Mycorrhizal Symbiosis Reprograms Metabolism and Gene Networks to Enhance Salinity Resilience in Quinoa

Soil salinity poses a major threat to global food security, compromising plant productivity by disrupting water uptake, nutrient homeostasis, and metabolic balance. Here, we demonstrate that arbuscular mycorrhizal fungi (AMF) enhance quinoa ( Chenopodium quinoa Willd.) resilience to salinity stress by orchestrating multi-tiered metabolic and genetic reprogramming. AMF-inoculated plants exhibit a significant increase in chlorophyll content and osmoprotectant accumulation, along with enhanced regulation of ion homeostasis under high salinity conditions. Metabolite profiling reveals a shift in central carbon metabolism, with elevated levels of phosphoenolpyruvate (PEP), 3-phosphoglycerate (3PGA), and glutamate, supporting enhanced photosynthesis and stress adaptation. RNA sequencing identified key regulatory modules enriched in chlorophyll biosynthesis ( GLK1 , PORA ), iron uptake ( CHLN ), and stress-responsive pathways ( CBSCBS2 , CMO , aspartic proteinase inhibitor genes), while repressing ABA-related stress signaling ( C2H2-ZFP , PYL4 ). Furthermore, weighted gene co-expression network analysis (WGCNA) identified several co-expression modules enriched in genes involved in osmoprotectant synthesis pathways in AMF-inoculated quinoa plants. Our findings establish AMF as a potent modulator of metabolic resilience, highlighting its potential as a sustainable tool to enhance crop tolerance against environmental stress.