Metabolomic Changes in Rice (Oryza sativa L.) Subjected to Herbicide Application through HPLC-HRMS and Chemometrics Approaches

Abstract

This study evaluated rice samples (Oryza sativa L.)─rice husk, husk and grain, polished grain, and unpolished grain─exposed to imazapyr, imazapic, and clomazone using high-performance liquid chromatography coupled to high-resolution mass spectrometry (HPLC-HRMS) and chemometric analysis. Partial least squares discriminant analysis (PLS-DA) was applied to HPLC-HRMS data, successfully distinguishing between herbicide-treated and control samples. Additionally, variable importance in projection (VIP) scores were then computed to identify key metabolites contributing to class differentiation, with higher scores indicating the most influential m/z values. These findings revealed metabolites affected by herbicide exposure and variations in the rice matrix. Furthermore, the most relevant m/z values were putatively annotated using spectral libraries, enabling the assessment of herbicide-induced metabolomic changes in rice. Herbicide treatment resulted in reduced free sugar levels across all rice matrices and led to a decrease in flavonoid content in the husk, indicating a potential suppressive effect on flavonoid accumulation. In addition, the herbicide treatment markedly disrupted the phenylpropanoid biosynthesis pathway. Overall, the combination of HPLC-HRMS analysis with multivariate approaches proved effective in detecting significant variations in the rice metabolome cultivated under herbicide application, paving the way for understanding the effects of herbicides in crop cultivation.