We use the terms dominant and recessive to describe the effects the alleles of one gene have on the other copies of that same gene. This can also be seen in the abbreviations used when writing them down: a dominant allele is capitalized, while a recessive one is denoted by lower cased letters.
A dominant allele will always show (unless it cannot due to other factors), no matter the variant of the second allele. A good example is the black allele on the extension gene. The black version (E) always turns a horse's coat black, no matter the form of the second allele. From phenotype (coat colour) alone, it is impossible to determine whether the horse has two copies of E, or if a second, recessive allele is hidden behind it.
The opposite, a recessive allele, will always be suppressed. It only shows when the other allele at the same gene is of the same variant. This situation, called homozygous recessive, will always show (unless it is prevented of doing so by other factors) and will always pass on to the horse's descendants, though it will depend on the second copy obtained from the other parent whether is will show or remain hidden.
A third option is called incomplete dominant. It means one allele always shows, but its effect is different when a second copy of the same allele is present. A good example of this would be the cream gene, where one copy turns red pigment to yellow or gold, while two copies result in a overall cream-colored horse.
The fourth option is best explained by using the pearl alleles, a variant of the cream gene. It is often referred to as incomplete recessive, though the term is not entirely fitting. Pearl does not show in heterozygous state, but only when it is paired with another pearl allele (homozygous recessive), or with a cream allele of the same cream gene (incomplete recessive).
Sometimes we use the terms dominant and recessive also in conjunction with genes or colour names, though this usually requires some extra knowledge. For example, flaxen is often denoted as recessive, as the trait only seems to appear when the horse is homozygous for it.
The grey gene has two known alleles: G and g. The capital version is always expressed when present: it turns the coat white. The lower capital allele, g, is recessive and does not influence the horse's coat colour. This gives the following results:
- GG = grey
- Gg = grey
- gg = not grey
All non-grey horses have to be gg, for the presence of a single G would have turned them grey. A grey horse has to always have at least one G. But upon seeing the horse, it cannot be ascertained by vision alone whether the horse is homozygous or heterozygous for grey. It can both be Gg and GG.
To verify this, one can look at DNA test results, or check wth the horse's pedigree and/or descendent. If just one of them is not grey, the horse itself cannot be GG and always has to be Gg. If it wasn't, it couldn't have passed on the g, making the foal a non-grey.
Note: it has to be said the grey phenotype can appear quite late in a horse's life. A non-grey foal from at least one grey parent can be believed to carry gg, while in fact it has at least one G. The process of turning grey can appear much later in the foal's life and therefore surprise breeders with sudden grey foals.
Alleles can be dominant and recessive at the same time. The agouti allele is often theorized to have more than two alleles. For this example, we assume it has four:
- a, which means a black horse is unaffected by agouti
- At, which is used to denote the colour seal brown
- A, which denotes a bay colour
- A+, theorized to be the wild type bay
Much is not yet known of these variants, but for the purpose of this example we will assume the following dominance:
- A+ is dominant over A, At and a
- A is dominant over At and a
- At is dominant over a
- a is always recessive
This means At is dominant over a, but recessive to A and A+. The same goes for A; it is dominant over a and At, but recessive to A+.
Note: As black always becomes bay in the presence of the dominant agouti alleles, it is often said agouti is dominant over black, referring to the colour instead of a particular allele.