Journal of Tea Science Research, 2025, Vol.15, No.1, 1-11 http://hortherbpublisher.com/index.php/jtsr 6 synthesis-related genes in purple tea, especially anthocyanin synthase (ANS), have copy number variations and functional variations, and these changes are the key factors determining the purple phenotype (Maritim et al., 2021; Cai et al., 2022; Tariq et al., 2024). Modeling of the regulatory network further revealed that, the co-expression modules composed of structural genes (e.g., PAL, 4CL, F3’H, DFR, UFGT), and transcription factors (such as MYB, bHLH, NAC, WRKY), play a synergistic role in anthocyanin synthesis and accumulation (Maritim et al., 2021; Cai et al., 2022). Figure 2 A total of 22 representative cultivars of tea plant were selected for the pangenome analysis. a, The 736 resequenced tea genomes were subjected to principal component analysis to reveal their genetic diversity. The coloured dots indicate the cultivars chosen for pangenome analysis, which collectively represent the broad genetic diversity of C. sinensis species. PC, principal component. b, Phylogenetic analysis of the 22 representative tea cultivars was conducted on the basis of 1,063 single-copy genes, with C. lanceoleosa as an outgroup. The selected cultivars are highlighted with different colours: CSA samples have a red background, CSP is indicated by yellow and CSS samples are represented by light blue. On the right, the images illustrate the morphological differences between CSA and CSS. The numbers on the branches represent the bootstrap values supported, with higher values indicating stronger bootstrap support (Adopted from Chen et al., 2023) Taking the new variety of purple bud tea "Zikui" (ZK) as an example, Cai et al. (2022) revealed the molecular mechanism of its purple leaf formation through the integration of metabolome and transcriptome analysis. The research found that the accumulation of anthocyanins in the leaves of the purple sunflower reached its peak (4.97 mg/g) at 15 days, significantly higher than that of the green control variety N61. The relative abundance of the three main anthocyanins - cyanidin 3-O-glucoside, cyanidin 3-O-galactoside and cyanidin 3-O-glucoside - was the highest (Figure 3). Further analysis indicated that the high expression of CsMYB90, and its targeted genes F3’H and ANS was closely related to the enrichment of the above-mentioned anthocyanins, clarifying the molecular association between transcription factor regulation and metabolite accumulation (Cai et al., 2022). These findings provide a theoretical basis, and practical targets for the molecular breeding and metabolic engineering of anthocyanin-enriched tea tree varieties. 6 Prospects of Functional Genomics in Tea Breeding 6.1 Trait-associated markers and genomic selection With the development of pan genome construction, and high-throughput sequencing technology, researchers are able to identify functional SNPs and haplotypes, associated with key traits of tea trees, such as flavor, stress resistance, and leaf color. These variations were discovered through genome-wide association analysis (GWAS),
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