Multi‐omics dissection of interactive cross‐stress tolerance to Penoxsulam and salinity in Echinochloa crus‐galli

BACKGROUND: Herbicide resistance and soil salinization increasingly co-occur in rice paddies, yet how evolved penoxsulam resistance shapes the fitness of barnyardgrass (Echinochloa crus-galli) under combined salt and herbicide stress remains poorly understood. This study aimed to resolve the physiological and molecular basis of such cross-stress tolerance. RESULTS: penoxsulam, and their combination, integrated phenotyping, untargeted metabolomics and RNA-seq revealed that the two biotypes were equally suppressed by salinity alone but diverged under penoxsulam exposure; under combined dual stress, resistant plants maintained 3.78-fold greater aboveground biomass, corresponding to an antagonistic buffering interaction quantified by Bliss independence modelling. Sequencing of eight ALS codons associated with target-site resistance detected no mutation in either biotype, indicating a nontarget-site (metabolic) basis of resistance. Metabolome-wide profiling showed that susceptible plants mounted a costly defensive burst of flavonoids and anthocyanins (Group 9), whereas resistant plants preferentially sustained lignin precursors and accumulated rosin-type diterpenoids (Group 15). Weighted gene co-expression network analysis resolved two antagonistic transcriptional programs: a damage-responsive module marked by the DNA-repair gene MSH4, and a growth-homeostasis module enriched in lipid transfer proteins. CONCLUSION: Penoxsulam resistance in E. crus-galli operates through constitutive homeostasis maintenance and targeted carbon partitioning rather than amplified defence, providing a mechanistic framework for integrated resistance management in saline paddy fields.