Preface

The aim of this introduction is assist anyone wanting to learn about the basic principles of genetics, particularly with regards to rats, and how they relate to the breeding of these animals. This is not intended as an all inclusive resource for the study of genetics but rather as a supplement to the many fantastic Rat Genetics Explanations already available around the web. If this is your first introduction to some of the concepts explained here then it is recommended that you also go to the genetics section of our links page and visit some of the sites listed therein, in order to get a broader perspective.

Genetics

So what is Genetics?

Genetics is a science which involves the study of heredity (the passing of specific traits between parents and offspring) and genes (the basic units of storage for genetic information).

Genetic information provides the basis for the creation of an organism. As the organism grows and forms, this information directs the organism to grow in specific ways; what size to be, what colour, etc. The organisms eventual form is largely dependant on this information, though it can also be affected to varying degrees by events that may occur during that organisms life; for example if it doesn't get enough food it may not grow to its intended size. The result of this is that most organisms will become a combination of their genetic information and their life experiences.

Genetic information is stored and tranferred in the form of DNA.

DNA

The blueprints for the growth of a lifeform.

DNA (deoxyribonucleic acid) is a substance which carries the information for the development of cell-based organisms, including rats, in the form of microscopic strands. The entire collection is divided into a number of very long, continuous strands which are known as chromosomes, which assists with the organisation of DNA. The basit units for the storage and delivery of genetic information are called genes, and they inhabit specific locations along these strands of DNA.

All rats have precisely 42 chromosomes, a copy of which exists in every cell in the rats body with the exception of the sex cells (sperm and eggs), which hold 21 chromosomes. When two opposing sex cells meet to form an embryo, the embryo receives 21 chromosomes from each parent, thus giving it a full set. The embryo then repeatedly divides, replicating this DNA, until it forms a whole new rat. When a rat is producing its own sex cells, it divides it's own DNA (in a semi-random fashion) in half, giving these half-pieces of DNA to each sex cell.

Genes

The basic unit of storage for genetic information.

DNA is a made up of many components, most of which still remain a largely unknown, but the ones that concern us most are certain segments known as genes. It is these segments specifically that store information regarding an organisms development, with almost every gene contributing in some way to the growth of that organism. Furthermore, every gene has a specific place on a specific chromosome that it calls home, and in almost every creature of that species the same gene (or an allele of that gene, see below) will be found in the same place. These locations have been given the names locus (singular) or loci (plural) and specific loci are often referred to based on the genes they can carry of traits they affect, eg. Agouti-locus.

The loci which are most relevant to us are the ones on which certain mutations have occurred, which have caused significant changes to the rats colour, coat or markings, giving us the various types we have today. There are many different loci in this category and although many are not mentioned here it is recommended that you visit other rat genetics sites if you wish to learn more about them.

Mutations + Alleles

As genes are transferred from parents to offspring, occasional errors can occur that lead to slight modifications in the information that gene carries. This event is rare, and often the change has no discernible effect, or will not hold due to instability or health problems caused by the change. Sometimes, however, this change does hold and has a noticeable effect (such as changing the coat colour, eye colour, etc.) and is able to passed on to further generations. When this occurs the new gene is known as a mutation, a stable variation of an already established gene, and the original gene is referred to as the wild-type gene.

Different variations of a single gene are also referred to as alleles, the wild-type gene and its corresponding mutation/s can be said to be different alleles of the same gene. The loci that we are interested in have two or more alleles, which in different combinations can create different noticeable effects.

Dominant VS Recessive

Chromosomes often come in matching pairs, of the 42 chromosomes rats possess 40 of them can be grouped into pairs, with each member of the pair containing precisely the same loci in the same order. The result of this is that effectively an organism will carry two genes (of any possible allele) of a given locus, which combine effects to influence specific traits. When an organism is without mutations, these two genes will be of the wild-type. When an organism holds two mutation alleles then this will cause a different effect. However, when an organism holds two alleles of different types two possibilities could occur:

1. The alleles could display incomplete dominance, meaning that the two alleles will combine their effects to create a new kind of effect. An example of this could be the berkshire coat, being the combination of a self coat gene and a hooded coat gene.

2. One of the alleles could be dominant, meaning that this alleles take complete control over the related trait/s. This results in the other allele generally having no influence at all over the outcome of the organism, even though it is always present, and so this second allele is considered recessive. An example of this could be the Agouti coat colour vs the Black coat colour, if an Agouti allele is present it will completely override the effects of a non-Agouti or Black allele, causing the coat colour to be an Agouti type.

