Revealing the intrinsic relationship between gene interactions and phenotypes is a key issue in life science research. Most phenotypes are controlled by multiple genes in a coordinated manner, exhibiting complex genetic effects such as dominance and epistasis in addition to additive effects. In a recent study, a “hybrid” population of rice containing 18 421 recombinant inbred lines was constructed, successfully identifying 96 high-confidence candidate genes controlling 16 agronomic traits. The study analyzed the epistatic effects among genes, constructed a genetic interaction network consisting of 19 hub genes, revealed potential interactions among genes, and discovered 170 “masking” epistatic interac-tions. This research provides important data and material resources for genetic studies in rice, establishes a new paradigm for crop genetics research, greatly accelerates the discovery of genes related to important traits, advances the functional analysis of quantitative trait gene interactions, and provides genetic resources and theoretical support for mole-cular breeding.