Multiple layers of cryptic genetic variation underlie a yeast complex trait

Cryptic genetic variation may be an important contributor to heritable traits, but its extent and regulation are not fully understood. Here, we investigate the cryptic genetic variation underlying a Saccharomyces cerevisiae colony phenotype that is typically suppressed in a cross of the lab strain BY4716 (BY) and a derivative of the clinical isolate 322134S (3S). To do this, we comprehensively map the trait9s genetic basis in the BYx3S cross in the presence of three different genetic perturbations that enable its expression. This allows us to detect and compare the specific loci harboring cryptic genetic variants that interact with each perturbation. In total, we identify 21 loci, all but one of which interacts with just a subset of the perturbations. Beyond impacting which loci contribute to the trait, the genetic perturbations also influence the extent of additivity, epistasis, and genotype-environment interaction among the detected loci. Additionally, we show that the single locus interacting with all three perturbations corresponds to the coding region of the cell surface gene FLO11. Nearly all of the other loci influence FLO11 transcription in cis or trans. However, the perturbations reveal cryptic genetic variation in different pathways and sub-pathways upstream of FLO11, suggesting that multiple layers of cryptic genetic variation with highly contextual effects underlie the trait. Our work demonstrates an abundance of cryptic genetic variation in transcriptional regulation and illustrates how this cryptic genetic variation complicates efforts to study the relationship between genotype and phenotype.