Integrated multi-omics reveals the mechanisms of sunburn-induced peel browning in wampee fruit

Sunburn is a major abiotic stress in fruit crops, leading to significant economic losses due to reduced fruit quality and marketability. Wampee ( Clausena lansium ), a tropical specialty fruit with growing industrial interest, is particularly vulnerable to sunburn-induced peel browning during ripening. To elucidate the underlying mechanisms, we conducted comprehensive field surveys and integrated physiological, biochemical, metabolomic, and transcriptomic analyses. Our integrated analyses suggest that strong light exposure is a key environmental trigger for sunburn, while shading treatments effectively mitigated damage despite elevated bag temperatures. Physiological assessments revealed that sunburn progression involved reactive oxygen species (ROS) accumulation, membrane lipid peroxidation, and dynamic changes in antioxidant enzymes (SOD, CAT, APX) and osmotic regulators. Metabolomic analysis identified 277 differentially accumulated metabolites, with significant enrichment of phenylpropanoid and flavonoid compounds such as coniferol, dihydrokaempferol, and naringenin—under severe stress. Transcriptomic data further highlighted coordinated upregulation of phenylpropanoid biosynthesis, flavonoid biosynthesis, and heat stress response pathways. We identified 28 structural genes and 56 transcription factors (including WRKY28 , bHLH30 , and HSFC1 ) as central regulators. Integrative analysis suggested that WRKY and bHLH transcription factors are associated with the upregulation of key genes (e.g., PAL and 4CL ) and the accumulation of antioxidant metabolites, implying a potential role in improving photo-thermal tolerance. This study provides valuable physiological and molecular insights into sunburn response in wampee fruit and offers potential strategies for breeding resistant varieties and developing postharvest management practices to enhance fruit quality in industrial cultivation. • Field and multi-omics analyses identify intense light as the key environmental trigger for sunburn in wampee, while bagging effectively alleviates damage despite elevated bag temperatures. • Sunburn induces oxidative stress (ROS accumulation, lipid peroxidation) and triggers dynamic changes in antioxidant enzymes and osmotic regulators. • Metabolomic and transcriptomic profiling highlights the crucial role of phenylpropanoid and flavonoid biosynthesis pathways in the sunburn response. • We identified a core regulatory network involving 28 structural genes and 56 TFs, with WRKY28 and bHLH30 potentially key to enhancing photo-thermal tolerance by activating PAL and 4CL.