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Genetics 101: Introduction to Genetics Terms and Concepts for Understanding Rabbit Coat Color Genetics

A lot of jargon and terminology used in genetics can be confusing to someone who has not taken a genetics class. This article is not a complete list of every term and concept in genetics--my purpose is to give rabbit breeders and hobbyists interested in rabbit coat color genetics a basic, solid understanding of the field.

We can start this lesson with the most basic of basics. Where do the sperm and egg come from that became our favorite bunny? These cells come from the doe's and buck's gonads. In the doe the gonads are called ovaries and in the buck they are called the testis. The doe produces several eggs during her estrous cycle. For rabbits, this occurs every 16-18 days, provided the doe is not pregnant. Does usually become "receptive" to bucks at about 3 months of age and are capable of conception at 4 or 4 months.2 This is when she is in "heat." The buck has a supply of sperm in the testis all the time and is always ready to mate.


The sperm and egg contain genetic material that when combined form the genome of their offspring. You have probably heard of the word genome by now. If you have not, you have probably been on a desert island--were you the last survivor? You could buy many rabbits with that money! With all of the cloning and genetics research being reported in the news today, the word genome might be misunderstood. Genome refers to the complete set of genes or genetic material that makes an organism unique. A gene is one of many discrete units of hereditary information located on the chromosomes and consisting of DNA. DNA is a set of nucleic acids that are usually localized in a cell's nucleus and that form the molecular basis for heredity in most organisms. A chromosome is a long strand of DNA that is wound tightly around little ball-like proteins called histones. Each of us has our own personal genome, locked in to every cell of our bodies, that makes each of us the people that we are. The word genome can also be generically used to refer to the unique set of genes that makes all apes, apes, or that makes all rabbits, rabbits (i.e., the rabbit genome).

The Rabbit Genome

The rabbit genome contains 22 pairs of chromosomes; 21 pairs are autosomal chromosomes. That is to say, they do not determine the sex of the rabbit. The last pair is the sex chromosomes. The infamous X and Y or X and X. A doe has two X-chromosomes, and a buck has an X and a Y chromosome. If a gene is on a sex-chromosome, then the gene is a sex-linked gene. If two genes are on the same chromosome, they are called linked genes. In some species, specific traits appear in only males or in only females. The genes that control these traits are mostly likely located on the X and or Y chromosome.

In each pair of chromosomes, one comes from the buck (sire) and on comes from the doe (dam). This is where the duplicate letters come from in genetics (i.e., AA, Aa, BB, Bb, or DD, Dd). Each pair of chromosomes is known as homologous chromosomes. Each letter represents one allele for a gene from each parent. An allele is each possible form of a gene.

The homologous chromosomes are not identical! They each contain the same number of genes in the same sequence running along the strand of DNA and each has its own mutations. They're like two parallel streets with the same number of houses. The location of the gene along the strand of DNA is called the locus, or the physical address of the gene (i.e., 432 Fairmount, 432 Haven = gene A on chromosome 1A and gene A on chromosome 1B). Each chromosome can contain different alleles for each gene. The assignment of A and B to a chromosome is random because we cannot determine which one came from which parent under a microscope. It's like different people living in the corresponding houses on two different streets (the Jones live in 423 Fairmount and the Smiths live in 423 Haven = having an at on chromosome 1A and an A on chromosome 1B). The alleles for a gene are referred to as a series (A series = A, at, a; B series = B, b; C series = C cchd, cchl, ch, c; etc.). Therefore, if I want to talk about the alleles for the C gene, I would say, "the C series." Later we will talk about what each letter means in relation to the coat color of the rabbit.

The Wild Type

When talking about genes, it is usually good to start with a reference. In most cases, the gene of concern is compared to the wild type. Wild type refers to the allele that is the most common in the wild for a specific gene. For rabbit coat color, this is the chestnut agouti coat color. All of the alleles for a gene arise from mutation. Radiation, chemicals, UV light, free radicals from within the cell, and many other sources can cause these mutations. With reference to the wild type and other alleles for a gene, an allele can be classified as recessive, dominant, or codominant.

The E series for rabbit coat color is an excellent example of mutations that are dominant and recessive to the wild type. The allele for the E gene that produces a steel coat is Es; this is dominant to the wild type form for the gene E. The two other alleles for the E gene, e and ej, are recessive to the wild type, E.3 A good example of codominance is found in the snapdragon. The genes for flower color have several alleles. If you cross a red flowered plant with a white flowered plant, you get offspring with pink flowers.4 The pink is not the result of a different allele, but the expression of both the white and the red alleles at the same time.

