Extension: can the coat make black pigment?
The MC1R gene and its E, e and eᵃ versions
Two chestnut-based parents produce a chestnut-based foal, while two bay horses can also have a chestnut foal. Extension explains this difference. Other genes can then change the coat color you see.
Explanations and diagrams reviewed on 3 November 2026
Extension and Agouti: the combinations behind each base
Read each line from left to right: the pair at Extension (MC1R), then the pair at Agouti (ASIP). These lists show the combinations that can give each base, not their probabilities in a cross.
Start with the horse you can see
Chestnut hair is based on red pigment and ranges from light copper to very dark liver, with red or lighter manes and tails. A chestnut does not have the genetically black mane, tail and lower legs typical of bay. Both bay and black horses can make black pigment in their hair.
These are base colors. Dilutions, white markings and graying can change their appearance later, so a very dark horse is not necessarily genetically black.
What the letters mean
Extension is the usual name for the gene with the scientific symbol MC1R. This gene contains instructions for a receptor, a protein that receives signals. The receptor is involved in determining which pigment is produced: black-brown eumelanin or red-yellow pheomelanin.
A horse inherits one version of this gene from each parent. These versions are called alleles. E allows black hair pigment even when the other allele is a recessive version: E/E, E/e and E/eᵃ all allow black pigment. Without E, the pairs e/e, e/eᵃ and eᵃ/eᵃ give a chestnut base. The rarer eᵃ is another recessive version.
Example: two E/e parents
Suppose DNA tests confirm that both parents are E/e. Each can pass E or e with equal probability. Every conception therefore has a 25% chance of E/E, 50% of E/e and 25% of e/e. Only e/e is chestnut-based in this example. Four births need not include exactly one chestnut.
An E/E or E/e foal may have a bay or black base. That distinction also depends on Agouti, the ASIP gene. It determines whether black pigment is mainly restricted to the mane, tail and lower legs or can extend over the body.
What a DNA result adds
Appearance cannot distinguish E/E from E/e or E/eᵃ. An E/E parent always passes E and cannot produce a chestnut-based foal in this model. Two chestnut-based parents each pass a recessive version, so their foal is chestnut-based even if other genes change its final appearance.
A chestnut can carry any Agouti pair without showing its effect, because there is no black hair pigment for Agouti to redistribute. Agouti needs its own test. For Extension, check whether the laboratory tests both e and eᵃ before interpreting the result.
An example: what could this foal inherit?
MC1R
Both demonstration horses have the exact pair shown. These examples explain inheritance; they do not use the mare and stallion entered in the calculator.
MareE/e
StallionE/e
All possible pairs at each conception
- E/E25%
Two copies of E
- E/e50%
One E and one e
- e/e25%
Two copies of e
Where the explanations come from
Laboratory resources explain which variants are tested and how to read their results. Research papers describe the evidence, discoveries and remaining uncertainties. Each article links its explanations to the relevant sources. Published titles stay in their original language so you can find the exact work.
1 · Laboratory explanation
UC Davis VGL — Red Factor2 · Laboratory explanation
UC Davis VGL — Agouti (Bay/Black)3 · Research paper
Marklund et al. (1996) — MC1R and chestnut coat colour