SRP374717 PRJNA836875 AGO1 and HSP90 buffer different genetic variants in Arabidopsis thaliana Argonaute 1 (AGO1), the principal protein component of microRNA-mediated regulation, plays a key role in plant growth and development. AGO1 physically interacts with the chaperone HSP90 that buffers cryptic genetic variation in plants and animals. We sought to determine if genetic perturbation of AGO1 could also reveal cryptic genetic variation, and if so, whether AGO1-dependent loci would overlap with those dependent on Hsp90. To pursue these questions, we introgressed a hypomorphic mutant allele of AGO1 into a set of mapping lines derived from crosses of the commonly used Arabidopsis thaliana strains Col-0 and Ler. We found several instances in which this genetic perturbation buffered genetic variation; however, none of the AGO1-dependent loci overlapped with those buffered by HSP90 for the same traits. We focused on one buffered locus where AGO1 perturbation uncoupled the otherwise closely correlated traits days to flowering and rosette leaf number. Using a bulk segregant approach, we identified a non-functional Ler hua2 mutant allele as the causal AGO1-buffered polymorphism. Introduction of a non-functional hua2 allele in a Col-0 ago1 mutant background recapitulated the Ler-dependent ago1 phenotype, implying that coupling of these traits involves different molecular players in these closely related strains. Taken together, our findings demonstrate that even though AGO1 and HSP90 buffer genetic variation in the same traits, these robustness regulators interact epistatically with different genetic loci, suggesting that higher-level epistasis is uncommon. We also find evidence for rewiring of key regulatory pathways within the same species.