The Gene Labeling System

When genes are assigned letters to represent them, a capital letter usually indicates a dominant allele and a lowercase letter usually indicates a recessive allele. The superscript letters (Es) are used to differentiate between two dominant or two recessive alleles. Superscript letters are also used to differentiate between dominant alleles and the wild type (Ed, Es, E). Remember that the terms "recessive" and "dominant" are assigned to alleles in relation to the wild type allele. Using a system that keeps all alleles for a gene using the same letter makes it is easier to keep track of genes when doing pedigree analysis. It is true that the letter chosen for a gene is somewhat random. The genes are usually assigned in the order they were discovered. The first gene discovered for rabbit coat color was labeled A, the second one B , etc. Sometimes the letters are assigned to indicate what the gene is responsible for. For example, Du is the Dutch spotting gene or En is the English spotting gene. If you are the one that discovers a gene, you usually get the privilege of deciding the nomenclature, or name, that should be used for the gene.

It is hard enough keeping track of what an allele means--imagine if each allele were assigned a random letter or number to represent it. There would be a lot more people on the planet who were bald from pulling out their own hair! Figure 1 shows an example of the ease of comparing two rabbits, based on coat color, using the established system of using the same letter for all alleles of a gene. Figure 1 also shows how chaotic it would be, using the same two rabbits, if a random system were used. You can see that a direct comparison is much easier using the established system of naming.

Figure 1: The effectiveness of gene labeling systems

Assignment of gene labels
using established system
Assignment of gene labels
using random system
Rabbit 1
Rabbit 2

Genes in Rabbit Coat Colors

Table 1 shows the common naming of the genes involved in rabbit coat color and lists the alleles for each of the genes involved in the coat color of rabbits. In the table, they are listed in order of dominance with the most dominant listed first. Four important terms when talking about the genetic make up of an animal are genotype, phenotype, heterozygous, and homozygous. Heterozygous and homozygous refer to the combination of alleles the rabbit has for a particular gene. A heterozygous combination means the rabbit has two different alleles for the gene and homozygous means the rabbit has the same two alleles for the gene. Genotype and phenotype have to do with the genetic makeup and physical appearance of a rabbit. An easy way to help keep track of what each means is to think of them as thus; genotype = gene type, phenotype = physical type.

The genotype is comprised of all the genes in an animal, including genes that do not show in the animal's physical appearance. The phenotype is comprised only of the genes that show in the appearance of the animal. The phenotype comes from what we can tell about the animal by looking at it. If you have a solid chestnut agouti mini Rex, you know that the phenotype of the animal is ABCDEEnDuVWSi. These are the alleles for the genes that code for the chestnut agouti color. Now, each of these dominant alleles could be masking, or hiding, recessive alleles. Because we cannot tell what the second allele is for some genes, we use the underscore (_) to represent the alleles we do not know. The genotype for this chestnut agouti mini Rex would be A_B_C_D_E_EnEnDuDuVVWWSiSi.

To find out what the missing alleles are in a rabbit, we could breed this rabbit to others. (Yeah, I know, "Duh!") The breedings can help to fill in the missing alleles: when the offspring is born, you can look at the color of their coats. A pedigree with information about the rabbit's ancestors' colors can help to fill in the gaps, too.

There are times, though, that the pedigree will be of little use. If the rabbit is a red-eyed or blue-eyed white, it would be difficult using a pedigree to determine the other alleles in the rabbit. We could, however, find out what the missing alleles are in our chestnut agouti mini Rex by breeding him to other rabbits--hopefully other mini Rexs--that have recessive alleles. Ideally, this would be done in one cross with an aabbccddeeenenduduvvwwsisi rabbit. Realistically, this cross is achieved in several different breedings.

In the above cross, you can see that the phenotype of the recessive rabbit is long and contains information that we are not talking about. If the rabbit is solid in coat color and does not posses the silvering gene, we can shorten the phenotype to just the genes of interest, aabbccddee. This helps save keystrokes and ink. To shorten it even further, you can list only the recessive alleles. For a chocolate mini Rex, this would be aabb. In this case, the other alleles would be assumed to be C_D_E_. This works if you do not know the other alleles. If you do know something about the other alleles, then you could fill them in like this: aabbCc.

