I spoke before about all cats being basically black, genetically. I also discussed how this is actually dark brown, and is known by several different names, such as seal, or natural.
The brown gene can be expressed different ways and the different expressions (of any gene, not just this) are known as alleles. There are three alleles in this instance; brown (black, seal), a warmer brown called 'chocolate', or a rich, auburny colour called cinnamon. Cinnamon is not an accepted colour in the Tonkinese, but it's worth including it in the discussion.
The brown gene is not sex linked, like the orange gene is, so all cats will have two alleles in their genetic profile. These can be the same, for example, brown and brown, or different, for example chocolate and cinnamon. Having two alleles the same is known as being homozygous, two different alleles is known as heterozygous.
So which allelle eventually determines the cat's colour? Well, some allelles are dominant over others. Brown is dominant to chocolate and cinnamon. Chocolate is recessive to brown and dominant to cinnamon, and cinnamon is recessive to both brown and chocolate. A pecking order, if you will.
So a black (brown, seal, natural) cat might be homozygous (brown/brown) or heterozygous (brown/chocolate or brown/cinnamon) but it will still be a brown (black!) cat.
My black cat Sofia could be brown/brown, brown/chocolate or brown/cinnamon, genetically.
It's important though, as the recessive alleles can be passed on genetically, and when, for example, two chocolate alleles are passed on, one from each parent, the kitten will be chocolate and not brown. Which is why, in the cat fancy, you might see a cat described as 'brown, carrying chocolate' (for example). That means that the cat is heterozygous for colour. It's colour is brown, as it has one brown allele which is dominant. But it also has one chocolate allele, which it can potentially pass on to its offspring.
clear as mud- or chocolate- eh?
It's worth mentioning that the orange gene masks the colour gene, however it presents itself- brown, chocolate or cinnamon. Also the important word here is mask- not replace. The colour gene will be hidden but genetically still be present and will still be passed down to subsequent generations. This is what I got wrong last year!