Journal of Tea Science Research, 2024, Vol.14, No.5, 293-303 http://hortherbpublisher.com/index.php/jtsr 295 constructing pangenomes helps distinguish between core and variable genes, allowing for a more complete view of structural diversity across tea accessions. These approaches are not only useful for identifying trait-related structural variations, but also offer strong support for future studies in tea functional genomics and molecular breeding (Tong et al., 2024; Tariq et al., 2024). 3 Structural Variations in the Tea Genome 3.1 Characteristics of the Camellia sinensis genome Tea plants (Camellia sinensis) mainly include two cultivated varieties: the small-leaf type (var. sinensis, CSS) and the large-leaf type (var. assamica, CSA). Whole-genome resequencing of 30 cultivated varieties and 3 wild accessions by An et al. (2020) revealed 6,440,419 unique mutations in CSS and 6,176,510 in CSA, indicating clear genomic divergence between the two groups (Figure 1). The CSS subgroup shows higher genetic diversity, while CSA carries more nonsynonymous mutations. This pattern may reflect the effects of balancing selection. Further analysis showed that CSS is mainly associated with traits like cold tolerance and aroma biosynthesis. In contrast, CSA is more linked to leaf development and the synthesis of flavonoids and alkaloids. Huang et al. (2022) found that in CSA cultivars, the expression of CsAN1—a key transcription factor for anthocyanin biosynthesis—is significantly higher, especially in the anthocyanin-rich variety ‘Zijuan’. A deletion mutation in this gene led to the loss of anthocyanin synthesis in some F1 individuals. During the domestication of each group, specific trait-related genes and selective signatures were retained, reflecting adaptations to different environments and uses (Tong et al., 2024; Duan et al., 2024). Figure 1 Classification and distribution of identified SNPs/indels among 30 samples. (A) Annotation of SNPs identified in CSS and CSA subgroup. (B) The mutation pattern (SNP) and the length distribution (indel) of unique variations for CSS and CSA subgroup, respectively (Adopted from An et al., 2020) Image caption: The figure shows the annotation distribution and variation patterns of SNPs and indels in the two tea subgroups, CSS and CSA. Figure A indicates that most variants are located in intergenic regions, with more nonsynonymous mutations than synonymous ones. Figure B reveals that the number of CSS-specific mutations is slightly higher than that of CSA, and the indel length distribution also differs between the two. These findings suggest that the two subgroups have undergone substantial genomic divergence. In addition, CSS harbors a higher number of rare alleles, offering direct evidence for its greater genetic diversity and providing insights into its evolutionary history (Adapted from An et al., 2020)
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