Integrated transcriptomic and metabolomic analysis reveals spatiotemporal regulation of Cucurbitacin B biosynthesis in melon (Cucumis melo L.)

Cucurbitacin B (CuB), a triterpenoid compound in Cucurbitaceae crops like melon, significantly impacts plant defense and fruit bitterness. This study explores the spatiotemporal regulation of CuB biosynthesis using integrated transcriptomic and metabolomic analyses of two melon germplasms 14B46 and 14BY, differing in CuB decay rates. We found that 14B46 exhibits rapid CuB decline and enhanced growth, while 14BY maintains high CuB levels, correlating with delayed senescence and metabolic prioritization. Transcriptomic profiling reveals distinct expression patterns across developmental stages, identifying ABC transporters as key mediators of CuB degradation, with significant regulatory shifts at 20 days post-anthesis (DPA). Combined transcriptomic and metabolomic data highlight coordinated regulation between gene expression and metabolite profiles. At 10 DPA, photosynthesis and defense pathways are enriched, while at 20 DPA, plant hormone signaling and terpenoid biosynthesis dominate. ABC transporters show stage-specific expression, influencing CuB accumulation and degradation. The qPCR results of melon bitterness synthesis-related genes and ABC transporter proteins showed that the expression levels of the more bitter 14B46 were significantly higher than those of 14BY at all stages. The growth-defense trade-off in 14B46, prioritizing growth via rapid CuB clearance, results in higher fruit weight and chlorophyll retention, mirroring domestication trends where defense metabolites are reduced to enhance yield and palatability. This research delineates a comprehensive regulatory framework for CuB biosynthesis, transport, and degradation, offering actionable targets for developing high quality non-bitter melon melons while preserving ecological defense mechanisms and theoretical basis.