How Chicken Colour Genetics Works

1. Two pigments do all the work

Feather colour in the chicken is built almost entirely from two pigments, both made by the same pigment cells (melanocytes) from the amino acid tyrosine:

• Eumelanin — the black and dark-brown pigment.
• Pheomelanin — the red, gold, and buff pigment.

There is no blue pigment, no white pigment, and no lavender pigment in a chicken feather. What look like those colours are produced by controlling the two pigments above: white is the near-total absence of pigment, blue-grey is diluted eumelanin, and gold ground colour is pheomelanin showing through wherever black has been kept out. Almost every colour gene works by changing one of three things — which pigment is made, where on the body it is deposited, and how concentrated it is. Keep that framing in mind and the rest of the system follows from it.

2. Genes, loci, and alleles

A gene is a stretch of DNA with a job. The physical place a gene sits on a chromosome is its locus (plural loci). A chicken carries its chromosomes in pairs — one from each parent — so at most loci it holds two copies of every gene. The specific versions it holds are called alleles.

Take the Blue locus. It has two common alleles: Bl (the blue version) and bl+ (the ordinary, non-blue "wild-type" version). A bird can be bl+/bl+, Bl/bl+, or Bl/Bl — those three genotypes are the only combinations two alleles allow. When both copies match (bl+/bl+ or Bl/Bl) the bird is homozygous at that locus; when they differ (Bl/bl+) it is heterozygous.

Two distinctions matter constantly:

• Genotype vs. phenotype. The genotype is the allele combination the bird actually carries; the phenotype is what it looks like. Two birds can share a phenotype while carrying different genotypes — which is exactly why breeding results sometimes surprise people, and why a calculator earns its keep.
• Wild-type. The "+" allele (e.g. bl+, e+, s+) is the reference or ancestral version, the state of the red jungle fowl from which domestic chickens descend. Wild-type is a baseline for notation — not necessarily the most common allele in a given breed today.

3. Dominance: how two copies combine

When a bird's two alleles at a locus differ, which one you actually see depends on their dominance relationship:

• A dominant allele shows its effect with just one copy. Blue (Bl) and Dominant White (I) are dominant — a single copy already changes the bird.
• A recessive allele shows its effect only when both copies are present. Lavender (lav) and recessive white (c) are recessive — a single copy is carried silently and can travel hidden through generations until it meets another.

"Dominant" is not a statement that an allele is stronger or better; it is only a statement about how many copies are needed to see it, and it is decided locus by locus.

4. The foundation: the Extension (E) locus

If you learn one locus first, make it Extension (E), the master switch for the black/red balance. Its gene has been identified as MC1R, the melanocortin-1 receptor.² Extension decides how far eumelanin (black) is allowed to extend across the body, and correspondingly how much pheomelanin (red/gold) is left showing. Unusually, it has not two but a whole series of alleles, ranked in a dominance order.¹ Every variety begins from one of these as its base:

The conventional dominance order is E > eR > EWh > eb > e+,¹ so a bird carrying two different E-series alleles generally shows the higher-ranked one, though the boundaries between adjacent alleles are soft and other genes shift the result. Because a bird has only two E-locus slots, its whole colour story starts from at most two of these alleles — everything else is other genes acting on top of that base. Two adjacent alleles with a similar modifier layered on top can even converge on the same look — see Brown vs Wheaten base genetics for a worked example, and why the resemblance stops holding once you cross the two.

5. Building on the base: pattern & modifier genes

The Extension base is rarely the finished bird. A second group of genes redistributes, restricts, or organises eumelanin into the patterns breeders recognise. Crucially, most of these do nothing visible on their own — their effect depends on which E-base they are sitting on. When one gene's effect depends on another gene like this, geneticists call it epistasis, and it is the single biggest reason chicken colour feels complicated: you cannot read a gene in isolation, only in the context of the base it modifies.

• Columbian (Co) — restricts eumelanin to the hackle, tail, and wing tips, clearing the body. It is what turns a dark base into the crisp black-and-white "Columbian" or "Light" pattern.
• Melanotic (Ml) — pushes eumelanin the other way, extending black further through the plumage and darkening the bird.
• Pattern gene (Pg) — organises eumelanin into structured markings. On its own it produces barring or pencilling; combined with eb and Co it produces lacing, with eb and double Ml double-lacing, and with eR spangling. Pattern is the clearest example of a gene whose meaning is entirely contextual — worked through on the Pattern genes page.
• Dark Brown (Db) — shifts pheomelanin toward darker ocher and red-brown shades, deepening the ground colour.

Two of these — the molecular identities of Db and Ml — have only recently been mapped to specific chromosomal regions,⁹ a reminder that this is living science, not a closed book.

