A-Locus
The A-locus is where the alleles for agouti and black sit. Agouti (A) is the dominant trait, black (a) is recessive.
Rats can be:
AA - homozygous agouti, presenting as agouti-based.
Aa - heterozygous agouti, presenting as agouti-based but carrying black.
aa - homozygous black, presenting as black.
B-Locus
The B-locus is where the alleles for chocolate and non-chocolate sit. Non-chocolate (B) is the dominant trait, chocolate (b) is recessive.
Rats can be:
BB - homozygous non-chocolate, presenting according to their other inherited traits.
Bb - heterozygous non-chocolate, presenting as according to their other inherited traits but carrying chocolate.
bb - homozygous chocolate, presenting as chocolate-based.
C-Locus
The C-locus is where the alleles for shaded are located. There are a few variations.
C- - non-shaded, so the colour is expressed normally.
cc - albino, one version of Pink-Eyed White (PEW).
cc^h - himalayan
c^hc^h - siamese
c^mc^m - marten
cc^m - pale marten
c^hc^m - pointed marten
H-Locus
The H-locus is where some of the alleles for markings are located (roan and chinchilla are associated with other loci). There are a few variations:
HH - unmarked
Hh - berkshire
hh - hooded
H^ro - Essex (lethal dominant)
H^i - Irish
h^e - extreme hooded
Other modifiers exist, and their effect depends on selection and what they are in combination with. Some varieties can be made in a few different ways.
Modifiers are genes that affect the expression of other genes, affecting the likelihood that a certain phenotype will present (penetrance), the degree to which a gene is expressed (expressivity), etc.
Other Loci Influencing Colour
Most loci influencing colour involve recessive alleles, so two copies are required to be expressed. The below is not an exhaustive list.
dd for british blue
rbrb for russian blue
mm for mink
amam for American mink
rr for red-eyed dilute (RED)
pp for pink-eyed dilute (PED)
Other Loci Influencing Variety
Dumbo
Dumbo is caused by a recessive, so there are the following possibilities:
DmboDmbo - top ear
Dmbodmbo - top ear carrying dumbo
dmbodmbo - dumbo
Select for dumbo ears after the 6 week mark as this is when most creases form.
Rex
The rex gene is incomplete dominant, so has a different effect when homozygous. Rexing expresses better on bucks than does.
rere - standard coat
Rere - rex
ReRe - double rex
There is also the less common recessive rex gene:
rere - standard coat
refz - standard coat carrying recessive rex
fzfz - recessive rex
Black-Eyed
While Be is dominant, its expression is dependent on C-locus genes being expressed.
Dwarf
Dwarf the variety is different from dwarf the mutation. Dwarf is caused by a recessive.
DwDw - standard size
Dwdw - standard size carrying dwarf
dwdw - dwarf