The genotype-phenotype map has been analyzed in terms of several principal axes: epistasis, polygeny, pleiotropy, quasi-continuity, modularity, phenotypic plasticity, robustness, and evolvability.
- Epistasis: when the alleles at one locus change the phenotypic effects of genetic variation at another locus, the two genes are said to exhibit 'epistasis' in their interactions.
- Polygeny: when multiple genes contribute to a particular phenotypic character, the map is said to possess 'polygeny'. The genetic architecture in cases of polygeny can be further characterized by the spectrum of contributions of the genes, e.g. many genes of small effect vs. few genes of large effect.
- Pleiotropy: when multiple phenotypic characters are affected by a single genetic variation, the map is said to possess 'pleiotropy'.
- Quasi-continuity: when small genetic changes map to small phenotypic changes, the map is said to possess "quasi-continuity" (Lewontin).
- Modularity: when two different phenotypic characters can be mapped to mostly non-overlapping sets of genes, the map is said to possess 'modularity', though this concept is still in flux in the scientific literature.
- Plasticity: when a single genotype gives rise to a spectrum of phenotypes, the phenotype is said to have 'plasticity'. The plasticity may occur as different phenotypes among different individuals of the same genotype, or different phenotypes within the lifetime of a single individual, or different phenotypes in response to specific environmental conditions.
- mutational robustness'.
- Transgressive phenotype: when a phenotype is more extreme than the phenotype displayed by either of the parental lines.