How the five loci work
Every color on a domestic rabbit is built from just two pigments: eumelanin, which is black or brown, and pheomelanin, which is yellow or red. There is no blue pigment and no chocolate pigment. What breeders call blue is black pigment deposited more sparsely in the hair shaft, and what they call lilac is chocolate treated the same way. Five classical gene locations — written A, B, C, D and E — decide which of the two pigments gets made, how strongly, and where along each hair it lands. Get those five right and you have named almost every color in the standards.
Each locus carries two alleles, one from each parent, and within a locus the alleles have a fixed pecking order. A rabbit shows the phenotype of the most dominant allele it carries and silently passes on the other one. That is the whole reason a rabbit genetics calculator is useful at all: the hidden allele is invisible on the animal but very much present in the litter.
The A locus (the ASIP gene) decides the pattern of each individual
hair. A gives the agouti coat — every hair banded dark, then yellow, then dark
again, with a light belly. at gives the tan pattern: solid-colored
hairs on the body with a bright tan or cream belly, eye circles, nostril lines and a triangle
behind the ears. a is self: one solid color from skin to tip. The order is
A > at > a.
The B locus (TYRP1) chooses which eumelanin is made — B for black,
b for chocolate — and the D locus (MLPH) decides how densely it is
packed. Together they give the four base colors every other color is built on: black
(B_D_), blue (B_dd), chocolate (bbD_) and lilac
(bbdd). Both are simple two-allele, fully dominant genes.
The C locus (tyrosinase) controls how much pigment the enzyme can make at all,
and it is the one with the longest ladder: C > cchd >
cchl > ch > c. Full color,
then chinchilla-dark, then chinchilla-light (the shaded or sable allele), then Himalayan, then
albino. Chinchilla works by removing the yellow pigment: an agouti rabbit whose yellow band turns
white is a chinchilla. Himalayan is a heat-sensitive version of the enzyme, which is why the
points — ears, nose, feet, tail — are colored and the warm body is not, and why a Himalayan
raised cold carries darker points. And cc is epistatic: it stops
all pigment, so an albino rabbit is a ruby-eyed white no matter what the other four loci say.
Every one of them is still there, still being passed on, and completely invisible.
The E locus (MC1R) decides how far the dark pigment extends along the hair.
E is normal extension and lets A and C do their job. e, in the
homozygous ee state, stops dark pigment reaching the coat at all, leaving orange,
fawn or tortoise. ej — Japanese brindling — mosaics the two pigments
into the patches of a harlequin. Es is steel, a partial extension that
leaves tipped guard hairs, and it only shows on a rabbit that is also agouti.
The five loci at a glance
| Locus | Gene | Alleles, most dominant first | What it changes |
|---|---|---|---|
| A | ASIP | A > at > a | Banding along the hair: agouti, tan/otter, or self |
| B | TYRP1 | B > b | Which dark pigment: black or chocolate |
| C | TYR | C > cchd > cchl > ch > c | How much pigment is made: full, chinchilla, shaded, pointed, albino |
| D | MLPH | D > d | Density: black→blue, chocolate→lilac |
| E | MC1R | Ed > Es > E > ej > e | How far dark pigment extends: dominant black, steel, normal, brindle, none |
How to read a rabbit genotype string
A genotype is written as five pairs in locus order, so aaBBCCDdEE reads: self at A,
black at B, full color at C, one dense and one dilute at D, normal extension at E. That rabbit
is black and carries dilute. An underscore stands for “unknown, and it does not matter here” —
aaB_C_D_E_ is how you write “this rabbit is black and I have not proved the rest”.
Convention puts the dominant allele of each pair first, which is why you see Dd and
never dD. The calculator above writes both parents’ strings under their dropdowns so
you can copy them onto a pedigree.
