Important Terms


1 - INTRODUCTION

Mice have 2 pairs, or copies, of chromosomes. Chromosomes are made up of tightly bundled groups of DNA. The exact number will vary in different species, but there are still 2 copies of each. Mice, for example, have 20 pairs of chromosomes.

DNA is a blueprint for the body on how to build itself, which is why it’s important to have an extra copy. If mutations occur and render one of the copies unusable, the other copy can sometimes fill in the correct information to keep things running smoothly. Other times, the information overwrites the other copy entirely. This is why there are dominant and recessive mutations. Sometimes, the information is mixed, and both copies are used; leading to incomplete dominant or codominant mutations.

These mutations can occur in the same spot on a chromosome (the same locus) or at a new place. When two mutations occur at the same locus, they are mutations of the same gene, a specific section of DNA. This is when two different mutations of the same gene, called alleles, can interact. If the alleles are on different loci, they do not “code” for the same information, and thus do not compete for expression within the same gene.

Note: While the terms gene and locus are technically different, they are often used interchangeably. The terms locus and gene however, are not interchangeable with allele.

2 - ALLELES

A gene is homozygous when a mouse has two copies of the same allele. When the two copies are different it is called heterozygous. Recessive alleles are typically* ones that must be homozygous to express, while dominant alleles can express while heterozygous.
* Some recessive alleles can express together with other recessive alleles, often expressing a mix of the two alleles.

When the allele of a gene is not considered to be mutated, this is called wild type. 

"Wild type is defined by the frequency of the allele in the natural population. Any time it is the majority (more than 50%), an allele is considered the wild type." Source

In scientific documentation, wild type is given the + symbol. In the mouse fancy, it is usually given a symbol based on the mutation it is allelic to. For example, the wild type allele of the D locus is given a capital "D" to show that it is dominant over the recessive "d".

3 - MELANIN TYPES

When it comes to fancy mouse genetics, nearly all of the mutations we tend to focus on are mutations of the melanin or fur production processes. If we take a look at the ASIP gene in mice, the A locus, we can see what it codes for.

“In mice, the agouti gene encodes a paracrine signaling molecule (MSH) that causes hair follicle melanocytes to synthesize pheomelanin, a yellow pigment, instead of the black or brown pigment, eumelanin” (1)

There are some fancy words in there, but all it means is that ASIP codes for a molecule that signals melanocytes, melanin production cells, to produce pheomelanin, rather than eumelanin. This change is why there are bands of color on agouti mice. Without this change to produce pheomelanin, we get black self. Other loci can produce colors that have almost entirely pheomelanin, or no melanin at all.

If you're interested in learning more about how exactly a gene functions biologically to create different varieties, you should head over to this page: Gene Pathways

4 - 

Genotype

The composition of alleles that a mouse has is its genotype. The genotype can be described with words only, but it can also be described using symbols that condense the information. You could describe a mouse that is albino, a recessive mutation, as being homozygous for albino: meaning it has two copies and is expressing as albino. You could also describe the mouse simply as "c/c". These symbols are used in Punnett squares to predict litter outcomes.

Examples:
C = wild type
c = albino

C/C = Homozygous for wild type at the C locus (No mutation)
C/c = Heterozygous for wild type and albino
c/c = Homozygous for albino

Note: While these symbols are more efficient, it is not uncommon for some people to have difficulty reading them, such as some people with dyslexia and/or those new to the concept. Writing in both symbols and word form can increase accessibility in this regard, and is recommended when possible.

Mouse fanciers typically use simplified versions of these symbols. The full allele symbol usually includes the gene symbol as well. The A locus is often the only exception, as the full form uses the A itself as the gene symbol.

Example:

Simplified form: b = chocolate (brown)
Full form: Tyrp1ᵇ = chocolate (brown)

Simplified form: c = albino
Full form: Tyrᶜ = albino

Simplified form: d = blue (dilute)
Full form: Myo5aᵈ = blue (dilute)

Simplified form: e = recessive yellow
Full form: Mc1rᵉ = recessive yellow


Phenotype

The observable appearance of a mouse is its phenotype. There are some cases where a phenotype can be caused by multiple genotypes. To a mouse breeder, an infamous example is the yellow mouse, as it has 3 possible genotypes. This is why phenotype is not always 100% reliable when trying to ID a mouse's genotype.

(Optional)

Here you can see 4 mice. They would typically be nearly solid yellow in color, expressing primarily pheomelanin except for the light soot on their backs, expressing a small amount of eumelanin.

The 2 with black spots are A locus red mice (Aʸ, lethal yellow).The function the A locus/ASIP gene codes for is timing of black and yellow pigment. It uses the MSH protein to communicate when to switch to eumelanin, black pigment. So when A locus yellow mice were given a dose of MSH protein, they started to produce eumelanin instead of pheomelanin. 

The other 2 mice are yellow due to a mutation at the E locus instead though. They are yellow due to a different function, so adding MSH did not affect them at all.
Link

TERMS

Chromosome: Tightly bound DNA.
Ex: The D locus is found on chromosome 9.

DNA: Self replicating genetic information.
Ex: Novel mouse varieties can contain mutated DNA.

Locus: A location on a chromosome.
Ex: The C locus is very close to the P locus on chromosome 7.

Gene: A specific section of DNA.
Ex: The gene symbol for the D locus is, "Myo5a".

Allele: A specific variation of a gene.
Ex: The siamese (himalayan) allele is a fascinating example of temperature dependent enzymes.

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Dominant: Requires only one copy of an allele to express.
Ex: The lethal yellow allele is dominant to all others on the A locus.

Recessive: Requires two copies to express.
Ex: Extreme black is the most recessive allele on the A locus.

Incomplete Dominant: Requires only one allele to express "halfway" in tandem with another allele. Requires two alleles to express fully.
Ex: On the A locus, lethal yellow is codominant.

Codominant: Requires one copy to express fully, but only in certain spots, leaving the other allele to fill in the rest. Requires two alleles express fully in the mouse.
Ex: (Mice have no examples of codominance)

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Homozygous: A gene or locus that has 2 copies of the same allele.
Ex: The grey mouse is homozygous for blue (dilute).

Heterozygous: A gene or locus that has 2 copies of different alleles.
Ex: The agouti tan mouse is heterozygous for agouti and black tan.

Wild type: The natural or most common expression of a gene; one without mutations.
Ex 1: Agouti is the wild type phenotype of house mice.
Ex 2: The B locus is heterozygous for wild type and chocolate (brown).

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Pheomelanin: Yellow/orange/red melanin pigment.
Ex: Recessive yellow mice produce primarily pheomelanin.

Eumelanin: Black/brown melanin pigment.
Ex: Extreme black mice produce only eumelanin.

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Genotype: The genetic composition of an organism; which alleles it has.
Ex: The genotype of the black mouse is "a/a", homozygous for black (nonagouti).

Phenotype: The observable appearance resulting from the combination of the genotype and the environment; what the organism looks like.
Ex: The phenotype of the yellow mouse has multiple genetic causes.

Allele Symbol: The group of letters and numbers given to a specific allele.
Ex: The allele symbol for 

Punnett Square: A table for predicting possible outcomes of matings.
Ex: The punnett square shows a 3 different genotype and 2 different phenotype as possible results from the mating.