Integrated transcriptomics and physiological parameters reveal the husk browning difference between two cultivars of pomegranate fruit

•‘Tunisia soft seed’ showed better antioxidant activities than ‘Jingpitian’.•Chilling injury accelerated oxidation of phenolics and degradation of pigments.•Chilling injury upregulated cellular process genes, accelerated cell metabolism.•The regulatory network diagrams of genes associated with husk browning were made. Pomegranate fruits are prone to chilling injury during low temperature storage, resulting in husk browning. In this study, two varieties of pomegranate fruit, ‘Jingpitian’ and ‘Tunisia soft seed’ (‘Tunisia’) were chosen to compare the differences in husk browning after 60 days of storage at 4 ± 1 ℃. The transcriptomics was utilized to investigate the causes and differences of husk browning caused by chilling injury. At the end of storage, the relative conductivity of ‘Tunisia’ was 31.47% lower than that of ‘Jingpitian’, and the total phenols content was 3.11 times that of ‘Jingpitian’. ‘Tunisia’ showed lower browning index, polyphenol oxidase, and peroxidase activities, and higher cell membrane integrity, phenolics, phenylalanine ammonia-lyase, and catalase activities. The transcriptomics of husk samples indicated that 6329 differentially expressed genes (DEGs) were identified in the two varieties on the 60th day. There were 3453 up-regulated DEGs and 2876 down-regulated DEGs. Additionally, most DEGs were significantly enriched in carotenoid biosynthesis and flavonoid biosynthesis pathways, indicating the two pathways could be related to the husk browning of pomegranate fruits. Collectively, the genes involved in cellular process of ‘Jingpitian’ were up-regulated, resulting in the destruction of cell membrane integrity. This accelerated the reaction of polyphenol oxidase and phenolics, causing the husk browning. It was noted that the husk browning was accompanied by the degradation of pigments. These findings could provide theoretical support for the study of husk browning caused by chilling injury.