Genotype VS Phenotype

The term genotype refers to the specific genetic make-up of an individual, often in reference to one or more particular gene/s of interest. For example, the genotype of an Agouti rat which carries non-Agouti would specifically show one Agouti allele and one non-Agouti allele at the agouti-locus.

The term phenotype refers to the outward appearance of an individual, either as a whole or in reference to a particular trait. For example, the phenotype of an Agouti rat which carries non-Agouti would simply show that the individual possesses at least one copy of the Agouti allele at the agouti-locus, since this allele is dominant the resulting colour would be Agouti regardless of what other gene resides there, thus the second gene becomes irrelevant.

For example; in the case of an Agouti rat not carrying non-Agouti and an Agouti rat carrying non-Agouti, though the two rats are of different genotypes, they are said to be of the same phenotype.

Genetic Shorthand

Now we come to the method of abbreviating the genotype of our rat, in reference to the traits that we are interested in at any given time, for the purpose of a simpler way to express this information. In standard genetic shorthand, genes of a given locus are expressed as a single letter, or group of two letters, with different alleles being distinguished by upper case and lower case variations. The wild-type allele is always represented by upper case while a mutation is represented by lower case. If more than two alleles exist for that locus, additional alleles are distinguished by certain suffixes.

Example: The locus most responsible for common marking variations is the H-locus, here are three of the various alleles that are believed to exist for this locus;

H : the wild-type allele, a rat with two copies of this gene will have self marking,

h : the 'hooded' allele, a mutation, a rat with two copies of this gene will have a hood,

(Note that a rat with one 'H' and one 'h' will have a berkshire marking)

Hi / h<i> : Irish, a rat with one or two copies of this gene will generally have Irish marking.

When composing a genotype in this form, typically one would only show loci that are relevant to the purpose for which it is composed. For example it would not be necessary to show the H-locus if you are only interested in colours, also there are many more loci which would never be relevant to breeders at all. There are a few methods of composition with slight differences to appearance and though we use a widely accepted style here feel free to use a style that suits you. Our style can be viewed by the following example;

A/a M/m R/R p/p

Four loci are shown one after another, separated by spaces. The two alleles on each locus are separated by a slash. Though the ordering of the loci can be fairly flexible, the Agouti-locus is generally shown first when referring to colours.

A / a

The Agouti-locus, showing one allele to be the dominant wild-type ('A'), and one allele to be the recessive mutation, Non-Agouti (aka black). Note that where there are two different alleles at a locus, the dominant allele is always written first. Due to the Agouti genes dominance our resulting rat will now be of an Agouti type, though the exact colour may be affected other loci.

M / m

The Mink-locus, showing one allele to be the dominant wild-type and one allele to be the recessive mutation, Mink. Mink dilutes the coat colour, however since non-Mink is dominant the coat will not be diluted by this loci. Also note that since there are always two genes at any given locus, there will always be two letters in each group in the genotype.

R / R

The Ruby-eye locus, showing no mutations (both letters being upper case). Typically if a locus shows no mutations it can be left out of the genotype to save space, and it can be assumed that any locus not mentioned has known mutations. It has been included here for the purposes of example.

p / p

The Pink-eye locus, showing two copies of the recessive mutation, Pink-eyes (both letters being lower case). Because there are two copies of this gene, its recessive effects will now show, not being overridden by dominant effects, to result in this rat having pink eyes and a diluted coat colour.

So what colour will this rat be?

Pink-eyed Agouti, also known as SilverFawn or Amber.

Summary

Genetics is the study of genes and heredity.

DNA exists in the form of long strands and is the carrier of genes.

Chromosomes are groups of DNA strands that together form a creatures genotype.

Genes are segments of DNA which are the basic units of genetic information, carrying instructions that relate to specific aspects of growth or functioning.

Loci are specific locations on DNA strands where genes can be found.

Alleles are different variations of a single gene.

The wild type is the most common allele of a gene.

Mutations are rare alleles that differ from the wild type.

Dominant alleles will completely override the effects of recessive alleles.

Semi-dominant alleles will result in combined effects.

A creatures genotype is its specific genetic make-up.

A creatures phenotype is its outward appearance, which is derived at least partly but not always completely from its genotype.

Sources

North of England Rat Society; The Genetics of Rat Coat Colour and Pattern ::Farlex Inc.; The Free Dictionary by Farlex (Online Encyclopedia :: John Kyrk; Cell Biology Animations