3. Combining Genes

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Now that we know what the most common genes in mice are, we can work out how they go together to define the characteristics of our fancy mice.
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3.1 The Gene Sequence

At the beginning of this essay, I gave an example of a “wild” mouse: A_ B_ C_ E_ D_ P_ ww. Using the information on the genes, we know that A represents the agouti colouring, so this mouse has hair banded with yellow. The B locus is black, so the banded hairs are yellow/black. The C locus means that the mouse is full-coloured, so has no apparent effect. The E, D, and P loci are the same. Finally, the w allele means there are no markings. This mouse is therefore a common agouti mouse with black eyes and no markings.

This also works in reverse. Imagine you have a black mouse with a tan belly, black eyes, and no markings. You could surmise that it carries the a^t locus, giving the distinct tan belly; the B locus, due to the black colouration; C, E, D, and P loci as there is no colour dilution; and the ww allele for the lack of markings. You have therefore identified this mouse as: a^t_ B_ C_ E_ D_ P_ ww.
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3.2 Determining Inheritance

When pairing mice, especially if breeding for specific colours or properties, there is a simple way of determining the likely outcome using a punnet square. The punnet square was developed by Mendel and represents a simplified view of how loci are inherited from parents. As each parent donates one of thier loci to the offspring's genetic makeup, the punnet square lists the loci of one parent along the top of a matrix, and the other parent down the side. Matching up the rows and columns allows you to see what combinations the parents can produce.
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3.2.1 Punnet Square: Single Gene

In this example, we are going to cross an agouti mouse (AA) with a non-agouti mouse (aa). While the colour of a mouse is made up of more than just the agouti gene, we’ll start here with just one gene.

Each parent will give one of their two loci to their offspring. To work out what combinations this will result in, we put each parent in the punnet square as follows:

		Dam
		A	A
Sire	a	Aa	Aa
	a	Aa	Aa

Taking one locus from each parent gives each of the offspring the Aa gene. They will all be agouti, but carry the non-agouti gene. If we were to cross a brother and sister from this litter, it would look like this:

		Dam
		A	a
Sire	A	AA	Aa
	a	Aa	aa

This result already looks very different. Approximately a quarter of the offspring will get the dominant gene from each parent, and will have the A allele. Another quarter will get the recessive locus from each parent, having the a allele. The rest will receive a locus of each type; appearing as agouti, but carrying the non-agouti gene.
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3.2.2 Punnet Square: Two Genes

When looking at genes that determine the appearance of a mouse, we can build ever-increasingly complex punnet squares, showing the combinations of various interacting loci. For this example, we are going to look at the agouti and the black genes, both of which have obvious effects on appearance. For this example, we will cross a black agouti (AA BB) with a chocolate self (aa bb).

First of all, we have to determine all the possible combinations for one of each of the two genes. In this case, no matter how you mix them up, the father can only give A and B to their offspring; and the mother a and b.

		Dam
		ab
Sire	AB	Aa Bb

Again, all the offspring have a dominant and a recessive locus from each parent for each gene. If we were to cross a brother and sister from this litter, there are four potential combinations of loci.

		Dam
-		AB	Ab	aB	ab
Sire	AB	AA BB	AA Bb	Aa BB	Aa Bb
	Ab	AA Bb	AA bb	Aa Bb	Aa bb
	aB	Aa BB	Aa Bb	aa BB	aa Bb
	ab	Aa Bb	Aa bb	aa Bb	aa bb

Confused yet? To make it easier to work out what different results we have, we can colour-code the grid:

table here

table here

It wouldn’t be unreasonable for a mouse to have a litter of sixteen or even more kittens, but realistically, there is no way to tell the mice with dominant genes from the mice carrying recessive loci. From this litter, you could expect most of the kittens to be black agouti, a few brown agouti, and some black or chocolate selfs.
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3.2.3 Punnet Square: A Complex Example

The number of results in a punnet square increases significantly with each gene you add. Imagine you were pairing mice that had the following gene sequence: Aa Bb Cc Dd Pp ww Sasa. This is a standard agouti mouse, but carrying the recessive gene for a satin coat, and we’re crossing siblings to propagate this satin gene.

If we eliminate the w locus (ww crossed with ww will still result in all offspring having the w allele), that leaves six genes: a massive 64 potential locus-combinations from each parent. A punnet square using all 64 combinations will have 4096 results. The vast majority of these results will be physically indistinguishable.

Fortunately, for our purposes, we can treat each of these genes in isolation. For the degree of complexity used by fancier-breeders we can freely assume that each gene works in isolation and all combinations are possible. In reality, genes are linked to one another, and certain loci can only be found in certain combinations – but this is well beyond the level of complexity required for what we are doing.

