Basic Color Genetics

Basic Color Genetics

This page covers the five base alleles that affect the coat color of domestic rabbits. This article focuses strictly on genotype (the genetic makeup), not phenotype (how the color appears).

• Genotype* = the black-and-white formula on the gene that produces a color.
• Phenotype* = the observable color, often used in breed standards.

Understanding genotype is crucial for predicting offspring color in breeding.

A – Agouti

The Agouti gene has three alleles:

• A – Agouti (most dominant)
• at – Tan
• a – Self (most recessive)

The Agouti locus expresses the “wild color” banding along each hair shaft. Agouti hairs have alternating bands of eumelanin (dark pigment) and pheomelanin (yellow/red), producing a “ringed” appearance. Standard Agouti colors include Chestnut (Castor), Sandy, Copper, and Chinchilla (Squirrel). Other Agouti-based patterns modified by additional genes include Red, Steel, Harlequin, and Ermine.

• Tan (at) – Eumelanin on top, pheomelanin on the bottom; expressed across the back, ears, face, belly, and inside the ears. Dominant over a (Self), recessive to A. Examples: Tan, Marten, Otter.

• Self (aa) – Requires homozygous recessive alleles. Produces solid-colored hair shafts, typically expressing the base color at the B locus and sometimes modified by the D and E loci. Examples: Black, Chocolate, Lilac, Blue, Tort.

Summary Table:

• A = Agouti (banded hair shaft)
• at = Tan (solid color on top, pheomelanin on bottom)
• aa = Self (solid hair shaft)

B – Base Color

B Locus

The B locus controls the type of eumelanin expressed:

• B – Black (dominant)
• b – Brown/Chocolate (recessive)

Base color forms the foundation for many rabbit colors (e.g., Black, Chestnut, Chinchilla, Harlequin, Torts) and can be masked by other genes (white or pheomelanin-only expression).

C – Color Coverage

C Locus

The C locus affects color intensity and coverage. Four primary alleles:

• C – Full Color (dominant). Expresses complete eumelanin over the body; modified by at, d, e, and En loci. Examples: Solid Blacks, Chocolates, Blues, Lilacs, Chestnuts, Steels, Harlequins.
• chd – Dark Chinchilla. Strips most pheomelanin while leaving eumelanin intact; affects Agouti most. Produces Martin, Fox, Ermine, Chinchilla, Silver-Tipped Steel, Magpies.
• chl – Light Chinchilla. Co-dominant; partially strips pheomelanin. Agouti rabbits with chl- are Siamese; self and tan rabbits with chl- are Sable. Homozygous chlchl = Seal.
• ch – Himalayan / Californian. Temperature-sensitive; color restricted to cooler points (ears, nose, feet, tail). Recessive to C, chd, chl; dominant over c.
• c – Albino. Most recessive; masks all other loci when homozygous (cc), producing red-eyed white rabbits.

D – Density

D Locus

The D locus controls pigment density:

• D – Full Density (dominant)
• d – Dilute (recessive)

Dilution affects eumelanin: Black → Blue, Chocolate → Lilac. Think of it as a “brightness slider” for color intensity.

• Reference:* [A frameshift mutation in the melanophilin gene causes the dilute coat colour in rabbit (PMC)](https://pubmed.ncbi.nlm.nih.gov/24320228/)

E – Extension

E Locus

The E locus controls how far color extends along the hair shaft in Agouti rabbits:

• Ed – Dominant Black. Extends B locus color across entire hair.
• Es – Steel. Extends B color most of the way; tips show pheomelanin.
• E – Regular Extension. Normal banding along hair shaft.
• ej – Japanese / Harlequin. Co-dominant; alternating patches of color.
• ee – Non-Extension / Tort. Suppresses eumelanin; tips colored, rest pheomelanin.

• References:*
• [Mutations in the melanocortin 1 receptor (MC1R) gene in rabbits](https://pubmed.ncbi.nlm.nih.gov/16978179/)
• [Slc7a11 modulated by POU2F1 and pigmentation in rabbits](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6566412/)
• [ASIP gene characterization in rabbits](https://www.sciencedirect.com/science/article/pii/S0888754309002559)
• W.E. Castle, "Who Discovered the Dominant Black Rabbit?", Journal of Heredity, 1939