In the dihybrid crosses that we examined in Chapter 3, each locus had an independent effect on the phenotype. When Mendel crossed a homozygous pea plant that produced round and yellow seeds (RR YY) with a homozygous plant that produced wrinkled and green seeds (rr yy) and then allowed the F₁ to self-fertilize, he obtained F₂ progeny in the following proportions:

In this example, the two loci showed two kinds of independence. First, the genes at each locus were independent in their assortment in meiosis, which produced the 9 : 3 : 3 : 1 ratio of phenotypes in the progeny, in accord with Mendel’s principle of independent assortment. Second, the genes were independent in their phenotypic expression; the R and r alleles affected only the shape of the seed and had no influence on the color of the seed; the Y and y alleles affected only color and had no influence on the shape of the seed.

Frequently, genes exhibit independent assortment but do not act independently in their phenotypic expression; instead, the effects of genes at one locus depend on the presence of genes at other loci. This type of interaction between the effects of genes at different loci (genes that are not allelic) is termed gene interaction. With gene interaction, the products of genes at different loci combine to produce new phenotypes that are not predictable from the single-locus effects alone. In our consideration of gene interaction, we’ll focus primarily on interactions between the effects of genes at two loci, although interactions among genes at three, four, or more loci are common.