Epistasis and Bay, Black & Chestnut
by C. Williams

Epistasis refers to the presence of a certain allele or allele combination at one locus, which affects the expression of the genotype at a completely different locus. For the most part, this can be thought of as "masking". The Epistatic locus, when the right combination of alleles is present, masks the expression of the Hypostatic locus.

The best example of Epistasis in the horse, is the basic determination of Bay, Black and Chestnut colors.

All horses, underneath all other modifying colors and patterning are either Bay, Black or Chestnut. A person must be able to understand the genetic mechanism that creates these colors, in order to truly understand horse colors in general.

The Extension Locus

Horses are capable of producing two basic pigments within the hair shafts.

• Eumelanin = black pigment
• Pheomelanin = red pigment.

The Extension (E) locus controls which of these two pigments the horse is capable of producing. There are two primary known alleles at the E locus: a dominant E and a recessive e.

(Note: Sponenberg uses the nomenclature of E+ for the dominant E allele.)

The recessive e allele allows a horse to produce only Red Pigment or Pheomelanin in the hairs of its coat.

The dominant E allele allows a horse to produce Black Pigment or Eumelanin as well as Red Pigment (Pheomelanin) in the hairs of its coat.

EE or Ee Black Color

ee Chestnut Color

That's pretty simple and straighforward... however... we now need to add in the second locus.

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The Agouti Locus

The Agouti (A) locus controls where on the horse the black pigment shows up, (if the horse is capable of producing black pigment). The alleles involved here are a dominant A and a recessive a. The dominant A allele causes the black pigment to be restricted to the horse's Points.

Points of the horse for purposes of color determination include:

• Lower Legs
• Mane, Tail and Forelock
• Muzzle
• Eartips

The recessive a allele, does nothing. Therefore:

AA or Aa Bay Color

aa Black Color

Together, the E and A loci determine:

• whether or not a horse can produce black pigment
• where on the body the black pigment appears

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When dealing with the effects of two or more loci, a special shorthand is often used to indicate the presence of at least one dominant allele. In this case:

• A- = AA or Aa
• E- = EE or Ee

The second allele of the pair is irrelevant, because only one dominant allele is required to produce the effect.

These two loci together, E and A are Epistatic. What occurs at one locus, determines what happens as a result of the other. Geneticists consider that the E locus is epistatic to the A locus. What happens at E may cover up what happens at A.

More specifically, a horse who is chestnut, ee has no black pigment. Therefore, the A locus, which controls black pigment... has no effect in this case.

In the terms of epistasis:

The E locus is epistatic to (or masks) the A locus

The A locus is hypostatic to (or is masked by) the E locus.

It is important to note that even though a locus doesn't have any visible effect... doesn't mean the horse isn't carrying any alleles at that locus... they most certainly are! But those alleles won't be able to show themselves, until the right conditions occur in a later generation.

Possible Allele Combinations

	A E	a E	A e	a e
A E	AA EE Bay	Aa EE Bay	AA Ee Bay	Aa Ee Bay
a E	Aa EE Bay	aa EE Black	Aa Ee Bay	aa Ee Black
A e	AA Ee Bay	Aa Ee Bay	AA ee Chestnut	Aa ee Chestnut
a e	Aa Ee Bay	aa Ee Black	Aa ee Chestnut	aa ee Chestnut

If you study the chart above, you'll note that whenever a horse is ee-- recessive chestnut, it doesn't matter what alleles are present at A. Whether A is homozygous, heterozygous, dominant or recessive alleles, the horse remains Chestnut. This is why, when you breed two chestnuts together, you always get some form of chestnut.

For black color to show itself, the horse has to be "genetically black" at the E locus (carry at least one dominant E allele) ... AND the horse must also be recessive aa.

This may help to explain why black color can be so elusive to breed for in horses, and why it can suddenly pop up unexpectedly.

Unfortunately, there's a few additional factors when it comes to determining basic Bay, Black and Chestnut colors... which will be presented in the next section...

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Views expressed herein are those of the writers and compilers of the various information. Reference sources are cited where applicable. Copyrights are the property of the respective authors.