Let’s start simple. In the context of inheritance, a gene is a segment of DNA that produces an effect, like making your hair brown. Genes can tell your cells to make a protein, or they can control how other proteins are made, or they can regulate other genes directly, but in the end they do something.
A locus is the physical place on the chromosome where a gene is located. The plural is loci. This term is often synonymous with gene.
Many genes have multiple different versions that can produce different effects. These different forms are called alleles. Since we’re focusing on coat color genetics, lets use epistatic white as an example. Epistatic white simply removes all color from a cat’s coat, leaving them white. If a cat isn’t white, they still have the epistatic white gene, they just don’t have the epistatic white allele, the particular version of that gene that would make them white.
Animals and some plants have two copies of every gene, with one copy inherited from each parent. An individual’s genotype is the combination of alleles that an individual has. This is contrasted with phenotype, what the individual actually looks like.
To see how these are different, let’s go back to epistatic white. When the cat has two non-white alleles, it’s not white, and when it has two white alleles, it is white. In either of these cases, it is homozygous, meaning it has two of the same allele. But what if it is heterozygous, having one of each allele?
With epistatic white, heterozygous cats are white. Therefore, epistatic white is dominant to non-white, and non-white is recessive to white. Dominance does not mean a trait is more common or more likely - it just means that when there are two different alleles, the more dominant one is the one that shows. We denote this by using capital letters for dominant alleles and lowercase letters for recessive alleles.
This also means that an epistatic white cat could be either homozygous or heterozygous - there is no way to know unless we know enough about their ancestry, breed them, or get them genetically tested.
Many alleles have this dominant-recessive relationship, however, there are exceptions. For example, two alleles can be codominant, where both traits are expressed. An example of this is tortoiseshells, who have one “black” allele, and one “red” allele, giving them patches of color. Or, alleles can exhibit incomplete dominance, where heterozygotes exhibit an intermediate trait, such as how mink is an intermediate between colorpoint and sepia.
To further throw a wrench into things, there are traits that seem to fall along a spectrum, not neatly into two or three boxes. There are two causes for this. The first is variable expressivity, where the trait is caused by a single gene, but unknown factors or random chance can cause the trait to appear different. An example of this is white spotting, which can range from almost entirely colored cats to almost entirely white cats. The other possible cause is that the trait is polygenic, meaning there are many different genes that each have a small effect. This is the case with the “redness” of red tabbies. Practically speaking, this means that the offspring’s phenotypes will usually fall somewhere in between that of the parents.
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