Multi-omics elucidates organ-specific flavonoid and alkaloid metabolic pathways in Sophora alopecuroides under nitrogen-mediated salt stress

Soil salinization severely threatens agricultural productivity, while halophytic medicinal plants like Sophora alopecuroides offer sustainable solutions for marginal lands through stress-induced bioactive compound accumulation. Nitrogen (N) supplementation may enhance salt tolerance and metabolite production, but tissue-specific mechanisms remain unclear. This study identified optimal N regimes for salt-stressed S. alopecuroides and deciphered organ-divergent metabolic adaptations using integrated phenotyping, metabolomics, and transcriptomics. Phenotypic screening under 200 mmol/L NaCl stress demonstrated that 10 mmol/L mixed-N (NH 4 + : NO 3 − ratio 1:0) maximized growth and salt tolerance, significantly reducing underground salt sensitivity index (SSI) by 81.1% (vs. N0, p < 0.05) while concomitantly increasing salt tolerance index (STI) by 56.6%. Organ-specific responses were observed: above-ground SSI decreased by 22.5% at this treatment, consistently exceeding under-ground SSI across all N regimes. Metabolomic profiling detected 796 metabolites, with flavonoids (103 compounds) predominating; roots showed elevated accumulation of oxygenated organics, quinol lipids, and key flavonoids (hesperetin, astragalin), whereas leaves enriched alkaloids (sanguinarine). Transcriptomics indicated stronger root responsiveness (7,477 DEGs vs. 4,027 in leaves), with 3,936 root genes up-regulated. KEGG analysis highlighted divergent primary metabolism (cyanamino acid/tyrosine in leaves; glutathione/tryptophan in roots) but convergence on phenylpropanoid biosynthesis. Crucially, multi-omics integration elucidated two core adaptive pathways: flavonoid metabolites biosynthesis in roots positively correlated with SaCHS1∼3 expression, and isoquinoline alkaloid biosynthesis in leaves linked to SaTAT1 / SaAAT1∼2 . These findings identify candidate genetic loci for the improvement of salt tolerance and accumulation of medicinal compounds in S. alopecuroides .