ from one parent and ‘slow’ from another, then it would still be fast, because ‘fast’, big ‘F’, is dominant to ‘slow’, little ‘f’. The dominant allele trumps the recessive one.
Another way to look at this:
FF = fast horse
Ff = fast horse
ff = slow horse
The ‘extension’ gene: Black, or Red.
The first gene you have to understand when talking about horse colors is the ‘Extension’ gene. Never mind its name, think of this gene as the “black or red” gene. The letters are ‘E’ for black, and ‘e’ for red (chestnut). Black, big ‘E’, is dominant to red, little ‘e’. All horses have this gene, (all horses have every gene), even ones that are colors other than black or chestnut. The other colors exist because of the way other genes interact with the extension gene.
EE = black-based
Ee = black-based
ee = red (chestnut)-based
You might be wondering, if black-based is dominant to red-based, why are there so few black horses compared to bays or chestnuts? Keep reading.
‘Aguti’ makes Bay.
The ‘Aguti’ gene controls black distribution across a horse’s body. Since red-based horses have no black, they will have two copies of this gene, but they won’t play in role in determining the horse’s color. On a black-based horse, the aguti gene determines whether the black will be all over the horse or only on certain parts (like the mane, tail, and legs). There are three alleles for this gene: ‘A’ restricts black distribution the most, (black main, tail and legs only), ‘At’ restricts black a little, and ‘a’ does not restrict black at all.
AA = black restricted to main, tail, legs
Aa = black restricted to main, tail, legs
AtAt = somewhat restricted black
Ata = somewhat restricted black
aa = black is unrestricted, black all over the body
So, combine this with what you know about the extension gene and you get:
EE or Ee (black based) with AA or Aa (restricted black) = Bay horse.
EE or Ee (black based) with AtAt or Ata (some black restriction) = Seal brown horse.
EE or Ee (black based) with aa (unrestricted black) = Black horse.
The reason for few truly black horses is that there are many black-based horses, but most of those turn out bay. Why? Because the big ‘A’, which restricts black, making bay, is dominant to the little ‘a’, and there happen to be a lot more big ‘A’s floating around in the horse population than little ‘a’s.
Remember, the aguti gene does not matter on red-based horses.
It only controls black. So:
ee (red-based) with AA, Aa, or aa (or any combination of aguti alleles) = Chestnut horse.