Idiosyncratic and dose-dependent epistasis drives variation in tomato fruit size

Epistasis between genes is traditionally studied using mutations that eliminate protein activity, but most natural genetic variation is in cis-regulatory DNA and influences gene expression and function quantitatively. Here, we use natural and engineered cis-regulatory alleles in a plant stem cell circuit to systematically evaluate epistatic relationships controlling tomato fruit size. Combining a promoter allelic series with two other loci, we collected over 30,000 phenotypic data points from 46 genotypes to quantify how allele strength transforms epistasis. We revealed a saturating dose-dependent relationship, but also allele-specific idiosyncratic interactions, including between alleles driving a step change in fruit size during domestication. Our approach and findings expose an underexplored dimension of epistasis, where cis-regulatory allelic diversity within gene regulatory networks elicits non-linear, unpredictable interactions that shape phenotypes.