Multi-omics analysis to visualize the dynamic roles of defense genes in the response of tea plants to gray blight.

Gray blight (GB) is one of the most destructive diseases of tea plants causing considerable damage and productivity losses. However, the dynamic roles of defense genes during pathogen infection remain largely unclear. To explore the numerous molecular interactions associated with GB stress in tea plants, we employed transcriptome, sRNAome, and degradome sequencing from 1 to 13 days post inoculation (dpi) at 3-day intervals. The transcriptomics results showed that differentially expressed genes (DEGs) related to flavonoid synthesis, like chalcone synthase (CHS) and phenylalanine ammonia-lyase (PAL), were particularly induced at 4 dpi. Consistent with this, the contents of catechins (especially gallocatechin), which are the dominant flavonoids of tea plants, also increased in GB-infected tea leaves. Combined analysis of the sRNAome and degradome revealed that miRNAs could mediate tea plant immunity by regulating DEG expression at the post-transcriptional level. Co-expression network analysis demonstrated that miR530b-ethylene responsive factor 96 (ERF96) and miRn211-thaumatin-like protein (TLP) play crucial roles in GB response. Accordingly, gene-specific antisense oligonucleotides assays suggested that suppressing ERF96 decreased ROS levels, whereas suppressing TLP increased the levels of ROS. Furthermore, ERF96 was induced, but TLP was suppressed in susceptible tea cultivars. Our results collectively demonstrate that ERF96 was a negative regulator, while TLP was a positive regulator in the tea plant's response to GB. Taken together, our comprehensive integrated analysis revealed a dynamic regulatory network linked to GB stress in tea plants and provides candidate genes for tea plant improvement.