Comparative Transcriptomic Responses of Arabidopsis thaliana to Multiple Herbicides Reveal Distinct Transcriptional Signatures

In this study, we performed a comparative transcriptomic analysis of Arabidopsis thaliana exposed to seven herbicides (2,4-dichlorophenoxyacetic acid, acifluorfen, atrazine, glyphosate, imazethapyr, mesotrione, and paraquat) representing seven different modes of action, employing a factorial design with two time points (4 hour and 24 hour) and two dosage levels (IC50 and IC99) at each time point.

By focusing on herbicide unique differentially expressed genes under each treatment, we identified distinct transcriptional signatures comprising both mode-of-action-associated pathways and broader stress response processes. Temporal expression dynamics of these unique gene sets were resolved using k-means clustering, revealing characteristic response patterns across herbicides. Together, the differential gene sets and their associated expression patterns identify transcriptional signatures that provide a framework for herbicide mode-of-action inference, classification of novel compounds, and investigation of herbicide resistance mechanisms at the molecular level.