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

By J. Ross

There is a lot of jargon and terminology used in genetics. This can be confusing to someone that has not taken a class specifically in Genetics.  The following terms and concepts should help build a basic understanding for anyone.  Although this is not a complete list of every term and concept in genetics the purpose of this is to give a basic, solid understanding to rabbit breeders and hobbyists interested in rabbit coat color genetics.

We can start this lesson with the basics of basics.  Where do the sperm and egg come from that became our favorite bunny?  These cells come from the doe and bucks' 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.  Estrous cycle is the hormonal cycle for a female rabbit that allows for the release and subsequent fertilization of the eggs. For rabbits, estrous occurs every 16-18 days, provided she is not impregnated.  Does usually become quot;receptive" to bucks at about 3 ½ months of age and are capable of conception at 4 or 4 ½ months.2  When a doe becomes receptive to bucks it is said she is in "heat" or "receptive."

The buck keeps a supply of sperm contained in the testis all the time.  Due to keeping a constant supply of sperm, the buck can be rendered temporality sterile in hot climates.  The sterility is reversed with cooler weather and time.

So now for the genetics part!  You have probably heard of the word Genome by now.  If you have not, you have probably been on a dessert island, were you the last survivor?  You could buy many rabbits with that money!  With all the cloning and genetics research going on in the news today the word, "genome", can be misunderstood.  Genome refers to the complete set of genes or genetic material that makes an organism. Each of us has our own personal genome that makes us, locked in to every cell of our bodies.  The word genome can also be generically used to refer to the unique set of genes that make all apes, apes or all rabbits, rabbits (i.e. the rabbit genome.)

A chromosome is a long strand of DNA wound up tight around little ball-like proteins called histones. This is the ideal structure for keeping this vital string of information. Image if you had a string of beads with 10,000 beads on it. Each bead would represent a single letter. Now if you wanted to read any part of this string you could just pick it up and start reading the letters. What if you kept this important information piled in the corner of your room? It would become a tangled ball and when you reached for it, you would have to unwind and untangle it each time you wanted to use it. Animals keep there chromosomes in order by carefully wrapping them around little protein balls called histones. When genetic information needs to be read, the DNA is simply unwound from the histones and used.

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

Each chromosome is made from two strands of DNA. One comes from the buck (Sire) and on comes from the doe (Dam).  These individual stands are called chromatids. This is where the duplicated symbols come from in genetics (i.e. AA, Aa, BB, Bb, or DD, Dd).  Each pair of chromosomes are known as homologous chromosomes.  That says that both chromosomes contain the same genes but can have different alleles for those genes. Each letter represents one allele for a gene from each parent.

The homologous chromosomes are not identical!  They each contain the same number of genes in the same sequence running along the strand of DNA.  Each one with it's own mutations.  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 Sire Street = gene A on Chromosome 1A, and 432 Dam Street = 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.

Like different people living in the corresponding houses on two different streets (The Jones in 423 Sire Street and The Smiths in 423 Dam Street is equal to having an at on chromosome 1A and an A on chromosome 1B).  The alleles for a gene are referred to as a series (Here are a few gene series for rabbits: A series = A, at, a, B series = B, b, C series = C cchd, cchl, ch, c, D series = D, d, et.).  Therefore, if I want to talk about the alleles for the C gene I would say, "The C series."  Each possible form of the gene a rabbit can have is called an allele.  The word allele comes from allelomorphs.  So the alleles for the A gene series are A, a, at (Later we will talk about what each letter means in relation to the coat color of the rabbit).

Figure 1: Basic Stucture and layout of a chromosome.

