Cultivation altitude is a comprehensive environmental factor that significantly affects tea quality. To gain a deeper understanding of the effect of cultivation altitude on tea metabolites, a widely targeted metabolomic method based on ultra-performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS) was used to analyze tea samples derived from three altitudes (86 m, 256 m, and 880 m) of two cultivars, ‘Mingke 1’ (MK) and ‘Fuyun 6’ (FY). The results showed that distinct groups of tea samples from different altitudes and cultivars were observed based on PCA. A total of 64 and 56 altitude-related differential metabolites were identified in MK and FY, respectively. Among them, 16 compounds were consistent in both cultivars and were clustered in the metabolic pathways for flavonoid (11 compounds), amino acid (3), and fatty acid (2). The content of all flavonoids and one amino acid (L-aspartic acid) gradually decreased with increasing altitude; on the contrary, the others showed an opposite trend. Furthermore, we identified 57 differential metabolites between two cultivars. Two specific compounds (8-C-hexosyl chrysoeriol O-hexoside and pelargonidin 3-O-β-D-glucoside) were exclusively found in MK, while one compound (4-hydroxybenzoic acid) was present only in FY. These findings offer insight into the metabolic responses of tea plants to different altitudes, providing further understanding on the influence of the environment on tea plants.

Due to a labor shortage, the mechanical harvesting of tea plantations has become a focal point. However, mechanical harvest efficiency was hampered by droopy leaves, leading to a high rate of broken tea shoots and leaves. Here, we dissected the genetic structure of leaf droopiness in tea plants using genome-wide association studies (GWAS) on 146 accessions, combined with transcriptome from two accessions with contrasting droopy leaf phenotypes. A set of 16 quantitative trait loci (QTLs) containing 54 SNPs and 34 corresponding candidate genes associated with droopiness were then identified. Among these, CsEXL3 (EXORDIUM-LIKE 3) from Chromosome 1 emerged as a candidate gene. Further investigations revealed that silencing CsEXL3 in tea plants resulted in weaker vascular cell malformation and brassinosteroid-induced leaf droopiness. Additionally, brassinosteroid signal factor CsBES1.2 was proved to participate in CsEXL3-induced droopiness and vascular cell malformation via using the CsBES1.2-silencing tea plant. Notably, CsBES1.2 bound on the E-box of CsEXL3 promoter to transcriptionally activate CsEXL3 expression as CUT&TAG based ChIP-qPCR and ChIP-seq suggested in vivo as well as EMSA and Y1H indicated in vitro. Furthermore, CsEXL3 instead of CsBES1.2 decreased lignin content and the expressing levels of lignin biosynthesis genes. Overall, our findings suggest that CsEXL3 regulates droopy leaves, partially through the transcriptional activation of CsBES1.2, with the potential to improve mechanical harvest efficiency in tea plantations.