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To test for epistasis and allele-specific environmental responses among quantitative trait loci (QTL) involved in the evolution of maize from its ancestor (teosinte), teosinte alleles of two QTL previously shown to control much of the morphological difference between these plants were introgressed into an isogenic maize background. Plants of each of the four two-locus homozygous classes for the two QTL were grown in two environments. Three morphological traits and the level of mRNA accumulation for one QTL (teosinte branched1, tb1) were measured. tb1 has a large additive effect on morphology that was correlated with its message level. The second QTL had only negligible effects on morphology when isolated in an isogenic background, but exhibited a strong interaction effect on morphology in combination with tb1. This interaction is also evident in tb1 message levels, suggesting that this second QTL may act as an upstream regulator of tb1. The combined effect of the maize alleles at the two QTL makes tb1 message levels over fourfold higher. Plants homozygous for the teosinte allele at tb1 showed greater phenotypic plasticity across environments than plants homozygous for the maize allele. Our results support two hypotheses. First, maize plant architecture may have evolved by selection for a gene complex rather than the additive effects of individual loci alone. Secondly, selection during maize domestication for an allele of tb1 which lacks environmental plasticity may have led to the fixation of a morphological form that can be induced in teosinte by environmental conditions.