When we start 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 for that specific gene that is the most common in the wild.   For rabbit coat color, this is the chestnut agouti coat color.  All of the alleles for a gene arise from mutations.   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 for 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 incomplete dominance 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 the different alleles but the expression of only a single red allele instead of two red alleles. It is similar to mixing two cans of paint, one white and one red. Once mixed the white color will dilute the red color to pink

When genes are assigned letters to represent them, a capital letter usually indicates a dominant allele and a lower case usually indicates a recessive allele.  The super scripted letters (Es)are used to differentiate between two dominant or two recessive alleles.  It is also used to differentiate between dominant alleles and the wild type (Ed, Es, E).  Remember that recessive and dominant is assigned in relation to the wild type allele.  If the wild type "masks" or hides the affect of the other allele then it is classified as recessive. If the mutant allele "masks" or hides the affect of the wild type then it is classified as dominant. 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 , ect.  Sometimes the letters are assigned to indicate what the gene does.  For example, Du for the Dutch spotting gene or En for the English spotting gene.  If you are the one that discovers a gene, you usually get the privilege of deciding the nomenclature, or name, used for the gene.

Table 1 shows the common naming of the genes involved in rabbit coat color.  It is hard enough keeping track of what an allele means, image if each allele was assigned a random letter or number to represent it.  There would be a lot more bald people on the planet from pulling out their own hair!  Figure 2 shows an example of the ease of comparing two rabbits, based on coat color, using an ordered system.  Figure 1 also shows how chaotic it would be, using the same two rabbits, if a random system was used.  You can see that a direct comparison is easier using the established system of naming alleles.

Figure 2 : The effectiveness of gene labeling systems.

Ordered assignment of gene labels
Random assignment of gene labels





Table 1 lists the alleles for each of the genes involved in the coat color of rabbits.  In the table, they are listed in order of the dominance of the alleles with the most dominant allele for a gene series listed first.  Four important terms when talking about the genetic make up of an animal are genotype and 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 gene.  Genotype and phenotype have to do with the physical appearance and genetic makeup 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 of an animal is all the genes that make it.  Including genes that do not show in the physical appearance of the animal.  The phenotype is only 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 (castor) mini Rex, you know that the phenotype of the animal is this; 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 allele from the other parent. Since we can not tell what the second allele is for each gene we use the underscore, "_", to represent the alleles we do not know.  The genotype for this chestnut agouti (castor) mini Rex would be A_B_C_D_E_EnEnDuDuVVWWSiSi.

To find out what the missing alleles are we could breed this rabbit to others (Yeah, I know,"Duh!").  The breedings can help to fill in the missing alleles by looking at the color of the offspring.  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.  To determine the other alleles we would breed our chestnut agouti mini Rex to other rabbits, hopefully other mini Rexs, which have recessive alleles.  Ideally, this would be done in one cross with an aabbccddeeenenduduvvwwsisi rabbit.  Realistically, this cross is achieved in several different breedings. By using the rabbits in the herd that carry the desired reccesive genes. This types of "test" crosses are called just that, a Test Cross.

When talking about 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 we are talking about an animal that 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.

With each breed of rabbit, comes a different name for the same genotypes. The genotype A_B_C_D_E_ has different names depending on the breed you are talking about. This genotype is a chestnut agouti. In the Dutch it is called a Brown Gray, in the English Spot it is called a Gray, in the Flemish Giant it is called a Sandy, in the Rex and Mini Rex it is called a Castor, and in the Angora and Satins it is called a Copper. This can become confusing and one must struggle to keep them from being mixed up. With my compiled genotype list, you will find a color conversion chart compiled from several sources.


Gonads - The male and female sex organs; the gamete-producing organs in most animals.1

Genome - The complete complement of an organism's genes; an organism's genetic material.1

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. 1

Autosome- A chromosome that is not directly involved in determining sex, as opposed to the sex chromosomes. 1

Sex chromosomes- The pair of chromosomes responsible for determining the sex of an individual.1

Sex-linked genes- Genes located on one sex chromosome but not the other. 1

Linked genes- Genes that are located on the same chromosome. 1

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. 1

Gene- One of many discrete units of hereditary information located on the chromosomes and consisting of DNA. 1

Locus- A particular place along the length of a certain chromosome where a given gene is located. 1

Allele- An alternative form of a gene. 1

Wild type- An individual with the normal. 1

Mutation- A rare change in the DNA of genes that ultimately creates genetic diversity. 1

Recessive allele- In a heterozygote, the allele that is completely masked in the phenotype. 1

Dominant allele - In a heterozygote, the allele that is fully expressed in the phenotype.

