Basic Genetics
For any one trait, a rabbit will have two genes--one from its sire, the other from its dam. These genes can be the same, or different. When both genes for a trait are the same, the rabbit is said to be HOMOZYGOUS for that trait. For a rabbit to be homozygous, BOTH parents must have had that gene. When the genes are different, the rabbit is HETEROZYGOUS. ("Homo-" means "same", "hetero-" means "different"). When a rabbit is homozygous for a trait, it will have the look that gene makes. When a rabbit is heterozygous, the genes' dominance come into play.
Most simply, genes are either DOMINANT or RECESSIVE. A rabbit which has the looks of a completely recessive gene is always homozygous for the recessive trait, so many people will simply say that the rabbit is the recessive trait. If a rabbit is heterozygous, the dominant gene determines what the rabbit looks like. The recessive gene will not affect how a heterozygous rabbit looks, but can be passed on to the rabbit's offspring.
Parents have two genes for every trait, but only pass one of those genes to each offspring. Think of it as a coin flip. Each side of the coin represents each gene. If a rabbit is homozygous, both genes and sides of the coin will be same (two heads or two tails). If a rabbit is heterozygous, the sides of the coin will be different (a heads and a tails). When a rabbit inherits its genes from its parents, it gets the result of two coin flips: one from the sire, one from the dam.
To demonstrate this, we'll use a tool called a Punnett Square. It is a graphic representation that geneticists use to predict what the offspring will look like. To make a Punnett Square, you draw a 2x2 grid. Across the top, label the columns with each of the possible genes from one of the parents. Down the side, label the rows with the possible genes from the other parent. Inside each of the grid squares, record the combination of the column label and row label. Here's an example of two heterozygous rabbits:
| B | b | |
|---|---|---|
| B | BB (homozygous black) | Bb (heterozygous black) |
| b | Bb (heterozygous black) | bb (brown) |
In the above example, both parents are heterozygous for the black trait, which would be written as Bb. Each parent has a B (black) gene, which is dominant (indicated by being a capital letter), and a b (brown) gene, which is recessive. Because black is dominant to brown, the rabbits will look black. The table shows all possible genetic combinations for the offspring. Some will get a B (black) gene from both parents, making those offspring homozygous blacks. Others will get a B (black) gene from one parent and a b (brown) gene from the other parent, making them heterozygous blacks, just like the parents. Still others will get a b (brown) gene from both parents. Since there is no black gene to override the brown gene, these offspring will look brown.
Incidentally, the Punnet Square also gives you the likelihood of getting any particular offspring. In the above example, 1/4 of the squares are BB (homozygous black), 2/4 of the squares are Bb (heterozygous black), and 1/4 of the squares are bb (brown). This means that on average, you would expect 1/4 of the offspring to be homozygous black, 1/2 to be heterozygous black, and 1/4 to be brown. That doesn't mean that you won't get an entire litter of blacks, but it's less likely, especially in big litters.
Also, keep in mind that heterozygous and homozygous blacks look exactly alike. There's no way to tell whether a black rabbit is homozygous or heterozygous for a dominant trait (like black) unless you either test-breed the rabbit or both of the rabbit's parents were homozygous. To use the above example, you would expect 3/4 of the litter to look black, but any of them could be homozygous or heterozygous. In all probability, you could expect that 1/3 of the blacks to be homozygous, and the other 2/3 to be heterozygous, but you have no way of telling which are which until you have test-bred them.
A note about Punnet Squares with homozygous parents: When one or both of the parents are homozygous, the gene label for both columns/rows will be the same. For instance, a homozygous black parent only has B genes, so both columns or rows from that parent would be labeled as B.
Multi-gene Traits
Many "traits", like color, are actually controlled by several traits, each inherited independently. Punnett Squares can be expanded to allow for more gene combinations. We'll do an example with just two traits: Black/brown, Dense/dilute.
| BD | Bd | bD | bd | |
|---|---|---|---|---|
| BD | BBDD (homozygous dense homozygous black) |
BBDd (heterozygous dense homozygous black) |
BbDD (homozygous dense heterozygous black) |
BbDd (heterozygous dense heterozygous black) |
| Bd | BBDd (heterozygous dense homozygous black) |
BBdd (dilute homozygous black) aka BLUE |
BbDd (heterozygous dense heterozygous black) |
Bbdd (dilute heterozygous black) aka BLUE |
| bD | BbDD (homozygous dense heterozygous black) |
BbDd (heterozygous dense heterozygous black) |
bbDD (homozygous dense brown) |
bbDd (heterozygous dense brown) |
| bd | BbDd (heterozygous dense heterozygous black) |
Bbdd (dilute heterozygous black) aka BLUE |
bbDd (heterozygous dense brown) |
bbdd (dilute brown) aka LILAC |
To set up a two-trait Punnett Square, like the one above, remember to include all possible gene combinations from each parent. One easy way to do that is to take one trait, and alternate across the columns which gene for that trait you write. So, for this example, you would label the columns: D, d, D, and d. Then, take the next trait, and do alternate its labels in pairs. (B, B, b, b). If there was a third trait, it would be alternated in sets of 4; a fourth would be in sets of 8. Obviously, the Squares can get really big.
The same rule still applies about the Punnett Square showing probability of offspring. In this case, there are 16 possibilities, so each square is 1/16 possibility. For looks, this means that there is a 9/16 chance for each baby to be black, 3/16 chance to be blue, 3/16 chance to be brown, and 1/16 chance to be lilac.
Incomplete Dominance and Rufus Modifiers
If this weren't complicated enough, there are also genes which are incompletely dominant. That is, when a rabbit has only one copy of the gene, they will still partially show traits of the recessive gene. When a rabbit has two copies of the gene, the effect is more extreme or complete. A good example of this in rabbits is the Vienna gene, which is responsible for blue-eyed whites. Blue-eyed white rabbits have two copies of the V gene. Some rabbits get only one copy of the V gene, and are called "Vienna-marked" or VM. VMs often have blue eyes, but not necessarily, and will have areas of white, usually on the tip of the nose (up to a full blaze) and front toes (as much as their entire saddle).
There are also modifiers which can affect the intensity of some genes. These are called Rufus Modifiers, meaning that the mode of inheritance of them isn't completely understood, and most likely depend on several independent traits that are difficult to isolate. It has just been observed that rabbits which seem to be more extreme tend to produce offspring which tend toward that extremity, but may or may not be as extreme, and can even be more extreme. These modifiers can affect the amount of white on a VM (some VMs may not even show any signs of carrying the VM gene!) or Dutch rabbit, amount of spotting (or lack thereof) on a broken or Charlie rabbit, and the intensity and amount of red on red and tan rabbits.
There are also modifiers which can affect the intensity of some genes. These are called Rufus Modifiers, meaning that the mode of inheritance of them isn't completely understood, and most likely depend on several independent traits that are difficult to isolate. It has just been observed that rabbits which seem to be more extreme tend to produce offspring which tend toward that extremity, but may or may not be as extreme, and can even be more extreme. These modifiers can affect the amount of white on a VM (some VMs may not even show any signs of carrying the VM gene!) or Dutch rabbit, amount of spotting (or lack thereof) on a broken or Charlie rabbit, and the intensity and amount of red on red and tan rabbits.