Integrated transcriptomic and metabolomic profiling unravels the altitude-induced regulatory mechanism of quality-related metabolites in tea plants

Altitude is a pivotal environmental factor affecting tea quality through its regulation of plantation microclimate. To investigate how altitude shapes quality-related components in tea plants and the underlying molecular mechanisms, we conducted a controlled experiment on Mount Emei. Our findings demonstrated that high-altitude conditions significantly increased the contents of water extract and free amino acids, while decreasing the level of tea polyphenols. Metabolomic profiling identified 3819 metabolites, among which theanine and aspartic acid were most abundant at 1200 m, whereas epigallocatechin gallate was markedly reduced. Functional annotation indicated that the identified metabolites are primarily involved in amino acid metabolism and biosynthesis of secondary metabolites pathways. Integrated metabolomics and transcriptomics analysis further revealed 26 nitrogen metabolism-related genes and 40 transcription factors strongly associated with theanine biosynthesis, along with 25 differentially expressed genes correlated with EGCG accumulation. The identified upregulation of glutamate dehydrogenase 2 (GDH2, CSS0034454 ) and key transcription factors from the HD-ZIP and KNOX families points to their critical regulatory roles in driving the high-altitude accumulation of theanine and aspartic acid. This study provides valuable information to reveal the changes in quality-related metabolites in tea plants at different altitudes, offering a theoretical basis for understanding the eco-physiological foundation of high-mountain tea quality in Mount Emei. ● High altitude elevates amino acids but reduces polyphenols in tea tender leaves. ● Theanine and EGCG show opposite accumulation trends with increasing altitude. ● Omics show altered significantly amino acid and phenylpropanoid biosynthesis. ● Key genes ( CsGDH2 ) and 40 transcription factors linked to altitude effects.