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.