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

Abstract 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.