Integrated transcriptomic and metabolomic analyses reveal melatonin-mediated drought response in red raspberry at the squaring stage

BACKGROUND: Red raspberry (Rubus idaeus L.) cultivation is often constrained by drought stress, which reduces fruit yield and quality. Melatonin (MT) plays an important role in plant stress tolerance. This study examined how exogenous MT improves drought tolerance in red raspberry at the squaring stage. It focused on changes in photosynthetic performance, antioxidant capacity, leaves anatomical structure, gene expression, and hormone homeostasis. RESULTS: , effectively alleviated these drought-induced effects. MT increased net photosynthetic rate and stomatal conductance, reduced oxidative damage, and promoted osmotic accumulation. At the anatomical level, MT-treated leaves showed more compact spongy tissue, increased palisade tissue and leaves thickness under drought stress. Transcriptomic and metabolomic analyses further revealed coordinated molecular changes under MT treatment. These changes mainly involved photosynthesis, carbohydrate and starch metabolism, plant hormone signaling, and amino acid metabolism. Genes related to photosynthetic function (PNSL3 and PNSB4), carbohydrate metabolism (glgc and PYG), antioxidant defense (SOD1 and sodC), and auxin signaling (AUX1 and SAUR) showed marked expression changes under MT treatment. Metabolite profiling also revealed changes in sugars, amino acids, phenolic compounds, and hormone-related compounds. Several transcription factor families, including bHLH, MYB-related, NAC, WRKY, and ERF, showed strong responses to MT. These changes were associated with transcriptional regulation and metabolic adjustment under drought stress. CONCLUSIONS: showing the best overall performance. This protective effect was associated with improved photosynthetic performance, enhanced antioxidant capacity, and better maintenance of leaves structure. Integrated transcriptomic and metabolomic analyses further revealed changes in hormone-related and metabolic pathways. These findings indicate that MT enhanced drought tolerance in red raspberry through coordinated physiological, anatomical, and molecular responses.