Metabolomic and Transcriptomic Insights into Anthocyanin Biosynthesis in ‘Ziyan’ Tea Plants under Varied Photoperiod and Temperature Conditions

(1) Background: Anthocyanins, the main pigments in plants, are influenced by both temperature and photoperiod. However, the specific mechanisms underlying anthocyanin accumulation in tea plants in response to these two environmental factors remain unclear. (2) Methods: This study subjected potted ‘Ziyan’ tea plants to four types of day-length and temperature treatments (HL (28 °C, 16 h), HS (28 °C, 8 h), LL (18 °C, 16 h), and LS (18 °C, 8 h)), and then conducted targeted metabolomic and transcriptomic analyses of the samples. (3) Results: Long photoperiods and low temperatures both promoted anthocyanin accumulation in the new shoots of the tea plants. Furthermore, the enhancing effects of these two environmental factors on anthocyanin accumulation are additive and exhibit interactive effects. Through a combined analysis of metabolomics and transcriptomics, five key differentially accumulated metabolites (DAMs) and twenty-two key differentially expressed genes (DEGs) were identified, the latter being found to participate in the regulation of anthocyanin biosynthesis pathways under varying light and temperature conditions. In summary, extended photoperiods primarily increase the content levels of ten metabolites, including cyanidin and naringenin-7-O-glucoside, by upregulating <i>CHS</i>, <i>F3H</i>, and <i>ANS</i> genes. In contrast, low temperatures primarily enhance the synthesis of seven anthocyanins, including cyanidin and cyanidin-3-O-rutinoside, by upregulating the <i>ANS</i> and <i>UFGT</i> genes. (4) Conclusions: Collectively, the differences in the expression levels of <i>CHS</i>, <i>F3H</i>, <i>ANS</i>, and <i>UFGT</i> might be responsible for ‘Ziyan’ tea plants’ purple shoot coloration, providing important data towards the discovery of candidate genes and molecular bases controlling the purple leaves of these tea plants under varied photoperiods and temperatures.