Genotype and phenotype: Definitions, similarities, and differences

The takeaway: Genotype and phenotype are basic concepts in genomic science, but easy to confuse. Let’s look at them in more detail here.

Genotype and phenotype—what is the difference and why is it important?

What is a phenotype and what is a genotype? These two terms are fundamental to genomic sciences but easy to confuse. The distinction between the two, however, is essential to both biology and evolutionary theory.

What is genotype?

A genotype is the set of genes that an organism carries. In a person, it is their unique sequence of DNA. The genotype is the hereditary material, or DNA, that is contained within genes and passed from one generation to the next. A classic example in humans is eye color—a person’s eye color depends on the genes they inherit from their parents: A gene encodes eye color, with one allele inherited from the mother and the other from the father, and the mix of dominant and recessive genes determining what the child’s eye color will be. The same goes for everything from hair color to height. Taken one step further, genotyping is the process of determining the genotype. IDT has tools for genotyping, including the rhAmp™ SNP Genotyping System. Others may be found here.

What is phenotype?

A phenotype is all of the observable characteristics of an organism, with these characteristics being influenced by the organism’s genotype and the environment the organism lives in. Phenotype is how the genotype is expressed. It is how the organism looks and acts, and can depend on everything from the humidity in the air to epigenetic factors such as the modification of cells that can lead to cancer. An example in the animal world is the color of flamingoes—while most are pink the color of individual animals actually depends on what kind of food they eat. And what is phenotypic? Phenotypic refers to observable characteristics of an individual that are the result of the genotype and its interaction with the environment around it. Phenotypic characterization is explained in more detail here.

Where did these terms develop?

The terms were introduced by the Danish botanist Wilhelm Johannsen in the early 20th century. More specifically, he coined the terms in 1911 when proposing “the genotype conception of heredity” and seeking to distinguish two very different levels of biology.

Johannsen sought to dismiss the idea of transmission conception, in which the characteristics of an individual organism transmit directly to their offspring.

Johannsen performed a series of experiments using barley and bean plants that had bene self-fertilized. He measured the physical dimensions of the seeds in every generation and found that they could separate pure lines into distinct groups based on the characteristics of the seeds that the plants produced. Johannsen analyzed the seeds and resulting plants and found that the group that a plant belongs to was a stronger predictor of the seeds that it produced than the characteristics that the parent plant possessed. Johannsen first called this distinction “type” then later used the term “phenotype,” and later contrasted phenotype with genotype.

How are phenotype and genotype related?

While both functions are important, there are not clear connections between the two. Genome-wide association studies, which are a type of genetics research used to see if a variant is associated with a trait, show this clearly. Next generation sequencing (NGS) and whole-genome transcription profiling may help researchers predict phenotype from genotype., and DNA sequence changes have been linked to phenotype differences at both the individual and species level.

What is the difference between genotype and phenotype?

Observing a phenotype is simple—one may simply look at outward features and draw conclusions from them. Observing a genotype is more complex. Through whole genome sequencing, a powerful yet increasingly affordable technology, researchers can identify the raw sequences of the nucleotides that make up an organism’s DNA. Genotyping techniques include polymerase chain reaction (PCR), DNA microarrays, allele-specific oligonucleotide probes, and DNA hybridization.