Genotype-Phenotype Interactions

Mutations are the primary source of genetic variation within a species, creating variants of nucleotide sequences in a gene called alleles. While many alleles do not significantly affect gene function, some result in distinct phenotypic traits.

A classic example of allele variation is observed in pea plants, particularly in genes determining flower colour. In these plants, a gene encoding a protein which controls the production of a purple pigment called anthocyanin has two alleles. One allele codes for a functional protein, leading to purple flowers, while the other allele is faulty, resulting in no pigment production and thus white flowers.

Alleles are variants of a nucleotide sequence in a gene

Most multicellular organisms are diploid, meaning they possess two sets of chromosomes in their cells. Consequently, genes are typically represented by two alleles in a cell. If both alleles are identical, the organism is termed homozygous for that gene. Conversely, if the alleles differ, the organism is termed heterozygous.

In a heterozygous organism, if only one of the alleles affects the observable characteristics it is called dominant, while the second allele is called recessive. For instance, in pea plants with heterozygous alleles for flower colour, where one allele codes for a functional protein and the other for a non-functional protein, the purple flower trait is dominant.

Interactions between alleles can often be more nuanced than a binary dominant-recessive relationship. For example, human blood groups are determined by a gene with three alleles $I$$I^{A}$, $I$$I^{B}$, and $i$. This gene governs the presence of a specific carbohydrate on the surface of red blood cells, with each allele resulting in a different structure of this carbohydrate. Alleles $I^{A}$and $I^{B}$ lead to the production of carbohydrate structures A and B, respectively, while allele $i$ results in the absence of the carbohydrate. Both $I^{A}$and $I^{B}$ are dominant over allele $i$, meaning individuals with genotypes $I^{A}i$ and $I^{B}i$ will have blood A and B, respectively. Only individuals with the genotype $ii$ will have no carbohydrate on their red blood cells and will have the blood group O. However, individuals with the genotype $I^{A}I^{B}$ will exhibit blood group AB, indicating the presence of both carbohydrate structures. This type of allele interaction, where both alleles contribute to the phenotype in a heterozygous individual, is termed codominance.

Blood groups Image source: OpenStax College - Anatomy & Physiology, Connexions Web site. http://cnx.org/content/col11496/1.6/, Jun 19, 2013., CC BY 3.0, https://commons.wikimedia.org/w/index.php?curid=30148183 with changes

Examples of phenotypes discussed above demonstrate discontinuous variation, which means that every individual can be assigned to a particular group according to its phenotype. However, plenty of traits, such as human body mass or skin tone are distributed continuously, in other words, an individual can have any characteristic value within a certain range. Such characteristics are commonly polygenic, which means, they are controlled by multiple genes, and/or are influenced by the environment.

Skin tone is polygenic, meaning it's controlled by multiple genes. At least 150 genes are known to contribute to skin colour, and even a simplified model considering just 3 genes, each with 2 alleles, can illustrate polygenic inheritance and its effect on phenotype. In this model, an individual who is homozygous recessive for all three genes would have a very light skin tone, while a homozygous dominant individual would have very dark skin. The combination of different alleles of these genes produces the wide spectrum of skin tones observed in human populations.

A simplified model of polygenic inheritance of skin colour