Transcriptomic Insights into the Synergistic Mechanism of Spinosad–Indoxacarb Mixtures Against Cnaphalocrocis medinalis

The rice leaffolder, Cnaphalocrocis medinalis, has developed widespread resistance to conventional insecticides, severely threatening rice production. Pesticide combination is a critical strategy for enhancing efficacy and delaying resistance evolution. In this study, binary mixtures with distinct modes of action were screened against C. medinalis neonates. Bioassays indicated that mixtures of spinosad and indoxacarb exhibited significant synergism, while several other combinations showed antagonism. To elucidate the synergistic mechanism of the optimal 1:1 mixture, comparative transcriptomic analyses were performed. Results revealed a time-dependent dual-phase response. At 6 h, the mixture induced broader upregulation of detoxification genes and activated stress signaling pathways due to competitive enzyme saturation, impairing metabolic clearance and amplifying neurotoxicity. At 24 h, massive transcriptional reprogramming uniquely activated lysosome, autophagy, lipid metabolism, and neurodegenerative disease pathways. This study demonstrates that the synergism arises from early competitive inhibition of detoxification and late overactivation of the autophagy–lysosomal system associated with cellular damage. These findings provide transcriptomic evidence for the dynamic synergistic mechanism and offer a scientific basis for rational resistance management of C. medinalis.