Codominance - A phenotypic situation in which both alleles are expressed in the heterozygote.1

Incomplete dominance- A type of inheritance in which F1 hybrids have an appearance that is intermediate between the phenotypes of the parental varieties. 1

Genotype- The genetic makeup of an organism. 1

Phenotype- The physical and physiological traits of an organism. 1

Heterozygous- Having two different alleles for a given trait. 1

Homozygous- Having two identical alleles for a given trait. 1

Pedigree- A family tree describing the occurrence of heritable characters in parents and offspring across as many generations as possible. 1

TestCross- A cross in which one of the parents is homozygous for recessive alleles. Testcrosses are often used to determine whether an individual with a dominant phenotype is homozygous or hetrozygous.

Table 1: Alleles for coat color in rabbits.5,6

A Series (Agouti locus, color pattern.)




Normal agouti pattern. Banded (black and yellow) and ticked. White and light eye circles, under nostrils, belly, and underside of tail.


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.


Nonagouti.  Solid black coat.

B Series (Black locus, color)




Wild type, black eumelanin.


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 (Color locus, amount of color.)




Normal pigmentation.  Fully colored. Brown eyes.


Yellow pigment is reduced to white. Blue-grey or marbled blue eyes.


Black pigment reduced to sepia brown. Also called the sable gene. Color is shaded, typical sable when with non-agouti gene (a). Somewhat temperature-sensitive. Brown eyes.


Further reduces black pigment to pale brown. Also may be called sable gene. Debatable whether it is present in U.S. rabbits.


Himalayan.  Restricts all pigment to the extremities.  This allele is temperature sensitive. Pink eyes


Albino.  Eliminates all pigment. Pink eyes

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 lower case c indicates it is recessive to the C, normal pigmentation. Pigment in the eye is also reduced by the alleles in this series. There is debate whether the Cchm gene exists or if the resulting colors are a homozygous combination of Cchd and Cchl.

D Series (Dilute/Density locus, arrangement)




Normal pigmentation, black and yellow is intense.


Dilute pigmentation.  Black to blue and red to yellow. Pigment granules are clumped; colors appear different.

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 (Extension locus)




Reduces or eliminates the agouti band of phaeomelanin and darkens the belly. Black color is extended over the entire length of the hair shaft. There is debate as to whether this gene exists, or if the appearance is from a darker form of the Es gene.


The Steel gene. Super extension of black on the agouti hair shatf, almost all black with very little yellow anding and/or ticking; belly an dother normally light areas of agouti are dark. A weaker version of Ed. Considered more codominant with E than Ed.


Normal gray. Normal extension of the black and yellow pigments.


Japanese brindling.  Mosaic distribution of black and yellow pigmentation. Patches, bands, bars, or brindling of yellow and black. Can be diluted to Blue and Fawn, Lilac and Fawn, and Chocolate and Gold by the B and D series.


Fawn color.  Coat is yellow with a white belly

En Series (English Spotting)




English marking.


Self coloring.

Du Series (Dutch Spotting)




Self coloring.


Dark Dutch.  Minimal amounts of white. 


Light Dutch.  Extensive white spotting.

There is debate whether the Dutch coat pattern is caused by the dud and duw alleles or a single recessive du allele. There is evidence in Dutch herds that favors a single du reccesive allele.

V Series (Vienna White, BEW)




Wild Type.


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)




Normal agouti band.


Subterminal agouti band double in width.









1.     Campbell, Neil.  Biology Fourth Edition. The Benjamin/Cummings Publishing Company Inc., 2725 Sand Hill Road, 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. 525 B Street, Suite 1900, San Diego, California, 92101, 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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