The term phenotype refers to everything that we can see about a being, from morphology and colour to behavior. In horse colour genetics, we specifically refer to the horse's coat colour. The opposite, genotype, refers to the being's genes and hereditary information.
- Genotype: all genes
- Phenotype: everything we observe on the outside of a being, but it can be influenced by genetics and environmental factors alike.
When we see a horse with dark skin and common red hairs all over its coat and points (mane, tail, lower legs, ear tips), we may say its phenotype is chestnut . From this, we can gather its genotype is likely ee. But we cannot say whether the silver dilution is present, as it does not show on a chestnut coat.
Now, if we can tell the horse is a suffolk punch (because of its characteristics), then we may say the horse likely doesn't carry silver, as it has not been observed in suffolk horses before. But it still remains a guess until we test the horse's DNA.
So, phenotype tells us what a horse looks like and it can give us clues to a horse's genotype, but usually not a definitive answer.
Let's say we take the ordinary red horse from the first example above and paint it so it appears to be black (not recommended). Then we call the horse's phenotype black, but genetically, it's still a chestnut.
Now, we have a DNA sample from an unknown horse. It can be a random animal whose DNA has just been submitted for registration, or it can be ancient DNA from a horse that lived centuries ago. When we do a DNA test, it tells us the horse has the genotype Gg. Easy, this horse is a grey ! But we do not know whether it was a white grey, or a dappled grey, or a flea-bitten grey. Such colour details may partially be caused by genetics we do not yet know, but they are also influenced by age. If this horse was relatively young and greyed out real slow, it may not even have been identified as a grey by a random observer!
Genotypes tell us what a horse is likely to look like on the outside (or what it may pass on to its offspring), but other factors as age or food can still leave us quite a surprise and result in a horse we would not at first have identified to belong to the specific DNA sample.