Two shorthand habits are worth knowing. Breeders often skip loci where nothing interesting is
happening and write aaDd for the black-carrying-dilute above. And superscripts are
frequently flattened in typed text, so at becomes at,
cchd becomes cchd and ej becomes
ej. Both are fine as long as everyone reading the pedigree agrees.
A worked example, step by step
Take a black otter doe who carries chocolate, dilute and albino —
ata Bb Cc Dd Ee — over a chestnut buck who carries self, chocolate and
dilute but not albino: Aa Bb CC Dd Ee. That is the cross loaded in the calculator by
default, so you can check these numbers against the tool itself. It produces
18 distinct colors. The five most likely are:
| Color | Chance per kit | Why |
|---|---|---|
| Chestnut agouti (castor) | 21.09% | Agouti from the buck, full color, black base, dense, normal extension |
| Black otter | 10.55% | at from the doe with no A to outrank it |
| Black | 10.55% | aa from both sides — the buck’s hidden self allele surfacing |
| Orange | 9.38% | ee: both parents pass non-extension, so no dark pigment reaches the coat |
| Opal | 7.03% | Agouti again, but dd dilutes the black bands to blue |
The remaining thirteen run down through chocolate agouti (amber) and tortoise at 7.03%, the
dilute and chocolate otters, fawn, lilac agouti (lynx), and finally lilac tortoise at 0.78% —
the kit that needs the recessive allele from all three of B, D and E at once. Note what is
absent: no ruby-eyed white, because the buck is CC and cannot pass an
albino allele, so the doe’s c has nothing to pair with. One parent being clear of a
recessive removes that color from the litter entirely.
Why two black rabbits can produce a blue kit
This is the question that sends most people looking for a rabbit breeding color calculator in the
first place, and the answer is the D locus. Dilute is recessive. A rabbit with Dd
looks exactly as black as one with DD — the single dense allele is enough to make a
full-density coat, and there is no visual tell. Breed two Dd blacks together and
each kit has a one-in-four chance of drawing d from both parents. That kit is
dd, and it is blue.
Load the “two blacks carrying dilute” preset and the tool gives exactly 75% black and 25% blue.
The same logic produces every surprise in the hobby: chocolate out of two blacks (both carried
b), a ruby-eyed white out of two colored parents (both carried c), an
orange out of two blacks (both carried e). A recessive can travel silently through
generations and only announces itself when it meets a copy of itself.
Color, pattern, and what a rabbit color chart is really listing
A printed rabbit color chart usually mixes two different things. Most rows are colors —
black, blue, chocolate, lilac, chestnut, opal, chinchilla, Himalayan, ruby-eyed white — and those
are exactly what the five loci above determine. A few rows are patterns: broken, Dutch,
English spotting, banded. Patterns describe how white is distributed over the body and are
controlled by entirely separate genes, chiefly the spotting gene at the En locus.
They stack rather than compete. A broken black is a black rabbit — aaB_C_D_E_, all
five loci as above — that also carries one copy of the spotting allele. The color genes decide
which color the colored patches are; the pattern gene decides where they are.
That is why show standards name them together: “broken chestnut”, “broken tortoise”. It also
means a color calculator and a pattern calculator are answering different questions, and this
one answers the color question.
What this calculator cannot tell you
Being straight about the edges matters more than looking clever, so here is the honest list.
- Broken and Charlie. The
Enspotting locus is not modeled.Enenis a normal broken,EnEnis a Charlie with very little color left,enenis solid — a separate square you would run alongside this one. - Wideband and rufus modifiers. The depth of red on an agouti or an orange is set by polygenic modifiers with no clean allele symbols. They are the difference between a washed-out fawn and a rich red, and no five-locus model predicts them.
- Silvering, Vienna and dwarf genes. Silvering has not been pinned to an identified gene at all. The Vienna gene behind blue-eyed white, and the dwarf gene that turns a homozygous kit into a non-viable peanut, sit outside this system entirely.
- Shade grading. Sable, seal and smoke pearl differ by degree as much as by genotype, and the same pairing can be judged differently in two breeds.
