Comparative Transcriptomics Deciphers Quinclorac Selectivity in Rice and Tobacco

Quinclorac is widely used in rice cultivation; however, its persistent residue poses a serious risk to subsequent tobacco crops in rice-tobacco rotation systems, limiting the sustainability of this practice. Although rice and tobacco exhibit markedly different sensitivities to quinclorac, the molecular basis for this divergence remains unclear. In this study, we investigated the differential molecular mechanisms from stress perception to phenotypic response by integrating comparative transcriptomics, physiological profiling, and metabolic pathway analysis. Under quinclorac, the tobacco cultivar K326 (K326) suffered severe growth inhibition and oxidative damage, whereas the rice cultivar Nipponbare (NPB) maintained internal homeostasis. Comparative transcriptomics analysis revealed putative distinct response strategies. K326 may activate a defense response program characterized by strong induction of mitogen-activated protein kinase (MAPK) and ethylene/jasmonic acid signaling pathways, followed by large-scale transcriptional reprogramming dominated by MYB and WRKY transcription factors. In contrast, NPB may adopt a steady-state prioritization strategy, upregulating NAC transcription factors to enhance glutathione-based detoxification while sustaining the core metabolic processes, including photosynthesis. Collectively, our work provides a systematic framework for understanding the molecular basis of the differential quinclorac response in rice and tobacco.