The genotype is the part of the genetic makeup of a cell, and therefore of any individual, which determines one of its characteristics (phenotype). The term was coined by the Danish botanist, plant physiologist and geneticist Wilhelm Johannsen in 1903.

The genotype is one of three factors that determine phenotype, along with inherited epigenetic factors and non-inherited environmental factors. Not all organisms with the same genotype look or act the same way because appearance and behavior are modified by environmental and growing conditions. Likewise, not all organisms that look alike necessarily have the same genotype.

One's genotype differs subtly from one's genomic flash card sequence, because it refers to how an individual differs or is specialized within a group of individuals or a species. So, typically, one refers to an individual's genotype with regard to a particular gene of interest and the combination of alleles the individual carries (see homozygous, heterozygous).Genotypes are often denoted with letters, for example Bb, where B stands for one allele and b for another.

Somatic mutations which are acquired rather than inherited, such as those in cancers, are not part of the individual's genotype. Hence, scientists and physicians sometimes talk about the genotype of a particular cancer, that is, of the disease as distinct from the diseased.

An example of a characteristic determined by a genotype is the petal color in a pea plant. The collection of all genetic possibilities for a single trait are called alleles; two alleles for petal color are purple and white.

Any given gene will usually cause an observable change in an organism, known as the phenotype. The terms genotype and phenotype are distinct for at least two reasons:

 To distinguish the source of an observer's knowledge (one can know about genotype by observing DNA; one can know about phenotype by observing outward appearance of an organism).

    Genotype and phenotype are not always directly correlated. Some genes only express a given phenotype in certain environmental conditions. Conversely, some phenotypes could be the result of multiple genotypes. The genotype is commonly mixed up with the phenotype which describes the end result of both the genetic and the environmental factors giving the observed expression (e.g. blue eyes, hair color, or various hereditary diseases).

A simple example to illustrate genotype as distinct from phenotype is the flower colour in pea plants (see Gregor Mendel). There are three available genotypes, PP (homozygous dominant), Pp (heterozygous), and pp (homozygous recessive). All three have different genotypes but the first two have the same phenotype (purple) as distinct from the third (white).

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