Genetics and Mutations (ongoing project)

The basics...

Coming soon!
Wild type, Agouti and Black (understanding coat color)...

Beginning with the basics is probably best, so this first section features Agouti and Black and how color is produced in a rat's fur, which is critical to the understanding of other color mutations.

A rat's hair is made up of several layers, but it is the cortex of the hair that contains the pigments that make up the overall color of the rat. As one would assume, mutations to genes that affect pigment cells or their development and distribution can create a rainbow of colors and markings. Pigment cells are called melanocytes, and within them are vesicles or little sacs (melanosomes) with particles of pigment. These vesicles will rupture as they go to the surface of the cell, leaving behind the visible color on the rat’s fur. There are two main types of pigments that are important to understand rat colors, as well. The first is phaeomelanin, a yellow-red pigment. The second is eumelanin, a brown-black pigment. To further complicate matters, these two pigments can switch back and forth in production, creating a banded look to the hair. In rats with NO mutations or dilutions to color, this banded pattern will occur. This is the agouti rat, or wildtype. It is referred to as the wild-type because it is the original version with no modifications that in turn create differing colors and coat types. Rats that are non-agouti in color (those that have no banding of color on the hairs) have a mutation that makes the body stop producing the phaeomelanin pigments. They only produce eumelanin. In these rats, the mutation causes them to have none of the agouti protein, the protein responsible for the body’s switching back and forth of pigment production. Genetically, agouti is a dominant gene. This means you only need one copy of the gene to have the rat be agouti or with banded hairs. The gene letter used to represent agouti is ‘A’, and in it’s capital form, it indicates a dominant allele (one copy of the gene). So an agouti rat is ‘AA’ or ‘Aa’. If a rat has no copies of the dominant gene, it is ‘aa’ and will appear black in color because there is no banding on the hair. All rats have a base color of either agouti or black, and any mutations to coat color are in additional to this 'A' gene.

For RSA standards, an Agouti rat is “Golden chestnut brown with dark gray to black base fur and black guard hair. The line between the top color and belly color is to be sharp, devoid of irregularities and brindling. The foot color should match the top, and the belly color should be a silver gray. Eye color is black.” The RSA standard for a Black rat is "Deep solid black, devoid of browning or rusting. The base fur is to be black to the skin, with foot and belly color to match the top. Eye color is black." Similar standards are found in NFRS, AFRMA, and RatsPacNW.

RED and PED (coat color single mutations)...

One of the most common mutation discussed, either on it's own or in combination with other mutations, is the red-eye dilute or RED mutation. This mutation interferes with melanosome development. When their development is compromised, as in this case, those pigments that occur in the melanosome are not distributed properly to the hair and eyes, resulting in a diluted color from the standard black (aa) or agouti (A-). Of course, the final color produced by this mutation also depends on this base, as one has the banding of color and pigment types and one does not. An Agouti rat with a RED mutation is called Fawn. A Black rat with the same mutation is called Beige. Genetically, the RED mutation is recessive. This means that you need two copies of the mutated genet to have the rat's color be diluted. The gene letter used to represent RED is 'R', and in it's capital form, it indicates a dominant allele (one copy of a the gene). So, a Fawn rat is ‘AArr’ or ‘Aarr’, and a Beige rat is 'aarr'.
For RSA standards, a Fawn rat is "To be a rich, golden fawn evenly ticked with silver guard hairs. Undercolor to be pale blue/gray carried down to the skin. Belly fur to be silver. Top color to be even and carried well down the sides with a clear differentiation between belly and top color. Any tendency to sootiness or grayness of the top color to be penalized. Eye color is dark ruby." The RSA standard for a Beige rat is "A warm tan. Eye color is dark ruby." Similar standards are found in NFRS, AFRMA, and RatsPacNW.
Another thing that seems important to mention here is that anytime you have a mutation in a cell, there are often multiple things that are affected. Obviously, color is one in the RED mutation, but their are some less visible things that are also affected by it. For instance, Fawn and Beige rats may have abnormal platelet function, which reduces their ability to clot properly. The disorder is called Platelet Storage Pool Deficiency. Serotonin uptake disorder can also be found in RED rats. These can lead to any mood alterations ranging from depression and anxiety to bipolar or obsessive-compulsive behaviors. How does something like this result from a mutation in a pigment vesicle's development? Certain platelet dense granules have a common component in their development, so it is thought that the mutation affects this particular area. Platelets are also partially responsible for serotonin uptake. Since this is not the true purpose of the article, but still needs mention, here are a couple links to read more about it if you are interested. Visit http://physrev.physiology.org/cgi/content/full/84/4/11 and http://bloodjournal.hematologylibrary.org/cgi/reprint/66/5/1196.pdf.

