Comparative physiological and transcriptomic analyses of differential mesotrione tolerance in foxtail millet seedlings.

Foxtail millet is an important drought-tolerant crop, yet its production is threatened by weed competition due to limited herbicide options. The 4-hydroxyphenylpyruvate dioxygenase (HPPD)-inhibiting herbicide mesotrione shows promise but causes differential responses among varieties. This study investigated the physiological and transcriptomic responses underlying differential mesotrione tolerance in two foxtail millet cultivars, Jingu 21 (JG21, sensitive) and Zhangzagu 10 (ZZG10, tolerant). Physiological analyses revealed that ZZG10 maintained higher net photosynthetic rate (Pn), photosystem II (PSII) efficiency (Fv/Fm), and non-photochemical quenching (NPQ) compared to JG21. Chloroplast ultrastructure showed that ZZG10 preserved membrane integrity under stress, whereas JG21 chloroplasts disintegrated with ruptured thylakoid membranes. Enzyme activity assays demonstrated that ZZG10 exhibited stronger HPPD activity and higher cytochrome P450 monooxygenases (CYP450) and glutathione S-transferases (GST) activities. Transcriptomic analysis revealed that ZZG10 had higher basal HPPD expression and stronger induction of detoxification-related genes, along with upregulated uroporphyrinogen decarboxylase (UROD) and suppressed chlorophyllase (CLH) expression associated with chlorophyll homeostasis. Protein sequence alignment confirmed no amino acid changes in HPPD between cultivars, indicating that tolerance differences are associated with gene expression levels and non-target metabolic pathways. WGCNA identified a turquoise module significantly correlated with 12 phenotypic traits, representing a core gene network associated with potential detoxification, photosynthetic maintenance, and growth recovery. Collectively, these findings reveal a multi-level synergistic tolerance strategy in foxtail millet and identify candidate genes for future functional validation to support breeding herbicide-resistant varieties and the scientific application of mesotrione in sustainable agriculture.