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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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Rex

The rex gene is incomplete dominant, so has a different effect when homozygous.

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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

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