Integrative hyperspectral, transcriptomic, and metabolomic analysis reveals the mechanism of tea plants in response to sooty mold disease

Background Sooty mold (SM) is one of the most destructive diseases of tea plants, causing considerable damage and productivity losses. However, the roles of defense genes and metabolites in different SM-infected canopy layers of tea plants remain largely unclear. To investigate the immune mechanisms of tea plants, we utilized hyperspectral, transcriptomic, and metabolomic data from leaves of three canopy layers infected by SM (A1, A2, and A3). Results The hyperspectral analysis indicated that the spectral characteristics of the three canopy layers significantly differed, and three inflection spots were located close to the 552, 673, and 800 nm wavelengths. Transcriptome analysis showed that the differentially expressed genes were mainly enriched in metabolic pathways, biosynthesis of secondary metabolites, and plant-pathogen interaction. The cluster analysis revealed an elevated immune response in the A2 and A3 samples. A total of 733 metabolites were co-changed in leaves infected by SM, with alcohol, lipids (free fatty acids), hydrocarbons, and amino acids significantly accumulating in A1, while flavonoids were predominantly upregulated in A2 and A3. WGCNA analysis revealed that five hub genes (Dormancy-associated protein, Serine/threonine-protein phosphatase, ABC transporter, and some uncharacterized proteins) and two hub metabolites (D-Mannitol and 17-Hydroxylinolenic Acid) have significant relationships with the DEGs and metabolites. Further co-expression showed that tea plants mainly employed genes and metabolites related to the biosynthesis of secondary metabolites, plant hormone signal transduction, and plant-pathogen interaction to defend against SM. Conclusion This study established a foundation for elucidating the immune mechanisms of different canopy layers of tea plants infected by SM, and provided candidate genes and metabolites for improving tea plant breeding.