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The a, or agouti, locus; located on chromosome 2; is generally the first locus discussed when determining mouse genetics. This is because all mouse colourations "build" from this locus. The a locus determines the basic qualities of the coat colouration, and the various modifying and dilution loci act from there.
There are approximately a hundred known variations across 17 allelles of the agouti locus. I have detailed the seven genes that fancy mouse breeders are likely to encounter. The rest are either unknown in the fancy, or are simply visually indistiguishable from the ones shown here.
Dominance
Avy
Ay
Aw
A
at
a
ae
2.1.1 A — Agouti
Agouti is also known as the "wild type" coat in mice. It is the most common - despite not being the most dominant - coat type found in non-domesticated mice. The individual hairs of the agouti coat are banded or ticked with two colours: yellow and black.
2.1.2 a — Non-agouti
Non-agouti mice are non-yellow mice with no banding or ticking on the individual hairs. Mice that are non-agouti are sometimes referred to as "self" mice, though this term actually refers to non-agouti mice without markings. Yellow mice without banding or ticking have the yellow (Ay/Avy) gene, rather than the non-agouti gene.
2.1.3 Ay — Yellow
The yellow gene is known to create mice in colours ranging from sooty yellow, through delicate lemon fawn, through gold, all the way to rich orangey-reds. Not a lot is understood about what influences these tones and shades of yellow, though careful selection of mice can produce offspring in these colours. Yellow is, however, a lethal gene, and homozygotes do not live to birth. It should also be noted that both the yellow and viable yellow (see below) genes are linked to obesity.
The "red" colour is virtually unknown in Australia due to our limited gene pool.
2.1.4 Avy — Viable Yellow
The viable yellow gene is more commonly known outside Australia as "brindle". Until (very) recently, it was thought that we did not have this viable gene in Australia, but research indicates that brindle-patterned mice can only come from the Avy gene, not the lethal yellow version[5].
Viable yellow gene can produce the same sooty, lemon, fawn, or golden mice as the lethal gene, but depending on the mother's modifying genes, can also produce brindle-patterns. The stripes can appear as yellow on black or vice-versa, depending on how much black is present in the coat. Heterozygotes with the A locus will have agouti brindling, while those with the a locus will have black brindle-patterns[6].
2.1.5 Aw — White-Bellied Agouti
White-bellied agouti mice have agouti banding or ticking on their coats, but their belly is white or cream.
2.1.6 at — Tan
Similar to the white-bellied agouti gene, tan mice are "non-agouti" with tan-coloured bellies. However, while this gene acts as a dominant gene on the belly of the mouse, it acts as recessive on sides and back. An Aat mouse will be agouti with a tan belly, while aat mice are non-agouti. Dilution factors such as the chinchilla gene can affect this tan belly, making it appear white, which is referred to as "fox".
2.1.7 ae — Extreme Non-agouti
Mice with the extreme variation of the non-agouti gene have no yellow pigment in their coat at all. This gene also increases the dark pigment in the skin, where the skin inside the ears of a non-agouti mouse may appear yellowish; in the extreme non-agouti mouse it will appear dark[cite]. The extreme non-agouti gene is responsible for creating very dark black self mice.
This gene is currently unknown in Australia.
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