Genetics 101. Feel free to correct me if I incorrectly state something, I am not a genetics wiz I am going to try to simplify it. Feel free to ask questions.
This will all be based on rats but mice work in the same way. Obviously being a different species they have different genes. Use this Australian genetics table for mice as well as these sites (which are not Australian):
First of all, a lot of it is based on mendelian inheritance. Thanks Mr Mendel for figuring that stuff out. Click here to read about Medelian inheritance here.
Basically he discovered that in genes there are alleles that are dominant and recessive. Explaining alleles are tricky >< I had to google this one because I suck at explaining it. "One member of a pair (or any of the series) of genes occupying a specific spot on a chromosome (called locus) that controls the same trait." You get one allele from one parent and another from the other parent. Rats with one allele of a trait are heterozygous and those with identical alleles are homozygous. Click here to read more indepth about genetic terms.
Now for those that need this, I'll add it in. What are dominant and recessive traits? A dominant trait is one that will 'override' some others. For this example I will use Agouti and Black. Agouti is dominant over Black. So if a rat gets one Agouti allele from a parent and a black allele from the other parent, Agouti is what will express (be seen) on the rat. This rat will be Aa (A = agouti, a = black). You can do that with most colours.
Now in order to utilise Mr Mendel's law we use punnet squares. I suggest using the first example in the link until you 'get it'. Then you can progress onto the other if you wish.
So using the above example... We have a parent who is Agouti with two agouti alleles mated to an Agouti with one agouti allele and one black allele. The possibilities of what they could produce in a litter is below. You put one parent's alleles at the top and then one parent's to the side and fill it in.
A AA Aa
A AA Aa
So they theoretically will get 50% Agouti (AA) and 50% Agouti (Aa) rats. Each section of the punnet square is 25%, totaling 100%. Both types will LOOK exactly the same but genetically they are different. One of them is heterozygous (aka 'carries) black and the other is just plain homogenous agouti (this means it is 100% agouti - both alleles are agouti).
When I said theoretically, it doesn't always happen like that. Each bub has a 50% chance of being Agouti (AA) and a 50% chance of being Agouti (Aa). So it is entirely possible to have a litter of AA or AA rats.
Now you can do this same thing with Ruby eyes. R = Dominant (wild type/normal eyes), r = recessive (ruby eyes). Because R is dominant only rats with two r alleles (rr) will show or express ruby eyes. So if we put a ruby eyed rat (who would have two r alleles aka rr) to a rat that is a carrier ( Rr) you would get this in the litter.
R Rr Rr
r rr rr
So... sticking with colours/eye colours.. Note: Take it as only the same alleles interact (so C and c). I'm just including what is in Australia.
C = (Dominant) Normal wild type
c = (Recessive) Albino
A = (Dominant) Agouti (wild type)
a = (recessive) Black
T = (Dominant) Chocolate
t = (recessive) Normal (wild type)
*Note: Chocolate and agouti in the one rat will express both.
M = (Dominant) Normal (wild type)
m = (recessive) Mink
D = (Dominant) Normal (wild type)
d = (recessive) Blue (aka dilution hence the d)
R = (Dominant) Normal (wild type)
r = (recessive) Ruby eyes
P = (Dominant) Normal (wild type)
p = (recessive) Pink Eyes
So if I had a rat and it was blue mink it may look like this = aa dd mm. We are looking at the rats phenotype. If we look at what it carries as well (the rats genotype), it may look like this = aa dd mm Rr Pp. So while the rat LOOKS blue mink, it actually carries pink and ruby eyes as well. If you got a rat from a random source and had no idea about the parents or siblings then you could only tell what it is phenotypically. You would have no idea about what it carries unless you bred it to others (in this case a ruby eye or pink eye rat or a carrier of the two).
Just to be entirely confusing... after you get all of that, some traits do not follow the mendelian law. This is most coat types.
Most coat types are Codominant. What does that mean? It means that if a rat has only ONE allele of a non standard coat type, it will be expressed/shown on the rat. So a single rex rat will be Rere. Re = Standard coat, re = rex. Two alleles in the one rat (rere) means it will be double rex. So a single allele makes the whiskers curl a bit and adds a kink to the hairs of the coat. Two alleles kind of does the same thing but a lot more. Just to be confusing, a single rex and a double rex CAN look the same. If you have heard of someone say a rat is a 'poor' rex this means that the whiskers aren't as curled and the coat isn't as kinked as it should be. So a poor double rex may look the same as a good single rex even though they are genetically different.
SO... if you have gotten through all of that and 'get it', it is now time to put it all together. Best way is using punnett squares for each individual trait (each set of letters). You can complicate it by using a few at once but not a good idea if you are just starting out.
Let's take two rats as an example. One is Blue Agouti single rex and the other is mink standard. The blue agouti is a carrier for pink eyes, mink and black, while the Mink rat is a carrier for pink eyes. This means that we will need to use five punnet squares. I will put the alleles for the first rat at the top and the other rat's at the side (it doesn't really matter which one goes where though).
a Aa aa 50% Agouti (Aa), 50% black (aa)
a Aa aa
d d 100% Blue hets (carriers)
D Dd Dd
D Dd Dd
M m 50% Mink hets (carriers), 50% minks
m Mm mm
m Mm mm
P p 25% Normal/wild type, 50% Normal/wild type that
P PP Pp are Pink eye carriers and 25% pink eyes
p Pp pp
Re re 50% Standard coats
Re ReRe Rere 50% Single Rex
Re ReRe Rere
When I say that something is 50% chance of getting that trait, it's unlikely you will get exactly 50%. What it means is that EACH baby has a 50% chance of having that trait. So it is entirely possible to have no minks at all in this litter. Unusual but entirely possible.
So the colours you would likely get in this litter are Agouti, black, mink, mink agouti, PE (pink eye) agouti, PE agouti mink, PE black and PE mink. As there is only a 25% chance of each bub having pink eyes, there is likely to be less pink eyed bubs in the litter than there is agouti based bubs.
You could also do the same thing with markings. Markings are easy.
HH = Self
Hh = Berkshire
hh = hooded
One marking that is a bit more complicated is bew. The allele for BEW is n and it is recessive.
N = Normal/wildtype
n = BEW (or REW or PEW)
Nn (a bew carrier) generally has a facial marking. This will usually be a headspot though it can be a blaze of some sort.
BEW stands for black eyed white. You can also get Ruby eyed white (REW) and Pink eyed white (PEW), that work the same but with different eye colours. Think of bew as a camouflage marking, like harry potter with his invisible cloak. Instead of it being an invisible cloak, it's a cloak of whiteness. Under the cloak, the rat may actually be a agouti blue mink berkshire rat. You can't tell though because it is covered by the BEW marking. Occasionally you will get a mismarked bew (aka spottie/dalmation). What has happened here is that the cloak has 'holes' in it that is allowing the marking underneath to show. If you breed two mismarked bews together, you are likely to make more. Over generations you will get ones that are heavily mismarked.
Now I HIGHLY recommend to learn all of this is you are breeding. When you 100% understand it and can do it yourself, feel free to have lazy days and use this rat genetics calculator. There are some traits that are missing from it as well but you can now work that out yourself...yay!
It's taken a while to spew that out of my head. I have obviously not made this all up, I have gotten it from many different sources over time. If you would like to share this in whole (not snippets), simply share it from this link: http://www.kirrascritters.com/genetics-101.html