*with an emphasis on Rex Rabbits (see the Un-Official Rex Standard here)
This guide assumes a knowledge of basic genetics. If you need a refresher, try: Dr. Dennis O'Neil, Behavioral Sciences Department, Palomar College, San Marcos, California

This site has a well-written introduction to genetics and to rabbit coat colours at Aurora Rabbits: Raising Rabbits.com

There is also an excellent description of rabbit coat colour genetics by Laurie Stroupe Of The Nature Trail Rabbitry. It deals with Holland Lops and so skips over a few details that pertain to Rex, but is very thorough with lots of tables and pictures.

Another site full of great pictures & descriptions (with lots of Rex photos) by Pamela Nock

The Three Little Ladies Rabbitry has a great colour chart.

When it comes to coat colour, believe it or not, there are only two Fundamental Pigments: Black & Yellow(red). The expressed colour is a function of how much black or yellow pigment exists in the hair, which can change not only from hair to hair, but also along the length of a single hair. In rabbits, there can be as many as five bands of colour on a single hair. In addition, most animals have two types of hair: 'outer' guard hairs which are stiffer, thicker, and often straighter than the finer, wavier, and softer undercoat hairs. The outer coat consisting of guard hairs protects the animal, while the undercoat provides insulation.

Rex rabbits have the same double coat as other rabbits, it's just that their guard hairs are the same length as the undercoat (usually the outer coat is longer). This has several effects:

1. The outercoat does not hold the undercoat down and the entire pelt appears to stand on end. In fact, a coat that lies flat is a fault in a Rex.
2. The coat has an amazingly plush feel - these really are velveteen rabbits.
3. The guard hairs carry the same amount of colour as a regular length hair but they are considerably shorter. This means that the colour of the hair appears more intense. Contrast that with long-coated rabbits like the angora when the same amount of colour is spread out over a MUCH longer hair; these rabbits always appear to have pale colours.

All genes come in pairs. If both genes of a pair are the same, it is said to be homozygous for that trait.

Genotype refers to the gene itself, while phenotype refers to what we can see. Sometimes a phenotype will imply a certain combination of genes but the actual genotype is different. The best way to discover an animal's genotype is through test breeding with an animal whose genotype is known.

There are 5 main groups of colour genes, each controling a different aspect of the colour and markings. The genes within each group are listed in decreasing order of dominance. A Capital letter denotes a dominant gene.

A = agouti
a^t = tan (otter)
a = self

The pattern gene controls how the colour appears on the hair. The dominance relationship for these genes is quite simple: each allele is completely dominant over the ones 'below it (as listed above). This means that the following pairs will all look exactly the same: AA, Aa^t, Aa. They will all look like agoutis. A tan (or otter) can be a^ta^t or a^ta, and a self can only be aa. Unless you know the genetic make-up of the parents, it is not possible to tell what the second gene is on an agouti or tan without test breeding.

Agouti is the basic “wild” colour. Hairs on different parts of the body are coloured differently, but will have three-five different coloured bands on each hair. This pattern looks different on a rex because of the shorter hairs. The bands are smaller and the colours appear more intense. The Castor is the name given to the black agouti (the standard wild colour). Their hairs should have at least three rings: the undercolour should be slate grey; the intermediate colour should be as rich an orange or rufous red as possible, and the tips should be black.

The otter (called tan in most other breeds) should have a solid body top colour with a lighter undercolour (next to the skin). The underside (from chin through belly to tail) should be white on the surface with a grey undercolour, and there should be a redish line between the body colour and the undercolour. The insides of the ears, and around the nose and eyes should also be reddish (i.e. red or orange in full coloured [black or chocolate] rabbits and tan or cream in dilute [blue or lilac] rabbits).

The self rabbits should be exactly the same colour all over their bodies right down to the skin.

A = Agouti [“wild” colour; multi-banded hair shaft]	at = Tan [giving tan or “otter” markings]	a = Self [solid colour]
agouti	otter	self (blue)

There are only two alleles in this group: the “black” results in more intense looking colours and the brown changes the black parts of the rabbit to brown. This means that in the Castor for example, the tips of the hairs become brown instead of black, making the rabbit look much redder.

B = Black
b = Chocolate

Chocolate (otter) vs Black (otter)	Castor (black agouti)	Amber (chocolate agouti)
Black	Broken Chocolate	Chocolate vs Amber

The shading (or colour) gene controls the amount of pigment in the hair; relative amounts shown as units of black 'B' and yellow( or red) 'Y' colour. Imagine that the total amount of pigment in hair is the same for all hairs. As a result, shorter hairs appear darker (and also why long-haired varieties look faded). This explains the shading pattern found in seals, sables, torts, and the pointed colours. The colour pattern of the chinchilla (c^chd) is essentially the same as that for the agouti except that is lacks the reddish colour in the mid-band.

