Integrated transcriptomic and physiological analysis highlights the candidate genes regulating enzymatic browning, antioxidant capacity, and lipid metabolism in pomegranate aril browning

Pomegranate fruit is highly susceptible to chilling injury during cold storage, resulting in aril browning and the decline of nutritional value and fruit quality. However, the underlying transcriptomic mechanisms remain insufficiently understood. In this study, the physiological traits and transcriptomic data in arils were investigated after 0 h (S0), 48 h (S1), and 120 h (S2) of cold storage at 4 °C. Compared to S0, the arils in S1 and S2 exhibited significantly higher browning rate and weight loss with lower sensory quality, and contained significantly lower phenolic and flavonoid contents. In S2, arils showed oxidative stress due to hydrogen peroxide (H₂O₂) accumulation and elevated activities of polyphenol oxidase (PPO) and peroxidase (POD), potentially leading to quality deterioration. Transcriptomic analysis identified 33,822 genes, including 3397 novel genes, and highlighted coordinated changes in the key pathways, including controlling antioxidant defense, phenylpropanoid biosynthesis, and membrane lipid metabolism during aril browning. Notably, reactive oxygen species (ROS) detoxification genes (PgSOD and PgAPX4) were downregulated, while oxidative enzyme–encoding genes, including PgAAO, PgGLO4-like, PgPPO, and PgPODs, were upregulated, indicating weakened antioxidant capacity and accelerated enzymatic oxidation in aril browning. Downregulation of membrane- and cuticle-related genes (PgSYT5-like, PgPSD1, PgFAR2/3, and PgCER1) suggested that lipid biosynthesis was retarded, and cell membrane integrity was damaged. Together, aril browning during cold storage was driven by ROS imbalance, membrane damage, and oxidation. Especially, these valuable candidate genes shed light on the mechanism of fruit browning.