Predicting the results of a litter is never going to be an exact science. If you take into account that we simply cannot know for certain what genes our mice carry, nor the intricate interplay of linking between genes, there will always be surprises. For the most part, two small punnet squares with just the genes you’re interested in should be more than enough.
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3.2.3.1 Using Multiple Punnet Squares

In this example, we are going to cross a pale silver doe (aa bb c^ec dd pp) with a chinchilla buck (Aa^t BB c^chc^ch Dd Pp). First of all, we can work out the base colour of the offspring with a punnet square for the A and B loci.

punnet square here

This punnet square shows us that the base colour of the kittens will either be black agouti, or black with a tan belly. Now, we need to work out what modifying genes the litter will have.

punnet square here

table here

This is just a rough guide to what effects these dilutions will have. In the case of the two non-blues with the c^chc gene, they will be chinchilla-like if they inherit the agouti locus, but they will be fox if they inherit the tan locus. To combine the results of the two punnet squares, simply assume that for each result in the second, roughly half will have the first base colour, the rest the second base colour.
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3.3 Fancy Mouse Colours

There is no definitive list of gene sequences that cause the colours recognised by the various fancy mouse societies around the world. The following sequences have been researched on the internet and are presented “as is” – I cannot vouch for the accuracy of the following sequences.
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3.3.1 The Cascade of Colours

Determining how genes affect colour types can be a complicated business. There are a number of phenotypes that can't be told apart. I tend to think of the colouration genes in a "cascade". Starting at the top, the cascade of genes affect the appearance of a certain order.

At the top of the cascade is agouti. All of the other colouration genes will affect the agouti/non-agouti colours, but typically won't change the baseline created by the a locus. Next is the b locus, which determines the darkness of black/brown in the coat (fawn mice skip this step in the cascade). Next is the c locus, which dilutes the colours to various degrees. Finally, the d locus, which if present turns to mouse to a blue shade determined by the genes that came before it.
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3.3.2 The C Locus

The C locus controls the intensity of pigmentation, and creates a large number of variations in fancy mice.

table here

3.3.3 The D Locus

The D locus is responsible for a whole range of lovely grey colours ranging from deep slate blue to a delicate dove.

table here

3.3.4 The P Locus

Certain colours are defined by the P locus. As the P locus dilutes colour and results in pink-eyed mice, certain colour standards exist for the pink-eyed “version” of other colours.

table here

3.4 Determining Genetic Make-up

If you bought your mouse from a fancier-breeder, you will probably have a good idea of exactly what genes your mouse carries. However, if your mouse is from a new breeding line, from a “backyard” breeder, or perhaps even rescued from a “feeder” breeder, then the genetic background is going to be a complete mystery.

While it’s not possible to tell what genes a mouse has without breeding, we can make an educated guess by looking at the mouse. Taking this educated guess, we can pair up mice that are more likely to reveal qualities we want, rather than random breeding.
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3.4.1 Connor

Since this was originally written, Connor passed away. Play well over the rainbow bridge, little man.

images here

This is Connor. I picked him up from a pet store because I was intrigued by his markings, despite all the reasons that would keep any sane mouse lover well at bay. He is off-black, with a white headspot, irregular white markings, and a pale tan belly.

Though the belly picture isn’t very good, Connor’s belly is cream, with a line of tan demarking the line between his belly and upper body. This is caused by have a tan belly (a^t locus), which is covered by a large white belly marking.

As Connor is black, we can assume that he carries the B locus, though he may be Bb due to his faded colour. Still, we can record B_ at this locus.

Connor shows no obvious colour or blue dilutions, and has lovely dark black eyes, so we’ll give him dominant loci at each of these.

As Connor has white markings, he either has dominant genes at the W locus, or recessive genes at the S locus. There’s no way I can tell without breeding which is the case, but the recessive s allele tends to create large markings, and Connor’s spots are all very small. Because we’re just guessing, we can put the W^v_ at this locus.

Finally, we will give Connor the hshs gene as he has a headspot, but remember that even if crossed with another headspotted mouse, his offspring may not demonstrate headspots.

Connor: aa^t B_ c^chc^ch D_ P_ W^v_ hshs

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3.4.2 Tristan

image here

Tristan is half of my very first pair of mice. I bought a pair of identical brothers because I found their colour so charming. Tristan and Nathaniel are both warm grey with bright black eyes, a pale stomach, and a white headspot.

At the A locus, we know that Tristan is a self, or non-agouti, giving him the aa gene. At the B locus, we might assume that Tristan carries the bb gene as he would be a dark slate blue if he had the dominant B locus.

Tristan has a pale belly; although the chinchilla gene can account for grey or pale bellies, we can’t be sure what gene is lightening his belly. Let’s err on the side of caution and give him the C locus.

Obviously, as a blue mouse, Tristan has the recessive allele at the d locus, or else he wouldn’t be the delightful grey colour he is.

There is no recessive yellow, his eyes are bright black, and there are no markings apart from his headspot; so we can give him dominant E and P loci, and the recessive w locus.

Although coat types apart from rex are virtually unknown in Australia, Tristan has a shiny coat that is soft to the touch and slightly greasy. His coat texture is definitely different to Connor’s, and noticeably shinier than Nathaniel’s. Let’s give him Gsgs.

Finally, we’ll add the headspot allele.

Tristan: aa bb C_ dd E_ P_ ww Gsgs hshs

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3.4.2.1 Attempting a Pairing

This section will return soon…

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