ABA orchestrates molecular networks linking antioxidant defense, sugar metabolism and circadian clock for combined stress tolerance in Quinoa (Chenopodium quinoa Willd.)

Quinoa (Chenopodium quinoa Willd.), an emerging model species for abiotic stress tolerance due to its exceptional environmental resilience, exhibits unique molecular adaptations to combined low temperature-drought stress. However, the mechanism by which ABA enhances combined stress tolerance in quinoa remains elusive. This study characterized the abscisic acid (ABA)-mediated regulatory network in quinoa using integrated physiological and transcriptomics analyses. We demonstrated that combined stress triggers ABA accumulation via significant up-regulating NCED - ABA biosynthesis genes (log₂(Fold Change) = 2.37 to 4.98, p < 0.05) while suppressing CYP707A - ABA catabolism genes (log₂(Fold Change) = −1.81 to −2.99, p < 0.05). Exogenous ABA application under low temperature-drought stress activated the PYR/PYL-PP2C-SnRK2 cascade, thereby enhancing antioxidant defenses (SOD, POD, CAT) and increasing the ratio of soluble sugars to starch, which mitigated oxidative damage. The ABA-responsive antioxidant module (MEwhite, 110 genes), identified via WGCNA, coordinates redox homeostasis and carbohydrate metabolism. This module relies on HSF-centered transcriptional networks to enhance stress tolerance. This module integrates ERF and WRKY transcription factors to coordinate stress adaptation, concurrently enhancing antioxidant enzyme activity for ROS scavenging while maintaining metabolic equilibrium under combinatorial stress. Crucially, circadian rhythm genes (CRY, GI, PRR5) coordinates both ABA-dependent and ABA-independent pathways enhance stress adaptation, revealing crosstalk between stress signaling and biological clocks. Fluridone-mediated ABA suppression exacerbated the inhibition of oxidoreductase activity and soluble sugar content, confirming ABA's pivotal role. These findings provide mechanistic insights into ABA-driven combinatorial stress adaptation, offering targets for breeding climate-resilient crops.