A dog’s genotype refers to the combination of alleles (a type of genetic variations) in their DNA and determines the traits the dog will exhibit. With so many different alleles, it may be difficult to keep track of which ones are responsible for what trait. But once you understand how this works, it’s pretty easy to see how the genotype controls what we see in our puppies. There are two sets of chromosomes that determine a dog’s genotype: autosomes and sex chromosomes. The autosomes are all the chromosomes that aren’t sex chromosomes. In dogs, that means there are two copies of every autosome except for the X chromosome and Y chromosome, each with their own unique set of alleles.

Autosomal Dominance

An allele that is dominant will always be expressed over the unexpressed allele in the presence of a trait controlled by a recessive allele. This means that even if both alleles exist in the genotype, the dominant allele will always be expressed. This is called autosomal dominance, and it’s the reason only one gene must be present for us to see a certain phenotype. Genetically, autosomal dominance can be seen as if there are double copies of the dominant allele. If a dog has a double version of the dominant allele, it will express the corresponding phenotype even if they have the recessive allele. Dominant alleles are usually capitalized and recessive alleles are usually lowercase. However, it is not common to capitalize all dominant alleles. Dominant alleles are also often abbreviated with a capital letter ‘D’.

How Genotype Determines Coat Colour in Dogs

The classic example of how genotypic expression works is in hair colour. German Shepherds, for example, always have either two copies of the e allele or two copies of the EM allele. The e allele is for the black/brown pigment and the EM allele is for the yellow/red pigment. A dog with only the e allele will have black/brown fur and a dog with only the EM allele will have yellow/red fur. But when a dog has both copies of the e and the EM allele, the expression of that gene is determined by which allele is dominant. So if the e allele is dominant, the dog will have black fur. If the EM allele is dominant, the dog will have red fur.


Co-dominance is a special case of genotypic expression where both alleles are equally expressed in the phenotype. With co-dominance, both alleles are present as double copies and neither allele is dominant over the other. Co-dominance is extremely rare, but it happens when two alleles are almost identical to each other. Co-dominance is usually seen when one allele causes an undesirable trait and another allele does not cause that trait. That’s because there is no single allele that only causes a desirable trait. So two alleles that don’t cause that trait are necessary for co-dominance. Co-dominance can also be found when an allele causes a trait that is desirable in one context, but undesirable in another context.

Genetically Determined Differences in Gene Expression

Genetically determined differences in gene expression are completely unrelated to genotypic expressions like co-dominance and dominance. Instead, this is when a specific allele causes a gene to be less or more active in the expression of a certain trait. This is when an allele causes the genetic expression of a trait, but that allele isn’t responsible for the trait itself. For example, the e allele is responsible for the black/brown hair colour and the EM allele is responsible for the yellow/red hair colour. But the e allele is also responsible for a black/brown nose colour and the EM allele is responsible for a yellow/red nose colour.

Merle Genotypes and Patterns

Merle puppies are not entirely black or fully one colour. Instead, their coat is a patchy mixture of two different colours. The patches can vary in size and contain a mixture of both colours. Merle dogs can be either Homozygous (H) or Heterozygous (H/m) for the merle gene. Homozygous dogs are fully merle and heterozygous dogs have a merle pattern. The genotype of a merle dog determines which specific genotypic expression of the merle phenotype the dog will have. The genotype determines where the patches are located and the phenotype determines the size and the ratio of the patches.

See our Cavoodle Puppies. They are a higher version of the Dog Breed.

Dominant Dilution Genotypes (DD)

Dominant dilution is the complete absence of a colour caused by a double allele of the recessive e allele. This is the only case of a genotypic expression that results in a completely different allele. The genotypic expression of a DD dog is as if they have a single e allele. This makes their coat colour more like the colour of the single e allele that is present in the genotype of an E dog. The colour is a diluted form of the normal colour, which means it’s lighter and less intense than normal. Homozygous DD dogs are commonly called Silver or Grey.

Epistasis and how it affects genotype based traits

Epistasis occurs when an allele on one chromosome negatively affects the expression of an allele on the other chromosome. Epistasis is completely unrelated to genotypic expression. This is when an allele on one chromosome inhibits the expression of an allele on another chromosome. For example, a dog with an E allele on one chromosome and an e allele on another chromosome will have a black/brown coat colour, but the e allele will be less expressed because of the E allele. A dog with both a recessive e allele and a recessive E allele will have a black/brown nose colour and black/brown eyes, but their coat colour will be a light grey.


When trying to decipher this complicated system, it is important to remember that it is not as simple as the expression of dominant alleles versus recessive alleles. Instead, genotypic expression is the complicated interplay of multiple factors. Epistasis and genotypic expression can both affect the genes that are expressed in a dog’s genotype. Even the environment can affect which genes are expressed in a dog’s phenotype. Although it can be difficult to understand, it’s important to keep in mind that the genotype determines the phenotype.