Table 1: Alleles for Coat Color in Rabbits5,6

  Allele Description
A Series
A Normal agouti pattern. Gray with white belly
at Black and Tan coat pattern. This allele gives the rabbit a white belly, black nonagouti on the dorsal surface, whitish eye circles, and tan on the foot pads, under the tail, and at the edge of the white belly.
a Nonagouti. Solid black coat
B Series B Wild type, black eumelanin
b Replacement of black eumelanin with brown eumelanin.
Notes: Agouti brown rabbits are cinnamon colored, where nonagouti brown rabbits are solid brown in color
C Series C Normal pigmentation. Fully colored
cchd Yellow pigment is reduced to white
cchm Black pigment reduced to sepia brown
cchl Further reduces black pigment to pale brown
cH Himalayan. Restricts all pigment to the extremities. This allele is temperature sensitive.
c Albino. Eliminates all pigment.
Notes: Mutations in the C series reduces pigmentation. The superscripted H for the Himalayan gene indicates that it is dominant to the other alleles and the lowercase c indicates it is recessive to the C, normal pigmentation. Pigment in the eye is also reduced by the alleles in this series.
D Series (Dilute locus) D Normal pigmentation, black and yellow is intense
d Dilute pigmentation. Black to blue and red to yellow.
Notes: The homozygous condition, dd, results in different pigmentation changes according to other alleles present: black to a blue-gray, brown to lilac, or yellow to cream.
E Series Ed Reduces or eliminate the agouti band of phaeomelanin and darkens the belly/TD>
Es A weaker version of Ed. Considered more codominant with E than Ed
E Normal gray
ej Japanese brindling. Mosaic distribution of black and yellow pigmentation
e Fawn color. Coat is yellow with a white belly
En Series (English Spotting) En English marking
en Self coloring
Du Series (Dutch Spotting) Du Self coloring
dud Dark Dutch. Minimal amounts of white
duw Light Dutch. Extensive white spotting
V Series (Vienna White, BEW) V Wild Type
v Vienna White. All pigment is removed from the hair. Pigment is also removed from the anterior surface of the iris, giving it a blue appearance.
W Series (Wide Band) W Normal agouti band
w Subterminal agouti band double in width
Silvering Si Normal
si Silvering


allele - An alternative form of a gene. The word allele comes from allelomorphs.
autosomal - A chromosome that is not directly involved in determining sex, as opposed to the sex chromosomes.
chromosome- A long, threadlike association of genes in the nucleus of all eukaryotic cells and most visible during mitosis and meiosis. Chromosomes consist of DNA and protein.
codominant - A phenotypic situation in which both alleles are expressed.
DNA - Short for deoxyribonucleic acid. Nucleic acids that are localized in a cell's nucleus and form the molecular basis for heredity in most organisms. DNA have a double helix of deoxyribose and phosphate, held together by hydrogen bonds.
dominant - The allele that is fully expressed in the phenotype.
gene - One of many discrete units of hereditary information located on the chromosomes and consisting of DNA.
genome - The complete complement of an organism's genes; an organism's genetic material.
genotype - The genetic makeup of an organism.
gonads - The male and female sex organs; the gamete-producing organs in most animals.
heterozygous - Having two different alleles for a given trait.
homologous chromosomes - Chromosome pairs of the same length, centromere position, and staining pattern that possess genes for the same traits at corresponding loci. One homologous chromosome is inherited from the organism's father, the other from the mother.
homozygous - Having two identical alleles for a given trait.
incomplete dominance - A type of inheritance in which hybrids have an appearance that is intermediate between the phenotypes of the parental varieties.
linked genes - Genes that are located on the same chromosome.
locus - A particular place along the length of a certain chromosome where a given gene is located.
mutation - A rare change in the DNA of genes that ultimately creates genetic diversity.
pedigree - A family tree describing the occurrence of heritable characteristics in parents and offspring across as many generations as possible.
phenotype - The physical and physiological traits of an organism.
recessive - The allele that is completely masked in the phenotype.
series - The alleles for a gene.
sex chromosomes - The pair of chromosomes responsible for determining the sex of an individual.
sex-linked genes - Genes located on one sex chromosome but not the other.
wild type - For a specific gene, the allele that is the most common in the wild.


1. Campbell, Neil. Biology, Fourth Edition. The Benjamin/Cummings Publishing Company Inc., Menlo Park, California, 1996
2 Manning, Patrick J. Newcomer, Christian E., Ringler, Daniel H., The Biology of the Laboratory Rabbit, Second Edition. Academic Press, Inc., San Diego, California, 1994 p. 32
3. Castle, W. E. The Genetics of Domestic Rabbits: A manual for students of mammalian genetics and an aid to rabbit breeders and fur farmers. Cambridge, Harvard University Press, 1930
4. Campbell, p. 248
5. Manning P. 7
6. Manning P. 12





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