Next is the pink-eye dilute or PED mutation. This mutation alters a protein that is in the membrane of eumelanosomes, the brown/black pigment producing cells, which changes the pH of these cells. Normally there is an acidic pH, and the eumelanin pigments are produced as usual. But the PED mutation alters the pH to a more neutral environment, and less of the eumelanin is produced. The other type of pigment found in a rat's hair, which you will recall is phaeomelanin (yellow/red pigment), is not affected by this mutation though. The result is a pale coat and pink eyes. In an agouti (AA or Aa) rat, this is Amber, and in black (aa) rats, this is Champagne. No significant health issues have been noted that coincide with this mutation, but melanosomes, in general, are usually fewer in number and can also be misshapen. Genetically, the PED mutation is a simple recessive. This means you need two copies of the mutated gene to have the rat's color be diluted. The gene letter used to represent PED is ‘P’, and in its capital form, it indicates a dominant allele (one copy of the gene). So an Amber rat is ‘AApp’ or ‘Aapp’, and a Champagne rat is 'aapp'.

For RSA standards, a Champagne rat is "to be a very light beige color with no sign of grayness. Belly color to match top. Eye color is pink." At this time, the RSA does not have Amber standardized, as it is quite uncommon in the US. However, AFRMA and RatsPacNW do have a standard for it, which is "a light golden fawn, evenly interspersed with light hairs. Belly color to be light, but not white. Eye color is pink."

Blue and Russian Blue (coat color single mutations)...
Another common set of color mutations are the blues. I'll start with Russian blue. When this mutation occurs, the transport of eumelanin (brown/black) pigment particles is affected. So, although normal pigments are produced, less of the pigment actually makes its way into the hair. The pigment that does get transported does so in clumps, producing a diluted color with a slate-like look. In the agouti (A-) rat, this look is still produced with the banding of color creating the Russian blue agouti. In black (aa) rat, the color is solid and called Russian blue. Genetically, this mutation is recessive. This means you need two copies of the mutated gene to have the rat’s color be affected. The gene letter used to represent Russian blue in America is ‘D’, and in its capital form, it indicates a dominant allele (one copy of the gene). So, a Russian blue agouti rat is ‘AAdd’ or ‘Aadd’, and a Russian blue rat is ‘aadd’.
For RSA standards, a Russian blue agouti rat is "an even blend of Russian blue and agouti ticking. Undercolor to be Russian blue down to the skin. Belly color to be silver. Foot color to match top. Uneven ticking causing the rat to appear either too blue or too brown is faulted. Eye color to be black." The Russian blue rat is "similar to Russian blue in cats. A deep medium gray-blue with a metallic sheen. Faint light speckling or a subtle ticking effect (heathering) and/or darker guard hairs throughout are usual for this variety and are not a fault. Color to be even; belly color to match top. Undercoat to be dark blue down to the skin. Brownish color or color too light are faulted. Eye color to be black." Similar standards are found for both colors in NFRS, AFRMA, and RatsPacNW.
The blue mutation also affects the distribution of eumelanin to the cells, but it’s method is less familiar. Just as in the Russian blue diluted rats, the phaeomelanin (yellow/red) pigments seem relatively unaffected. The result of this mutation is a diluted color, banded in the agouti (A-) rat and solid in the black (aa) rat. In the agouti rat, this color is called blue agouti (called Opal in the UK). In the black rat, it is called blue, and is sometimes referred to as American blue. Genetically, this mutation is recessive. The gene letter used to represent blue in America is ‘G’, and in its capital form, it indicates a dominant allele. So, a blue agouti rat is ‘AAgg’ or ‘Aagg’, and a blue rat is ‘aagg’.
For RSA standards, a blue agouti rat is "an even blend of blue and agouti ticking. Undercolor to be blue down to the skin. Belly color to be silver. Foot color to match top. Uneven ticking causing the rat to appear either too blue or too brown is faulted. Eye color to be black." The blue rat is "to be between a deep steel blue and a pale blue. Lighter shades have a pale silver base fur and underbelly. Darker shades to have a belly color matching the top; color may be lighter at the skin. Foot color to match the top. Patchiness or rusting to be faulted. Eye color to be black." Similar standards exist for both colors with NFRS, AFRMA, and RatsPacNW, but general favor seems to be given to the rat with color extending to the skin.
While it is not clear if it was the Russian blue (d) or blue (g) mutation of myosin V that was studied in the lab, this mutation, which affects a transport mechanism, also impacts calcium in the cells, which can lead to neurological deficits in some rats. It is more likely the blue (g) gene that was studied, though.
References...
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