6. Turning colour down: dilution genes

A third group doesn't move pigment around — it dilutes or removes it. These are the genes behind most of the "soft" and pale varieties:

• Blue (Bl) — dilutes eumelanin with incomplete dominance: one copy blue-grey, two copies splash (see section 3). It leaves pheomelanin untouched. Full walkthrough, with the cross ratios, on the Blue, Splash & Black page.
• Lavender (lav, also called self-blue) — a recessive that dilutes both pigments evenly, giving pale grey where black would be and straw where red/gold would be. Its gene has been identified as MLPH (melanophilin), which affects how pigment granules are transported within the cell.⁵ This even, both-pigment dilution is the key difference from Blue — see the dedicated Lavender page, or the FAQ, for the Lavender-vs-Blue comparison.
• Dominant White (I) — inhibits the expression of eumelanin, so a coloured base is turned largely white with a single copy. Its gene is PMEL17, involved in building the internal structure of the black-pigment granule.³ It is the basis of the "Paint" pattern when layered over a Blue or Splash base.
• Recessive White (c) — a completely separate route to a white bird, blocking pigment production only when two copies are present. Because Dominant and Recessive White are unrelated genes reaching a similar look by different means, two white birds are not necessarily "the same" underneath, and crossing them can give coloured chicks.

7. Sex-linked genes and why sons and daughters differ

In chickens the sex chromosomes are Z and W, and — unlike mammals — it is the female who carries two different ones. Roosters are ZZ; hens are ZW. A gene that sits on the Z chromosome is therefore inherited differently by the two sexes, because a hen has only a single Z to carry it:

• A rooster (ZZ) carries two copies of any Z-linked gene, just like an autosomal gene, and needs two recessive copies to show a recessive trait.
• A hen (ZW) carries only one copy — she is hemizygous — so whatever single allele sits on her one Z is what she shows, with no second copy to mask it.⁶

Three of the site's loci are sex-linked, all now traced to genes on the Z chromosome:

This asymmetry has a famous practical payoff: a cross set up so that sons and daughters inherit different Z-linked alleles produces chicks that can be sexed by colour at hatch — the basis of commercial "auto-sexing" and sex-linked hybrids, worked through with the actual crosses on the Sex-linked colour genes page. Because sex-linked genes are inherited differently by sons and daughters, the Breeding Outcomes tool reports frequencies based on the rooster's contribution and highlights cases where expected hen and rooster offspring ratios differ: for these genes, "50% of the offspring" is not necessarily the same statement for sons as for daughters. In practice this means the tool generates two separate offspring-frequency tables — one for sons, one for daughters, each totalling its own 100% — whenever a sex-linked gene actually produces different outcomes in the two sexes; when every sex-linked gene in the cross is fixed and the sons and daughters would look alike, the two collapse back into a single shared table shown on that same rooster (two-copy) basis, noting that hens carry only one copy of each Z-linked gene.

8. Linked genes and recombination

Genes assort independently only when they sit on different chromosomes. Genes that sit close together on the same chromosome tend to be inherited as a block, because separating them requires a physical crossover to happen between them during the formation of egg and sperm. The chance of that crossover is the recombination frequency: a small number means the genes travel together most of the time.

On this site the clearest example is the Db–Ml–Pg group, which lies together on chromosome 1. Their measured recombination frequencies are low — roughly 0.12 between Db and Ml and 0.10 between Ml and Pg¹⁰ — so they are usually passed on as a haplotype rather than shuffled freely. The Breeding Outcomes calculator applies these linked ratios by default when a cross involves two or more of them, because treating them as independent would overstate how often the rarer recombinant combinations actually appear.

9. From genotype to the bird in front of you

Putting the layers together, a chicken's colour is read in roughly this order:

1. The Extension base sets the starting black/red balance (section 4).
2. Pattern and modifier genes redistribute and organise the black on that base — their meaning depending on which base they sit on (section 5).
3. Dilution genes turn the resulting pigment down or off (section 6).
4. Sex-linked genes add their effects, differently in the two sexes (section 7).
5. Linkage shapes which combinations of the linked group are actually passed on (section 8).

Because these layers interact — the same modifier meaning different things on different bases, the same genotype looking different in rooster and hen — working a real cross by hand is genuinely error-prone. That is what the tools are for: Compare Standards lays two varieties' genotypes and standard descriptions side by side so you can see exactly which loci differ, and Breeding Outcomes runs the Punnett-square maths — including the sex-linkage and linkage subtleties above — to predict what a mating will actually produce, and how many eggs you would need to hatch to get a given result.

10. A note on sources

The inheritance rules and locus behaviour described here are standard chicken colour genetics, drawn from the primary scientific literature listed below and cross-checked against two long-standing breeder references: chicken-colors.info (which itself builds on the Dutch Kippenencyclopedie and on the scientific literature) for variety standards and phenotype descriptions, and kippenjungle.nl for genotype and linkage data. Where a statement rests on a specific study — particularly the molecular identity of a gene — it is numbered to the reference below. The Blue/Splash locus is described here by its inheritance pattern rather than a named gene, as its molecular basis is less firmly settled than the loci given gene names above; anywhere else we are summarising an established consensus rather than a single result, no number is attached.