Cats have genes for orange fur and black fur as well as genes for white patches. If cats have genes for both orange and black fur plus white fur, they're calico, and they're almost always female. Male cats can also be calico, although they're quite rare.
The Orange and Black
The genes that control orange and black cat fur are on the X chromosome. Females, XX, have two and males, XY, have one.
These gene varieties, called alleles, express as orange or black, never both, but female cats can have one of each.
The Y chromosome is smaller than the X chromosome and carries fewer genes. One of the absentees is the orange-black coloring gene. As such, multicolor orange and black coats are a sex-linked trait associated with females, not males.
Cats can also carry genes for piebalding. When activated, these genes manifest as patches of unpigmented skin -- that is, white fur.
This is completely separate from the genetic expression of orange fur, black fur or both. It has nothing to do with a cat's gender, either, because it isn't linked to sex chromosomes.
Regardless, it's a requisite trait for calico cats. Cats with orange and black fur who don't have piebalding are tortoiseshell cats -- not that there's anything wrong with that.
Female Cat Coloring
Female cats can carry two alleles for orange fur, two alleles for black fur, or one of each.
In the first case, the cat is orange. In the second case the cat is black.
The third case is more complicated. Theoretically, the orange-fur gene is dominant, but that's not how the genetics play out. One of the X chromosomes in a growing female embryo is randomly inactivated in each cell. (It supercoils into a structure called a Barr body via lyonization, if you want to get technical about it.) Cats with both orange and black alleles usually have patches of each color -- some with inactivated orange-fur genes, some with inactivated black-fur genes.
Add piebalding genes into the mix, and you have the classic calico cat.
Male Cat Coloring
The expression of cat color genes in males is straightforward: Cats with alleles for orange fur are orange, and cats with alleles for black fur are black.
Occasionally, though, male cats are born with an extra X chromosome, which makes them XXY instead of XY. This is called Klinefelter Syndrome, and it's rare. Such cats are almost always sterile, unless they have a genetic anomaly that's rarer yet.
All XXY male cats carry two genes for coloration and are subject to the same orange-black fur color outcomes as their sisters.
If an XXY male cat has piebalding, too, it's a rare elusive male calico cat.
- Cotton image by carroll2199 from Fotolia.com