Rat Basic Color Genetics

Colors, Loci, and Basic Expression

Just like everything about an organism, a rat's color is controlled by genetics. Our basic colors are mostly controlled by recessive genes. This means that 'most' of our colors cannot express unless a copy of that gene is inherited from each parent. Those RECESSIVE traits are noted with lower case letters of that locus. (A copy of Russian Blue, if present, is written as 'd'; If not present is is written as 'D'.)

If you consider a rats base color like a blank canvas, each dilute (Dilute - a gene whose expression modifies the base color) acts like a layer of paint. Our two base colors are Agouti (A/) and Black (aa). These are the canvases that we will paint. In this blog post, I will only touch on single simple dilutes...

Agouti Locus 'A'

Agouti - The genotype for agouti is A/. The slash means that either a capital or lower case letter can fill that space. Agouti is dominant, and is also the "wild" rat color. This gene creates banding on the hairs. The tips of the hair display a yellow to brown tone tone in varying shades with a gray toned shaft and black guard hairs (Guard hairs are the long, individual hairs that protrude beyond the length of the rest of the coat). If you have a rat with the genotype AA or Aa, that rat will be Agouti as its base color before you calculate in any dilutes.

  Agouti English Irish Dumbo - Reeces

Black - The genotype for black is aa. That means that there is NO agouti present. Since this color is able to be seen only with no Capital 'A' (Agouti) present, that means that Black is recessive to Agouti. Black is the solid color base, meaning that it does not have the same banding as is present in Agouti. This also means that if any dilutes are added to this Black base, they will not have banding either.

Black Banded Berkshire - Kitten

Brown Locus 'B'
Chocolate - This is a simple recessive color. This is not a common color and most rats that people see and believe is this color turn out to be very poor blacks who carry a single copy of multiple color genes. There is however a few U.S. Ratteries who have very good strong lines of chocolates. This color should be an even rich dark chocolatey brown tone. It should be even and not rusted. These are of course ideals. *I have no photos that are my own that include a Chocolate rat*

Albino Locus 'C'
This is a much more complicated gene, and can be a full blog entry all in itself. Suffice it to say today, that it is present.

Dilute Locus 'D'
Russian Blue - Another recessive gene. This color is a deeper medium blue gray. There is a speckling or ticking found in this blue (also known as heathering). There are frequently darker guard hairs also seen on these guys. Also unlike American blues, Russian blues have a dark under belly, very close in color to the top.In the UK and Australia this gene is in the 'RB' locus.

Russian Blue Mismarked Berkshire - Zero

Gray Locus 'G'
American Blue - This gene is a simple recessive gene. This means that, if a baby only gets one copy, they can not express this color. In order for this to be expressed, or see, they must have the genotype of 'gg'. This color is ideally a varying shade of blue, between deep blue and a pale blue, with a lighter more silvery base coat and lighter underbelly. *Please Note: In the UK and Australia the same color is represented under the the 'D' locus. *

 American Blue Irish - Bella

This will conclude this blog post because, for some, this may be a bit to absorb. Next post will include Mink, and most of the variations in the albino locus. ENJOY!
 *These Photo's are mine, of my rats, and may not be used without my permission except for educational purposes.* I apologize for the poor photo quality. I will be investing in an updated camera and a light box soon.

Basic Genetic Theories - Mendel Genetics

Medel Genetics

The person who first theorized much of we now know about simple heredity was an Austrian monk named Gregor Mendel. When you see reference to Mendel Genetics, Mendelian Genetics, or something similar, this is whom they are referring to. He found the basics regarding inherited traits through plants, but, the same things apply to most of the organisms who reproduce sexually (plants, insects, animals, etc). Keep in mind that his theories were much more advanced than what I am going to dive into but much simpler than that which a geneticist references. For our purposes though, it can be sufficient. One thing to understand that a "gene" is a unit of inheritance... It is a section of DNA that is passed to offspring.

First, a term that you should be familiar with, is Allele. An Allele is a letter reference to a specific gene. If you have looked at rat genetics in terms of genes, I'm sure you have seen that the first letters you see are aa, Aa, or AA. These 'A's are alleles. As I mentioned in the previous Blog, you inherit one copy of a gene from your mother, and one from your father, so that means you will usually have two alleles, one paternal, one maternal. The gene that it represents is called a Locus. (No... not the crop eating locust. LOL) 'A' is the Agouti locus.

