A-Locus
The A-locus is where the alleles for agouti and black sit. Agouti (A) is the dominant trait, black (a) is recessive.
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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.
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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.
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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
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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:
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HH - unmarked
Hh - berkshire
hh - hooded
H^ro - Essex (lethal dominant)
H^i - Irish
h^e - extreme hooded
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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.
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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.
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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:
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DuDu - top ear
Dudu - top ear carrying dumbo
dudu - dumbo
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Select for dumbo ears after the 6 week mark as this is when most creases form.
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Rex
The rex gene is incomplete dominant, so has a different effect when homozygous. Rexing expresses better on bucks than does.
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rere - standard coat
Rere - rex
ReRe - double rex
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There is also the less common recessive rex gene:
rere - standard coat
refz - standard coat carrying recessive rex
fzfz - recessive rex
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Black-Eyed
While Be is dominant, its expression is dependent on C-locus genes being expressed.
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Dwarf
Dwarf the variety is different from dwarf the mutation. Dwarf is caused by a recessive.
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DwDw - standard size
Dwdw - standard size carrying dwarf
dwdw - dwarf