Dose-response-defined physiological framework enables comparative analysis of transcriptional response dynamics...

Herbicides elicit diverse physiological responses in plants largely due to distinct modes of action of individual compounds. However, it remains unclear how plants differentially respond to herbicides with distinct modes of action when applied at herbicide-specific treatment levels corresponding to comparable degrees of growth inhibition. In this study, we integrated physiological and transcriptomic analyses to characterize the responses of Arabidopsis thaliana exposed to seven herbicides (2,4-dichlorophenoxyacetic acid, acifluorfen, atrazine, glyphosate, imazethapyr, mesotrione, and paraquat) representing seven different modes of action. Dose-response experiments were first conducted to determine herbicide-specific inhibitory concentrations, establishing a framework of physiologically defined treatment levels based on growth inhibition for subsequent RNA sequencing. Comparative transcriptomic analysis under a pairwise design with two points (4 hour and 24 hour) and two dosage levels (half-maximal inhibitory concentration and 99% inhibitory concentration) at each time point revealed herbicide-specific differentially expressed genes. Temporal expression dynamics of these unique gene sets via hierarchical clustering further resolved distinct herbicide mode-of-action-associated and shared broader stress response-related, growth inhibition-related, and detoxification-related processes with limited overlaps at the gene level. Together, these results demonstrate that plants display divergent physiological and transcriptional responses to different herbicides under comparable levels of growth inhibition yet converge on common stress-response biological effects. These findings indicate how plants coordinate physiological and transcriptional responses to adapt to distinct chemical perturbations. The identified differentially expressed gene sets and their associated expression patterns provide a framework for herbicide mode-of-action inference, classification of novel compounds, and investigation of herbicide resistance mechanisms at the molecular level.