Every concept appears twice, side by side: once the way a graduate seminar teaches it, and once in plain barnyard English. Read either lane, or both. The drawings and calculators sit between them so both lanes point at the same picture.
What a bird actually inherits, how it is packaged, and the notation breeders use to write it down.
Gallus gallus domesticus is diploid with 2n = 78: 38 autosomal pairs plus the sex chromosomes Z and W. The karyotype splits into macrochromosomes (GGA1β5 and Z) and roughly 30 pairs of microchromosomes. Microchromosomes are GC-rich, gene-dense and recombine at very high rates per megabase, because each bivalent needs at least one chiasma regardless of its physical length.
The current reference assembly (GRCg7b) is about 1.05 Gb with roughly 17,000 protein-coding genes, a third the size of mammalian genomes owing to fewer repeats and shorter introns. Domestic chickens descend mainly from the red junglefowl, with documented introgression from other junglefowl species; the yellow-skin allele at BCO2, for example, traces to the grey junglefowl.
Picture every chicken carrying a library of 39 pairs of instruction books. One book in every pair came from the sire, the matching one from the dam.
One pair is special: the sex books, Z and W. A cock carries two Z books. A hen carries one Z and one W.
Fun fact for leg-color fans: the gene for yellow legs and skin did not come from the red junglefowl at all. It was borrowed long ago from a different wild cousin, the grey junglefowl.
A locus is a position on a chromosome; alleles are alternative sequence states at that locus. Genotype is the allele pair; phenotype is what is observed, conditioned by other loci and environment.
Poultry nomenclature writes dominant alleles with a capital letter and recessive ones in lower case, marks the wild type (red junglefowl state) with +, and distinguishes members of an allelic series with superscripts: E, ER, eWh, e+, eb. Z-linked genotypes in hens are written with the W as the partner, for example B/W.
A gene is a recipe slot, say "comb shape". An allele is one version of that recipe: pea comb or straight comb. Every bird holds two copies of each recipe, one from each parent.
Breeders shorthand it: a capital letter means the version that shows even with one copy (P for pea comb). A small letter means the version that hides unless the bird has two copies (p). A + means "the way the wild bird has it".
So P/p reads "one pea copy, one straight copy". That bird shows a pea comb but can still throw straight-combed chicks.
Either P or p, each with 50% probability. He shows pea, but half his sperm carry straight comb.
Single genes, dominance, interacting genes and how to prove what a bird is carrying.
Mendel's first law: the two alleles of a heterozygote segregate into gametes in equal proportion. Under complete dominance an Aa Γ Aa mating yields a 3:1 phenotypic ratio; under incomplete dominance the heterozygote is intermediate and the ratio is 1:2:1.
Pea comb (P, a duplication within intron 1 of SOX5) is effectively dominant. Blue (Bl) is incompletely dominant: bl/bl black, Bl/bl blue, Bl/Bl splash. Creeper (Cp) is dominant for the short-leg phenotype but recessive lethal, so Cp/cp Γ Cp/cp hatches a 2:1 ratio.
Each parent flips a coin to decide which of its two copies goes into the egg or sperm. The chick gets one copy from each flip.
Want all blue chicks? Mate black Γ splash. Every chick gets one dose from the splash parent and none from the black parent.
R) and pea (P) are separate genes. A bird with both shows walnut; a bird with neither shows the straight (single) comb.Pick a gene and both parents' genotypes. The square and the expected chick ratios update instantly.
Bateson and Punnett (1905) crossed rose- and pea-combed lines; the F1 were walnut and the F2 segregated 9 walnut : 3 rose : 3 pea : 1 single. Two independently assorting loci produce a novel phenotype when both dominant alleles are present, a textbook case of gene interaction.
Rose comb is a ~7.4 Mb inversion on GGA7 that relocates MNR2 expression; the original R1 allele is associated with poor sperm motility in homozygous males, which a recombinant R2 allele avoids.
Think of comb shape as two light switches: a rose switch and a pea switch.
Practical warning: some rose-comb cocks carrying two rose copies are poor fertilizers. If a rose-comb cock is throwing clear eggs, that is a known cause.
R/r P/p both). Sixteen equally likely egg-sperm combinations give 9 walnut, 3 rose, 3 pea and 1 straight comb.To classify a dominant-phenotype bird as A/A or A/a, mate it to a/a. If it is heterozygous, each offspring independently has probability Β½ of showing the recessive; the chance of missing the carrier after n dominant-phenotype offspring is (Β½)n.
Mating to known heterozygotes instead requires about 11 offspring for 95% confidence, since each chick shows the recessive with probability ΒΌ: (ΒΎ)11 β 0.042.
You have a pea-combed cock and want to know if he secretly carries straight comb. Put him over straight-combed hens.
This works for any hidden gene where you have a hen that shows the hidden version.
About 20. Two-copy creepers die in the shell, so the hatch splits 2 creeper : 1 normal instead of 3 : 1.
Modules 1 and 2 are free. HOTCOCKER members get the whole course, with every calculator, plus the podcast, the Heritage Archive and the feed AI.
Start your free 7 daysEach term in one line, readable from either track.
Additive variance (ΟΒ²A) The part of variation that parents pass on predictably.
Allele One version of a gene.
BLUP / EBV The statistical method, and the breeding value it predicts for each bird.
Coancestry (f) The chance two birds share a gene copy from a common ancestor; equals F of their chicks.
Epistasis One gene changing or hiding the effect of another.
Generation interval (L) Average age of parents when their replacement chicks hatch.
Heritability (hΒ²) Share of differences between birds that parents reliably pass down.
Heterosis Cross offspring beating the parents' average.
Hemizygous Having only one copy, as hens do for Z genes.
Inbreeding (F) Chance a chick got the same gene copy from both sides.
Linkage Genes close together on a chromosome tending to be inherited together.
Locus A gene's address on a chromosome.
Ne Effective population size: how big your flock "acts" genetically.
Phenotype What you can see or measure.
Selection differential (S) How much better the chosen breeders are than the average.
Z / W Sex chromosomes. Cock ZZ, hen ZW.