Physiological and multi-omics analyses reveal BCAA-related responses and photosynthetic preservation associated with differential nicosulfuron tolerance in sweet maize

Nicosulfuron, an acetolactate synthase (ALS)-inhibiting herbicide widely used for post-emergence weed control in maize, can cause severe genotype-dependent phytotoxicity in sweet maize. At 80 mg L −1 nicosulfuron, the sensitive genotype HK320 showed 100% mortality, whereas the tolerant genotype HK301 maintained an average survival rate of 97.31% across three environments. To elucidate the basis of this differential tolerance, physiological, transcriptomic, proteomic, and metabolomic analyses were integrated in HK301 and HK320. Nicosulfuron induced distinct responses between the two genotypes, with HK301 maintaining stronger antioxidant responses, and differential regulation of ascorbate–glutathione, glyoxalase, and phytohormone-related processes, together with a more modular and less densely connected network. Transcriptomic analysis revealed increasing divergence between the genotypes after treatment, while weighted gene co-expression network analysis identified photosynthesis-related genes with high module connectivity and two branched-chain amino acid (BCAA) metabolism-associated candidate bridge genes linking distinct co-expression modules, highlighting candidate genes associated with the nicosulfuron-responsive molecular network. Multi-omics integration further revealed genotype-dependent patterns of BCAA-related metabolic adjustment. In the sensitive genotype, ALS transcripts were induced and 3-Isopropylmalate dehydrogenase (IPMDH) showed coordinated transcript- and protein-level regulation, whereas the tolerant genotype preferentially maintained photosynthetic processes and accumulated metabolites associated with phenylpropanoid, flavonoid and ubiquinone biosynthesis. Together, these findings indicate that differential nicosulfuron tolerance is associated with distinct BCAA-related responses and preservation of photosynthetic function, together with differential regulation of defense-associated metabolism. This study provides a systems-level view of genotype-dependent nicosulfuron responses and identifies candidate biological processes and genes for further investigation and breeding-oriented screening in sweet maize.