Although Mendel chose seven unrelated traits in peas to study gene segregation, most traits involve multiple gene interactions that create a spectrum of phenotypes. When the interaction of various genes or alleles at different locations influences a phenotype, this is called epistasis. Epistasis often involves one gene masking or interfering with the expression of another (antagonistic epistasis). Epistasis often occurs when different genes are part of the same biochemical pathway. The expression of a gene might depend on a gene product in the same biochemical pathway.

Epistatic analysis

The study of epistatic interactions allows researchers to determine the functional relationship between genes, the ordering of genes in a pathway, and how different alleles quantitatively impact phenotypes. Consider a biochemical reaction catalyzed by multiple proteins coded by different genes. The genes involved in such biochemical reactions can mask or inhibit other genes involved in the same biochemical pathway, a phenomenon called epistasis. Such genes are said to be in one epistasis group. By analyzing the epistatic relationship between different genes, scientists can construct an order-of-function map that shows the sequence of events and genes involved in a pathway. This process is called epistatic analysis. The alleles selected for the epistatic analysis must have distinct phenotypes.

As such, since the concept of epistasis was introduced, it has become increasingly clear that most biological systems involve many genetic elements that interact with one another in multiple and complex ways.