Effects of dark treatment on 'Yinhongli' plum phenolic biosynthesis and antioxidant capacity analysed through transcriptomic and metabolomic approaches

• Light plays a positive role in phenolics biosynthesis and antioxidant capacity in the Chinese plum cultivar ‘Yinhongli’ plum. • Integration of metabolome and transcriptome data for comprehensive analysis. • Differentially expressed genes (DEGs) and pathways associated with phenolics in ‘Yinhongli’ plum peel were identified. • The discovery of metabolic network of light-inducing phenolics biosynthesis in plum peel. • TFs such as MYB were identified as regulators for phenolics biosynthesis in plum peel. 'Yinhongli' is a typical light-dependent plum ( Prunus salicina Lindl.) cultivar for anthocyanin biosynthesis, and its peel color changes in response to direct light exposure. However, the effects of light on 'Yinhongli' color and quality and its metabolic regulatory mechanisms are remain unclear. In this study, transcriptomic and metabolomic analyses were conducted to investigate the changes in plum fruit quality under dark treatment. The results indicated that dark treatment led to decreased phenolic content and antioxidant activity in plum fruits. 1268 differentially expressed metabolites and 665 differentially expressed genes were identified in 'Yinhongli'. Transcriptome and metabolome analyses indicated that the alterations in phenolic substances following dark treatment were primarily attributed to changes in the expression levels of three photoreceptors (CRYs, PHYs, and UVR8), which subsequently influenced the expression of HY5. Additionally, variations in the expression levels of BBX24 and BBX31 genes within the BBX families might contribute to the observed reduction in phenolic content. Furthermore, changes in HY5 activity, along with modifications in certain transcription factors (such as MYB4, MYB111, and MYB123), might be likely account for the structural gene alterations within the phenolic synthesis pathway. Moreover, 11 structural genes that play crucial roles in light-regulated phenolic synthesis were identified. In summary, these findings highlight the distinct alterations in phenolic compounds under dark treatment and provided valuable insights into the study of light-tunable phenolic synthesis.