Integrated transcriptomic and hormonal analysis suggests a trade-off between salt/drought tolerance and thermotolerance in Brassica rapa
Introduction Brassica rapa plants often face combined or sequential abiotic stresses, but the potential negative association between salt/drought tolerance and thermotolerance remains poorly understood. Most studies have focused on individual stress responses, leaving the regulatory networks that may constrain broad-spectrum resilience largely unexplored. Methods Here, we propose a hormone- and anthocyanin-centered framework for understanding this apparent negative association in B. rapa, based on integrated physiological, transcriptomic, hormonal and metabolic analyses across diverse inbred lines. Results Physiological characterization of 11 lines revealed an apparent negative association (salt vs. heat: r = –0.555; drought vs. heat: r = –0.339). Time-resolved transcriptomics uncovered stress-specific temporal patterns: a triphasic response under salt stress, a 'rapid response–readjustment–reactivation' pattern under drought, and a biphasic mechanism under heat stress. Hormonal profiling identified ABA and ethylene biosynthesis-related metabolites as correlates of osmotic adaptation. The chalcone synthase gene BraA10g024990.3C (CHS) showed genotype- and stress-specific expression and correlated with anthocyanin accumulation. Exogenous hormone treatments indicated that ABA and ethylene induce, while GA represses, CHS-mediated anthocyanin production. Discussion Despite the correlative nature of these data, this study provides a candidate regulatory axis and suggests that hormone-directed anthocyanin metabolism may contribute to the negative association between osmotic tolerance and thermotolerance in B. rapa, offering targets for breeding multi-stress-resilient crops.