The next terms to have a basic understanding of are 'Dominant' and "Recessive'. There are variations of these, but for now, simple is better.
A DOMINANT trait means that, if a rat possesses one copy of the dominant gene out of the "usually" two alleles possible, that trait will be seen in the rat. A dominant trait is written using capital letters when the gene is present, and lower case letters when the gene is not present. Take the gene for the Rex coat. This is 'Re'. That means that if you have a "Rex" rat, it's alleles under the Rex locus will be 'Rere' ('Re' for the dominant trait that you are seeing, 're' for the one inherited from the other parent)
A RECESSIVE trait isn't exactly the opposite, but it is easy to understand in the same terms. A recessive trait can only be seen if two copies are present. This means that one copy needs to come from each parent. They can go undisplayed in the parent and still be passed on to the offspring. Recessive traits are written using lower case letters when the gene is present, and capital letters when the gene is not present. In rats, many of our color genes are recessive. We can use "Mink" as an example in this case. The locus for mink is "M". For a rat to display the Mink color dilution, the two alleles within this locus must be 'mm'. ('Mm' means that the rat carries the gene, the capital 'M' means that gene is not present, the lower case 'm' means that the gene is present. It does not show because TWO copies are not present. This means that 'MM' does not carry mink.)

Mink babies

Photo Courtesy of Cathy Wingo

You may often see the terms Homozygous and Heterozygous. Homozygous means that the two alleles are the same, both present or not present (aa -or- MM). Homozygous Black rat will be 'aa' or "black". Heterozygous means that the alleles are not the same, one present, one not. Heterozygous Rex would be 'Rere' or "Rex".

Two other terms that you may see with some frequency are, Phenotype and Genotype. They sound pretty similar, right? They are, and they aren't. A Genotype describes the genes that something has. It included every carried trait in that organism. A part of a rats Genotype includes its carried, not expressed recessive genes. A Phenotype is the way the animal looks. A Mink (aamm) rat is an example of a phenotype, but that rat may carry Russian Blue (aammDd) which is it's genotype, regardless of the fact that the blue isn't expressed.

The next entry will teach a few of the known color Loci found in the rat genome, as well as beginning on how to use a Punnett Square to help you to determine expected offspring from rats. Stay Tuned!

Understanding Genetics - Reproduction

There are so many things to learn when you begin to understand genetics, not only for rats, but for anything. Yes, we understand that we inherit traits in our DNA from our parents, but how? That is today's topic!

Chromosomes
So... what are chromosomes??? Chromosomes, in a very simplified explanation, are tightly wound chunks of DNA. In this image you can see that there are pairs, also know as homologous pairs. In pair 1, one of the chromosomes some from the mother, the other from the father. It is the same for each of the following pairs. One thing to remember is that even though these chromosomes come from different beings (mother and father), as long as they are within the same species, the same genetic information should be present at the same place on each of the individuals in a pair. If the gene for, say, having a widows peak or not, were found on chromosome one, right at the top end on moms chromosome, the gene should be at the same spot on dads also.

As humans, we have 46 chromosomes that are grouped in 23 pairs. One of each of the chromosomes in a pair come from each of our parents. Essentially, half of our DNA comes from each parent. The same is true for rats. The difference is that they have 42 chromosomes, 21 pairs. Every bit of how that rat will turn out is programmed on those tiny clumps of protein and nucleic acid, the building blocks of DNA (and RNA, but that is a different story).

Our Sex Cells - Eggs and Sperm
The next thing to have a basic grasp of is how these genes all get passed to offspring, through sex cells, also called gametes. I will run through sperm cell production as it is slightly less complicated and goes through mostly the same processes.

Stem cells, located in the semeniferous vesicles (you can just know that this is in the testicles), are the origin for sperm cells. They have all of the same genes that we have present in each of our body cells. When it is time for that stem cell to become sperm, it undergoes something called spermatogenesis (Sperm making). First, there is a period where each of the chromosomes undergo a duplication phase, so each of those chromosomes that you saw up top make an identical twin attached to it. This is also known as Sister Chromatids.

 This image, showing what is known as Meiosis (cell division that makes sex cells), walks through the basic steps development from a stem cell to sex cells (but only using 2 homologous pairs). In the first cell you see 2 pairs of chromosomes. There is a red (from mom maybe) and a blue (from dad possibly) of each. After going though the duplication period you get to the second cell. Note that there are stuck together identical copies of each of the chromosomes. The following cell lines them up in preparation for the first division. The fourth cell, under B, shows something called crossing over, which is simply a means of genetic variation. This is ONE way that a parent is able to have 20 children and no two be alike unless they are paternal twins. C shows the first division. One of the long duplicated chromosomes went to each cell, and one of the short duplicated chromosomes went to each cell. The last stage, that gives you your gametes, pulls those duplicated chromosomes apart and separates them into two different cells. This means that each gamete, or sex cell, ends up with HALF as many chromosomes as the original stem cell.

Why is this??? This is because this is for one sperm. And ovum (egg) forms in a similar manner, and when they combine, you then have the full number of chromosomes and all of the needed genetic information in the offspring. I hope that provides a general understanding that will be the foundation for all of the future blogs in this series! If there are questions, please comment and I will do my best to answer them.