GUIDE · EQUINE COAT COLOR GENETICS
Learn which genes influence horse and pony coat colors, then explore how EquiGenes estimates possible foal coats from parent information and pedigree.
Coat color is polygenic, and some patterns show variable expression. The model simplifies these effects to make inheritance easier to follow; it is not a substitute for genetic testing or advice from a veterinarian or coat-color specialist.
01 / GENETICS
A horse or pony foal inherits one copy at each locus from its dam and one from its sire. The combination of variants, called its genotype, contributes to its phenotype: the coat we can observe.
The Extension locus (MC1R) affects the production of black or red pigment. Agouti (ASIP) influences where black pigment appears: with a functional Extension allele, it helps distinguish bay from black. In this representation, chestnut corresponds to the recessive e/e model.
Cream (SLC45A2) is represented with one or two copies; Dun (TBX3), Champagne (SLC36A1), and Silver (PMEL) use simplified variants. Their visible effect can depend on base color: Silver, for example, mainly affects black pigment.
Tobiano, Sabino 1, Splashed White, Leopard complex (LP with PATN1), and classic roan are included as simplified loci or locus combinations. White patterns can vary widely in extent and overlap, so their appearance does not always fit a single category.
Loci are treated as independent in the calculation, though genetic linkage and interactions can occur. Pattern expression, rare variants, bloodline effects, and actual allele frequencies are not estimated. Percentages therefore reflect the model’s assumptions and the information entered.
02 / CALCULATION METHOD
The calculation follows allele transmission one locus at a time, then groups foal genotypes into visible coat categories.
For an observed coat (phenotype), the model collects genotypes it considers compatible with that appearance. For a known genotype, it uses the two entered alleles at each locus. Phenotype alone does not always reveal whether a horse carries a recessive variant.
When grandparents are entered, the model simulates the genotypes they can pass to the parent. It keeps genotypes compatible with both the parent’s phenotype and pedigree. Without grandparents, compatible phenotype genotypes receive equal weights; this is an assumption made because population frequencies are unavailable.
At each locus, each parent passes on one of its two copies. If the copies differ, each has a 1-in-2 chance in this model. The weights of possible parental genotypes are accounted for, then maternal and paternal transmissions are combined.
Probabilities across loci are multiplied to form possible foal genotypes. Each combination is converted to a phenotype using the model’s rules; probabilities for combinations with the same coat are added. Displayed results are rounded to two decimal places.
At a locus where both parents are heterozygous (A/a), each can pass A or a with a one-in-two chance. The combinations are theoretically A/A: 25%, A/a: 50%, and a/a: 25%. The associated appearance then depends on dominance and the other loci.
In Advanced or Expert mode, the section below the probabilities shows the parental genotypes considered, their weights, and then the outcomes at each locus. It makes the assumptions for this specific mating visible. Probabilities across different loci are not added together; each describes one part of the genotype.
The model evolves as knowledge and supported coat colors expand. For breeding or health decisions, confirm genotypes with a qualified laboratory.
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