Genetic sequencing (Phenotype and Alleles)

Now that we have established the basis for colour itself, we can look more closely at colour production and its various forms of expression. What decides whether our dog's coat colour will be a result of eumelanin or phaomelanin? This is due to the genetic makeup of the animal, in particular, we are looking at the coat colour. (Coat type, length and varity is not the main focus here.) This genetic makeup, or genotype, is the unique blueprint for what colours are expressed, and, more interestingly, carried.
Below are these basic genetics/genotypes explained.

Genotype - The genetic makeup of an organism that it carries within its genetic code. In this instance, our genotype is the genetic information expressed or present which affects the overall production and appearance of coat colour.

Phenotype - Defined as the expressed physical traits of an organism. In other words, while our dog is genetically black, because of certain recessive/dominant factors, he is visually a black, tan and white Swiss Mountain Dog! At what point did the colours change? This question will be further discussed.
An example of a phenotype:

 

This is actually only the very basic pehenotype and there are many other alleles included in the phenotype.

The above phenotype is that which would typically be exprected for, say, a black Labrador. 

Allele/s - An allele is the individual factor which determines the resulting phenotype (we established our dog's genotypeis black, however our genotype has been affected by recessive/dominant traits and we now have a cream coloured dog.)
The picture is an example of a singular and pair of allele/s. (Shown as "B" and "BB".)

Alleles work using Dominance and Recession factors. Alleles, in the phenotype of dogs, are grouped in twos, and each allele does have some effect on either the end result appearance or of inheritable traits passed along.

(Below - Complete dominance in simplest form - our Black Labrador.)

Dominance is a well known factor in how our end resulting phenotype looks. Dominance is simply the act of one allele being dominant over the other, and due to this dominance, only that allele may be expressed. This, is, of course, dependant on whether the alleles are Heterozygous or Homozygous. A Dominant allele is expressed using upper case lettering. In the case of the Black/Red factor (B,b), our Dominant allele is "B". This is then sequenced as "BB" or "Bb" depending on the phenotype.

 (Below - Complete recessiveness as expressed in this Yellow Labrador.)

Recessiveness is the result of a lack of dominant alleles. Recessive alleles are often only expressed when no dominant traits are present in that sequence. (This is not always a rule in dog colouration, however, as some colours are a result of incomplete dominance, where the two alleles work together.)
Recessive alleles are written in lower case form, and these may be carried ("Bb") or expressed ("bb"), depending on the placement of dominant alleles.

Heterozygous - different, opposite alleles. These are expressed using dominance and recessive means. And example of a Heterozygous set of alleles is "Bb" - in which case the upper case "B" is still dominant.

Homozygous - alleles that are alike. These can be either dominant or recessive. Examples include "BB" or "bb".

Now that we have established what all these genetic terms mean, we can begin to understand how to sequence and 'interpret' our phenotype. This is where it gets interesting, and I will further explain each allele's position in the genotype. This, of course, is subject to change depending on those phenotypical changes.