Standards and Genetics

This section of the website will be sharing the NFRS standards for varieties, some of the main loci that we have learned about through working with different varieties, and linking any photos that I have. I've also compiled some information on breeding each variety that I've found through discussions with judges and other breeders and through general research. I hope it is helpful. If anything is unclear, incorrect, or you would like me to add/remove something, please get in touch. The below section will discuss genetics more generally for those who are unfamiliar/need a refresher. If something doesn't make sense then it means I haven't done my job well enough, so please contact me in that event!

A rat's variety is made up of multiple factors: colour, shading, markings, eye colour, coat type, ear type and size. The NFRS provides variety standards against which, along with general conformation, rats are judged. Understanding the genetics behind each variety can be useful for breeders so that they know what "ingredients" are required to make a particular variety and what matings to do. Breeders can also use an understanding of genetics to predict what a particular mating could produce, though unknown recessives could manifest and statistical probability will likely differ from actual results.

As we know, some traits are inherited, some are a result of our environment, and most are a mix of the two. Variety is determined purely by genetics, though some faults like rusting can be influenced by diet. Inherited traits, like coat and eye colours, are controlled by genes. Different versions of a specific gene are called 'alleles', and you need two alleles to make up a gene. Kittens receive half of their genetic material from each parent, so they are a blend of the two parents' genetic material. One allele is inherited from each parent, and those two alleles together determine what trait is expressed.

Alleles can be dominant, recessive or codominant:

Dominant - only one allele is needed for the trait to be expressed.

Recessive - two copies of the allele are needed for the trait to be expressed. Individuals can be carriers.

Codominant - both alleles are expressed.

When discussing genetics, the following terms are also used:

Genotype - the genes involved.

Phenotype - the trait that is expressed visually. The rat's phenotype will differ according to what is expressed at each locus.

Homozygous - the two alleles inherited are the same.

Heterozygous - the two inherited alleles are different.

Locus - a location for a gene. Loci is the plural.

There are also some genes that are lethal when homozygous. If the rat inherits two copies, they die in utero or soon after birth. Lethal homozygous varieties include Pearl, Essex, Silken and Chinchilla.

Letters are used to represent different alleles to make discussing them easier. Upper case letters are used for dominant alleles, and lower case letters are used for recessive alleles. Each individual will receive two alleles from their parents, so usually two letters are used to write their genotype for a locus. A hyphen can be used alongside a dominant allele where the second allele is unknown, or to show that it doesn't matter what the second allele is.

Let's use agouti and black as an example, and use the terms mentioned above. Agouti and black are on the same locus, where agouti is the dominant trait, and black is the recessive trait. The agouti allele is therefore denoted using an upper case 'A' and the black allele is denoted using a lower case 'a' to reflect this. Only one copy of agouti is needed for a rat to be agouti-based as it is a dominant allele, and two copies of black are needed for a rat to be black-based as black is a recessive allele. 'A-' can be used when discussing a rat who is agouti, but it cannot be certain whether they are heterozygous or homozygous for agouti.

The parents in the diagram below are agoutis, but they carry black, so they have a copy of each allele and this makes them heterozygous. Their genotype, or allele combination, is Aa. Their phenotype, the expressed visual trait, is still agouti as agouti is dominant to black. Their offspring will be a mixture of agouti (homozygous, AA), agouti carrying black (heterozygous, Aa) and black (homozygous, aa) as the offspring will randomly take one allele from each parent.

You can more easily calculate which genotypes and phenotypes a pairing will yield by using Punnett squares. Punnett squares make a grid of all of the options, which you can then use to calculate probabilities of various varieties.

So for the mating above, the Punnett square would look like this:

Both parents have the genotype 'Aa', so this goes around the edge of the Punnett square. You then match the letters up to make a full genotype inside each smaller square, which shows you the possible resulting genotypes and phenotypes of the offspring. So some offspring will be AA (agouti not carrying black/homozygous agouti), Aa (agouti carrying black/heterozygous agouti) and aa (black). You can also use Punnett squares to calculate the probability of a certain phenotype. The Punnett square is divided into 4, so each square represents a 25% likelihood. There is therefore a 25% chance of each kitten being AA (homozygous agouti), a 50% chance of them being Aa (heterozygous agouti), and 25% chance of them being aa (black). There is a 75% chance of the offspring being agouti overall, and 25% chance of them being black.

If that makes sense, we'll take things a step further and add another loci. Let's use mink. I'll summarise the genotypes and phenotypes (variety):

aa mm = black + mink = mink

A- mm = agouti + mink = cinnamon

aa M- = black + non-mink = black

A- M- = agouti + non-mink = agouti

So if we have 1 parent who is agouti, heterozygous for agouti and mink (Aa Mm), and the other parent is cinnamon, heterozygous for agouti (Aa mm), this is what the Punnett squares would look like:

As before, there is a 25% chance of AA/homozygous agouti, 50% chance of Aa/heterozygous agouti, and 25% chance of aa/black. Phenotypically speaking, there is a 75% chance of being agouti-based and 25% chance of being black-based. There is a 50% chance of a kitten being heterozygous for mink (Mm), and a 50% chance of a kitten being mink (mm). To work out the probability of the two loci together, you multiply them together. So the odds of a kitten being mink (aa mm), is 0.25 * 0.5 * 100 = 12.5%. The odds of a kitten being cinnamon (A- mm) is 0.75 * 0.25 * 100 = 18.8%. While they initially look overwhelming, it can be easier to view combinations and their probabilities using a probability tree, especially when even more loci are at play.

To calculate the probabilities of each genotype, you multiply the likelihood of each event going left to right along the tree. If some of the resulting phenotypes are the same, you can add them together. So for the above:

Probability of agouti = (0.25 * 0.5 + 0.5 * 0.5) * 100 = 37.5%

Probability of cinnamon = (0.25 * 0.5 + 0.5 * 0.5) * 100 = 37.5%

Probability of black = 0.25 * 0.5 * 100 = 12.5%

Probability of mink = 0.25 * 0.5 * 100 = 12.5%

If you add up all of these percentages they make 100%, which is one way to double check your working!

Coming Soon (well, eventually):

- Linkage and cross-over events

- General principles in population genetics

- Any other requests/ideas!