Genetics

Basic Terms
Genes are why your rat looks the way it does. They are the blueprint for making a particular animal.

DNA stands for deoxyribonucleic acid. It is a double helix made up of two strands which hold the information to make an organism. The mother's egg contains one strand and the father's sperm contains another strand. When the egg is fertilized, these two strands come together and start to build a baby!

Locus is a group of alleles that affect a certain part of the rat’s appearance. For example, all the alleles in the R-Locus control the eye color.

Alleles are part of the blueprint needed to make the rat. In each locus, the rat can only have two alleles; one from the mother and one from the father. These are responsible for more specific aspects of the rat's appearance, such as whether it will have red eyes or black eyes. Alleles are denoted as letters, such as A, p, and B. Some alleles have two letters, like Re. Dominant alleles have capital letters, and recessive alleles have lower-case letters.

Dominance determines which alleles will affect what the rat looks like. Since the rat has two alleles, and they may be very different, there must be a way to determine which one will be the one that controls the rat's appearance. This is where dominance comes in. Some traits such as the black-eyed allele R are dominant over the recessive red-eyed allele r. This means that if the mother's DNA provides a R and the father's DNA provides a r, the baby will be Rr. The dominant R takes over the recessive r, giving the baby black eyes even though it carries the gene for red eyes. The only way for a rat to have red eyes is if both its parents' DNA provided a r, making it rr, and therefore it will have red eyes.

Homozygous is the term for when two alleles grouped together are the same. An example of this is the black-eyed gene R. When homozygous, it is RR.

Heterozygous is the term for when two alleles grouped together are different. An example of this is again the black-eyed gene R. If one parent provides the R and the other parent provides a r, the offspring will be heterozygous and have Rr.

Punnet Squares are an easy way to tell what the offspring of your critters will look like, provided that you know what genes the parents have. Let’s say, for example, you have a female rat with black eyes, and you know her mother had red eyes. You now know for sure that her genetic code for eye color is Rr. You also have a male rat, who has red eyes. You know that red eyes are recessive, so he must be rr. You are planning to breed them. Here’s how to use a Punnet square to predict the eye color of the babies.

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It looks like a tic-tac-toe board. You put the father's alleles in the top two rightmost boxes (shown in blue) and the mother's alleles down the left side in the two bottom-most boxes (shown in pink). Then you first take the father's alleles and copy them into each of the four boxes below them. Since they are both r, each box will contain a r. Then you take the mother's alleles and copy them into the two boxes to the right of each one. The R goes into the two boxes to the right and the r goes into the other two boxes to its right. Now you have four boxes with two alleles in each box. As we can see, there are two Rr's and two rr's. This means that there is a 50% (2 out of 4 boxes = 50%) chance of an individual offspring having black eyes (Rr) but carrying the red-eyed gene, and a 50% chance of an individual offspring having red eyes (rr). This works for most of the other alleles too.

Phenotype is a fancy term for the rat's appearance. It does not mean the genes behind the appearance, just the appearance.

Genotype is the term for what genes and alleles the rat has and not its appearance.

Finding Out Genotypes
So how can you know what your rat's genes are if you don't know what its parents looked like? With most genes, you can't tell until you breed that rat and see what the outcome is. Only a few traits can be identified instantly. If your rat has red eyes, it is definitely rr. Russian blue is definitely dd. But if your rat has black eyes, it could be RR or Rr. The only way to find out is by breeding. If you mate this rat to a rat with red eyes and the offspring are all black-eyed, then your black-eyed rat is definitely RR. If some have black eyes and some have red eyes, then you know he or she is Rr. Most other traits can be found out this way.

Rat Gene Table

There are many many different genes that make up a rat's appearance, but we will go over only the basic ones here.

The A-Locus (Agouti Locus)
This locus provides the basic backdrop to the rat's color. This color may later be affected by other genes, making other colors and color combinations.

is the agouti gene. When homozygous or heterozygous with a, it produces an agouti, or wild-type rat.

is the non-agouti or black gene. When homozygous, and not affected by other genes, it will produce a black rat.

The B-Locus (Brown Locus)
This locus has only two different alleles controlling whether the rat's base color will be diluted or not.

is the full color gene. Whether homozygous or heterozygous, there will be no effect on the phenotype.

is the brown gene. This gene dilutes certain colors into lighter ones. Here are some examples:

black becomes chocolate
agouti becomes cinnamon

The C-Locus (Albino Locus)
This locus has lots of complicated genes, including the albino gene. What makes this locus unique is that it is home to the two ‘masking’ genes, which are genes that, when homozygous, will override any other genes that determine color.

is the full color gene. Whether homozygous or heterozygous, there will be no effect on the phenotype.

is the albino gene. When homozygous, this rat will be albino no matter what its other genes are.

is the himalayan gene (also called the siamese gene). When homozygous, it will produce a seal-point siamese. The color of the points will depend on the rest of its genes. When heterozygous with c, it produces a himalayan.

