What Is a Locus? Why Dog Coat Genes Have Letters
A locus is a fixed position in the genome, often used to mean a gene and its versions. Here's what the word means, why dog coat colour genes go by letters like E, K and A, and how loci connect to traits.
By PuppyGenes · How we research and write our guides
A locus (plural loci) is a fixed position in the genome, such as the place where a particular gene sits on a chromosome. In dog genetics, the word is often used to mean a gene together with its versions, or alleles. That's why the genes behind coat colour are known by locus letters: E, K, A, B, D, M and S.
The short version
- A position: a locus is a fixed place on a chromosome.
- Plural: loci.
- Alleles sit at loci: a dog carries two versions, or alleles, at most loci.
- Coat colour loci have letters, each matched to a gene, such as E for MC1R.
- A locus can be a gene, a region or a single DNA letter.
The coat colour loci
| Locus | Gene | What it does |
|---|---|---|
| E (extension) | MC1R | Two copies of the e variant limit a dog to red and yellow pigment |
| K | CBD103 | One copy of the dominant black variant gives a solid coat and hides the A locus patterns |
| A (agouti) | ASIP | Sets the pattern when K allows it: sable, agouti, tan points or recessive black |
| B (brown) | TYRP1 | Two brown versions turn black pigment brown |
| D (dilute) | MLPH | Two dilute versions lighten the coat, for example black to grey |
| M (merle) | PMEL (SILV) | An insertion dilutes colour in patches |
| S (white spotting) | MITF | The major white-spotting gene |
Many of these letters were in use before the genes behind them were identified. Later studies matched them to genes, such as MC1R for E in 2000, TYRP1 for B in 2002 and CBD103 for K in 2007. Our coat colour hub explains how the loci work together, and our merle guide covers the M locus in depth.
How a locus differs from a gene
A gene is a stretch of DNA with a job, usually making a protein. A locus is simply a position. Many loci contain a gene, so people often use the words interchangeably, but a locus can also be a single DNA letter, such as a SNP, or a region whose gene isn't known yet.
That second use is common in research. A 2007 study of body size first found a region on chromosome 15 with a major influence on size within one breed, then traced it to a single gene, IGF1. Our guide to whether DNA can predict adult size explains what that gene does.
Loci in a DNA report
A DNA test compares dogs at many loci at once. Each trait prediction rests on the loci linked to that trait: in the PuppyGenes physical appearance section, for example, the coat length prediction is based on FGF5 and the furnishings prediction on RSPO2. Our glossary explains the other terms you'll meet in a report.
Frequently asked questions
- What is a locus in genetics?
- A locus is a fixed position in the genome, such as the place where a gene sits on a chromosome. The word is often used to mean the gene at that position and its versions.
- What is the plural of locus?
- Loci. You'll see it in phrases like "coat colour loci", meaning the set of genes behind coat colour.
- What are the coat colour loci in dogs?
- The main ones are E (MC1R), K (CBD103), A (ASIP), B (TYRP1), D (MLPH), M (PMEL) and S (MITF). Together they shape a dog's pigment, pattern, dilution, merle and white markings.
- What's the difference between a locus and an allele?
- A locus is the position; alleles are the versions of DNA that can sit there. At the E locus, for example, a dog might carry two copies of the usual allele, two copies of the e allele, or one of each.
From general to personal
See how this applies to your dog specifically.
Our at-home Complete Dog DNA Test adds your dog's own results to these tips across six report sections: breed ancestry, coat colour, physical appearance, temperament and size predictions, genetic diversity and oral microbiome. The report does not include genetic disease or health screening.