- Anything about the animals themselves. Probabilities per kit, nothing more — no litter sizes, no health, no welfare.
Where the sources disagree, and what we chose
Hobbyist charts contradict each other most often at the C and E loci, so it is worth stating which reading this tool implements and where the disagreement lies.
The E locus has five alleles, not four. A great many breeder pages list
Es > E > ej >
e and stop there. Both the OSU Extension write-up and the molecular work on the
rabbit MC1R gene describe a fifth and more dominant allele, Ed, dominant
black — rare, but real, and confirmed by segregation in F1 and F2
families. We include it, marked rare, and default it to off.
The shaded allele is less certain than the others. OSU is explicit that the
existence of cchl and its relationship to the sable phenotype “has been
speculated, but not confirmed with DNA evidence”. We keep the allele because it is how breeders
actually record sables and seals, but treat any cchl result as the
least-supported output on this page.
One deliberate departure. The OSU text says Ed fixes the
color from B and D “no matter what the A and C genotypes are (except cc)”. We apply that to the
A locus, but not to ch: the C-series alleles are mutations of tyrosinase
itself, so a Himalayan simply cannot manufacture full-body pigment however hard the MC1R gene
signals for it. We flag the departure rather than bury it — if you are working strictly to the
published text, read an Ed_ chch result as
contested.
Frequently asked questions
- What color will my rabbit’s babies be?
- There is no single answer — a litter is a probability distribution, not one color. Enter both parents’ alleles at the five loci above and the calculator lists every kit color that cross can produce with its exact percentage. If you only know what the parents look like, you can still narrow it down: a rabbit’s appearance fixes its dominant alleles but hides the recessive ones it carries, so start from the visible color and try each plausible hidden allele in turn.
- How is this different from a plain rabbit Punnett square calculator?
- A Punnett square handles one locus at a time. Rabbit color needs five simultaneously, and the loci interact — cc hides every other gene, ee removes the dark pigment the A locus was arranging, and steel only shows on an agouti rabbit. This tool runs all five squares, multiplies the independent results into a joint distribution, then applies those interaction rules to name the color a breeder would actually write on the pedigree.
- Why do the percentages not match my last litter?
- Percentages describe the chance per kit, not a guaranteed split of the litter. A 25% chance in a six-kit litter most often produces one or two, but zero and six are both perfectly possible. Each fertilization is an independent draw, and a doe that threw four blacks in a row is no more likely to throw a blue next time.
- Can a bunny color calculator tell me the genotype from a photo?
- No, and neither can an experienced judge. Appearance tells you the dominant allele at each locus and nothing about the second one. A black rabbit is aaB_C_D_E_ — the underscores are genuinely unknown until you test-breed it, look at its pedigree, or send a sample for commercial coat-color genotyping.
- I searched for a rabbit colour calculator — is this the same thing?
- Yes. Rabbit color calculator and rabbit colour calculator are the same tool; we use the American spelling on this page because that is where most of our readers are, and the genetics are identical either way. Only the colour names drift between countries. The same rabbit is a castor in a Rex, a chestnut agouti in a Netherland Dwarf, and simply an agouti across much of Europe. Where two names are in common use we show both, but always check your own club’s standard before entering a rabbit in a show.
Sources
- Understanding the genetics behind rabbit coat colors: Part 1 — introduction — Oregon State University Extension Service, EM 9707 (Stern & Cruickshank, 2022), peer reviewed. Dominance, alleles and the two pigments.
- Part 2 — coat color genes — the allele list and the dominance order of all five loci implemented above, plus the spotting and silvering genes we deliberately leave out.
- Part 3 — your rabbit — working backwards from a rabbit you can see to the genotype you would type into this calculator.
- Fontanesi et al., “A composite six bp in-frame deletion in the MC1R gene … Japanese brindling coat color in rabbits”, BMC Genetics — independent confirmation of the five-allele Extension series and its dominance order.