The D-Locus (Density Locus)
This locus, like the B-Locus, has only two alleles, one of which (if homozygous) changes the color of the rat.

is the full color gene. Whether homozygous or heterozygous, there will be no effect on the phenotype.

is the density / dilute gene. When homozygous, it dilutes the rat's color. Here are some examples:

black becomes russian blue
agouti becomes russian blue agouti
fawn becomes russian blue fawn
beige becomes russian blue beige

The Du-Locus (Dumbo-Eared Locus)
This locus determines whether a rat will have standard ears (sometimes known as 'top ears') or dumbo ears.

is the standard ear gene. Whether homozygous or heterozygous, the rat will have standard ears.

is the dumbo gene. When homozygous, it gives the rat ears that are wide, rounded, and set farther down on the head than the standard rat.

The G-Locus (Grey Dilute Locus)
This locus has only two alleles, one of which (if homozygous) changes the color of the rat. Though it is called the grey dilute locus, it produces the color known as slate blue.

is the full color gene. Whether homozygous or heterozygous, there will be no effect on the phenotype.

is the density / dilute gene. When homozygous, it dilutes the rat's color. Here are some examples:

black becomes slate blue
agouti becomes blue agouti
fawn becomes blue fawn
beige becomes platinum

The H-Locus (Hooding Locus)
This locus controls some of the types of markings the rat can have, including hooding, berkshire, and irish. This is a confusing locus, as it is one of the few that deal with incomplete dominance.

is the standard gene. When homozygous (HH), it produces a rat with no white markings: a self rat. When heterozygous with h (Hh), it produces a berkshire.

is the hooding gene. When homozygous, it makes the rat hooded. When heterozygous with H (Hh), it makes a berkshire.

is the irish gene. When homozygous or heterozygous with H (Hhi), it makes the rat irish. Other complicated modifiers determine how much white is on the belly, and where the white is placed. It can also be heterozygous with h (hhi), making a hooded rat with a broken and / or shortened stripe.

The Hr-Locus (Hairless Locus)
This locus controls whether or not the rat will be hairless.

is the standard gene. When homozygous or heterozygous, the rat will have a normal coat of hair.

is the hairless gene. The rat will have no hair at all (except for whiskers and some very short hairs around the muzzle and genitals) and have thick, wrinkly skin. The rats develop normally from birth, grow hair, and then lose it at weaning age.

The K-Locus (Velveteen Locus)
This locus determines if a rat will have a velveteen coat.

is the velveteen gene. When heterozygous, the rat will have fluffy, wavy hair and curled or kinked whiskers. When homozygous, the rat will be a double velveteen, meaning that the rat is hairless in some spots and has very thin, sparse wavy hair in others.

is the standard coat gene. When homozygous, it makes the rat have the normal, straight coat. When heterozygous with K, the rat will have a velveteen coat.

The M-Locus (Mink Locus)
This locus, has only two alleles, one of which (if homozygous) changes the color of the rat.

is the full color gene. Whether homozygous or heterozygous, there will be no effect on the phenotype.

is the density / dilute gene. When homozygous, it dilutes the rat's color. Here are some examples:

black becomes mink
agouti becomes cinnamon
fawn becomes havana agouti
beige becomes havana

The P-Locus (Pink-Eye Locus)
This locus generally describes the eye color of the rat. However, the recessive pink-eye gene, when homozygous, also affects the fur color.

is the full color gene and the black-eye gene. Whether homozygous or heterozygous, there will be no effect on the fur color, but the eyes will be black (unless modified by other eye color genes)

is the pink-eye gene. When homozygous, this rat will have pink eyes and the fur color will be affected. Here are some examples:

black becomes champage
agouti becomes amber
blue becomes silver
mink becomes platinum

The Pe-Locus (Pearl Locus)
This locus, when combined with mink, determines whether or not a rat will be pearled.

is the pearl gene. Homozygous fetuses with the genotype PePe will die in utero. When heterozygous, this rat will have white tips to its fur and also have some fully white hairs in its coat. This only appears if the rat is also homozygous for mink (mm).

is the full color gene. When homozygous, there will be no effect on the fur color. When heterozygous with Mm or MM, there will also be no effect on the fur color.

The R-Locus (Ruby-Eye Locus)
This locus generally describes the eye color of the rat. However, the recessive red-eye gene, when homozygous, also affects the fur color.

is the full color gene and the black-eye gene. Whether homozygous or heterozygous, there will be no effect on the fur color, but the eyes will be black (unless modified by other eye color genes)

is the red-eye gene. When homozygous, this rat will have red eyes and the fur color will be affected. Here are some examples:

black becomes beige
agouti becomes fawn
blue becomes blue-beige

The Re-Locus (Rex Locus)
This locus determines if a rat will have a rex coat.

is the rex gene. When heterozygous, the rat will have curled hair and whiskers. When homozygous, the rat will be what's known as a patchwork or double-rex, meaning that the rat is hairless in some spots and has very thin, sparse curly hair in others.

is the standard coat gene. When homozygous, it makes the rat have the normal, straight coat. When heterozygous with Re, the rat will have a rex coat.

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