Mycorrhizal inoculation modulates metabolism and gene networks to enhance salinity tolerance in quinoa

Arbuscular mycorrhizal fungi (AMF) are increasingly recognized for their role in enhancing tolerance to salinity stress. Here, we present an integrative analysis combining metabolic, ionic, and transcriptomic profiling to investigate early vegetative-stage responses of quinoa ( Chenopodium quinoa Willd.) to salinity and AMF inoculation, an approach that remains underexplored. Plants were exposed to different salinity levels with or without AMF inoculation, and growth, chlorophyll concentration, ion accumulation, metabolite profiles, and gene expression patterns were analyzed. AMF-inoculated plants displayed slightly enhanced growth, reduced Cl - accumulation, and significantly higher chlorophyll (Chl) levels under high salinity. Metabolomic analysis revealed a shift in carbon flux toward Chl biosynthesis, characterized by decreased glucose levels and sustained accumulation of key intermediates and Chl precursors, including 3-phosphoglycerate (3PGA), phosphoenolpyruvate (PEP), 2-oxoglutarate, malate, oxalic acid, and glutamate. These changes were accompanied by increased levels of amino acids (alanine, isoleucine, proline) and phenolic compounds (ferulic acid, benzoic acid, and p-coumaric acid), suggesting improved osmotic adjustment and stress tolerance. Transcriptomic analysis revealed upregulation of genes involved in Chl biosynthesis ( GLK1 , PORA ) and enrichment of pathways related to carbon metabolism, photosynthesis, starch and sucrose metabolism, and the tricarboxylic acid cycle in AMF-inoculated plants. In addition, stress-responsive genes (e.g., CMO , aspartic proteinase inhibitors, CBSCBS2) were upregulated, while other stress-signaling genes ( C2H2-ZFP , PYL4 ) were repressed. Weighted gene co-expression network analysis further identified gene modules correlated with metabolites and traits related to Chl biosynthesis, carbon metabolism, and stress-responsive pathways. Overall, our findings indicate that AMF inoculation is associated with coordinated metabolic and transcriptional adjustments that contributed to enhanced salinity tolerance in quinoa.