C = Normal [BBBBYYY]
c^chd = Dark Chinchilla [BBBBY–]
c^chl = Light Chinchilla [shaded : seal & sable] [BB—–]
c^h = Himalayan [BB—–]
c = White [Albino : absence of colour] [——-]

Dark chinchilla removes most of the yellow band. It makes the skin look brown but takes the red colour out of the hairs. Note that a chocolate chin retains the brown hue in the tipping but has completely lost it from the midband.

normal (C-)	dark chinchilla (cchd-)	white (cc)

Controls the “intensity” of the colour: a diluted black is a blue, and a diluted brown is a lilac. The dilution affects the whole rabbit, not just the hair colour. This includes the pigmentation in the skin and the eye colour.

D = Full Strength
d = Diluted

We can look at the colour (black vs brown) and the dilution genes together:
– B- – D- – = Black (where the – represent A, C, and E)
– B- – dd – = Blue
– bb – D- – = Chocolate
– bb – dd – = Lilac

Together, these two genes account for the four main colour variations of all the other shades and patterns. For example in the agouti group we have: castor (black), opal (blue), amber (chocolate), lynx (lilac).

Full Colour (Castor)	Dilute (Opal)
Full Colour (Amber)	Dilute (Lynx)

Full Colour (Black)	Dilute (self Blue)
Full Colour (Black Otter)	Dilute (Blue Otter)

a black & blue (the same blue as below)	note the differences in eye colour
both of these rabbits are dilute: the blue is Bb dd and the lilac is bb dd

These alleles control the presence, and extent of black on tips of hair and in undercolour. More extension causes the tipping to extend further down the shaft of each hair, and less extension keeps it at the tips. Non-extension gets rid of the tipping altogether, and the Japanese allele causes the black to appear in patches rather than on each hair, similar to the calico pattern of cats.

E^d = Dominant [not accepted in REX]
E^s = Steel [ not accepted in REX; causes the black on the hair to be extended, often covering the middle band with dark.]
E = Normal
e^j = Japanese [ not accepted in REX [excpet for tri-colour]; responsible for harlequin patterns]
e = Non-Extension [helpfulfor Red]

Normal Castor (E)	Steel Castor (Es)
Black-Orange Tri (Ej)

The E-series has some partial dominances which can cause the second e-gene of a heterogygous pair to show through.

The Dominant Black (E^d) makes agoutis look like blacks. For this reason it is only 'useful' in solid coloured rabbits (selfs).

The Steel (E^s) causes the darker undercolour to be extended. The ticking may also appear longer. This turns the short-haired areas dark and makes an agouti rabbit look like the top coat is too heavy. It also tends to turn the underside (belly) dark.

Next is normal extension (E) which allows the banding and colours to show through 'naturally'.)

The japanese extension (e^j) has a randomizing effect on the distribution of colour. In a solid rabbit, it is responsible for the harlequins. It is the only e-series gene that is acceptable in harlequin rabbits. The black-orange and blue-cream carry C for full colour, and the magpies (black-white and chocolate-white) carry the chinchilla gene (c^chd). An agouti or otter with one full extension (E) and one japanese gene (e^j) will always show the randomizing effect which is most notable inside the ears and around the eyes.

In Rex, a self (no white: enen) harlequin and a broken (En-) is a tri-colour and will show the dark parts as actual spots on an orange background. The full colours will have either black or chocolate spots on an orange background and the dilutes are similar only with blue or lilac and cream. Black spots on a cream background is undesirable.

The final allele is the non-extension gene (e) and is recessive to all of them. It eliminates all banding. On a self coloured rabbit (aa) it will appear as a tortoiseshell (tort) and on an agouti (A-) it will eliminate the ticking which is necessary for reds and creams.

White markings are called “broken” in rabbits (en = english spot). This allele is influenced by various modifiers that can cause the white markings to vary from tiny amounts under the chin and on the chest to the markings on finds in a Hotot which has only a fine coloured line around the eyes. In Rex, the ideal broken pattern allows for 10-50% colour. It can be a blanket pattern or spots, but the ears must be coloured and there should be colour on either side of the nose. When the nose marking straddles the nose, it's called a butterfly marking. Spots on either side are also OK. Markings that look like they have single white hairs scattered through the coloured parts are NOT desirable.

There's also a good article here (Nature Trail, Laurie Stroupe)

En = Broken Pattern
en = Self [Normal]
{there are others but they are not significant in Rex}

White markings fall into 3 categories:

It is not usually possible to distinguish between an “undermarked” broken and a true (genetic) charlie. The only definitive means is through test-mating. If a cross between the undermarked broken and a self (solid coloured) rabbit produces even a single self baby, then the broken is not a charlie.

too much colour [Enen]	broken [Enen]	broken [Enen]
(broken calls for 10-50% colour)	(lilac)	(blue otter)
'almost' charlie [Enen]	Charlie [EnEn]	Charlie [EnEn]
(black)	(tri-colour)	(chinchilla)

Judith Graf, Color Basics 1991 (self-published booklet)

Glenna M.Huffmon, The Basics of Color Genetics in Rabbits (I have the 1995 third edition)