Journal of Tea Science Research, 2024, Vol.14, No.5, 293-303 http://hortherbpublisher.com/index.php/jtsr 298 tea samples from southern Guizhou. They identified 11 candidate genes linked to leaf tip shape and seven associated with overall leaf form. Some leaf development-related genes showed clear differences in allele frequency across production regions. These structural variations offer a genetic basis for the phenotypic diversity observed among different tea germplasms. SVs also contribute to regulating branching patterns and flowering time in tea plants. Several candidate genes have been identified as related to plant architecture and developmental stages (Lu et al., 2021). For example, Xia et al. (2021) found that the CsLAZY1 gene plays a central role in controlling branch gravitropism and branching angle. CsLAZY1 is mainly expressed in stem tissues and is localized on the plasma membrane. When introduced into Arabidopsis, it enhanced the plant's gravitropic response, indicating that this gene is involved in the regulation of branch orientation and affects the overall shoot structure of tea plants. The continued presence of such structural variations in wild and ancient populations suggests their lasting role in adaptive evolution and trait differentiation. 6 Case Studies 6.1 Structural variations in ancient tea genomes Ancient tea trees distributed across Southwest China are valuable materials for studying the evolution and domestication of tea plants. Lu et al. (2021) conducted whole-genome resequencing of 120 ancient tea individuals and identified over 410 million SNPs and nearly 19 million InDels. Many of these were nonsynonymous mutations and frameshift indels, indicating a high level of structural variation within the genomes of ancient tea trees. These variants were widely distributed across both coding and regulatory regions. The dN/dS ratio was close to 1, suggesting that strong genetic diversity has been maintained under natural selection. Population structure analysis revealed that the samples clustered into three main groups, which were further divided into seven subgroups. This pattern reflects genetic divergence driven by geographic isolation. Through genome-wide association studies (GWAS), researchers identified several candidate genes associated with important traits. Multiple nonsynonymous mutations were found to be significantly related to leaf color, tooth density, tooth depth, and plant type. For example, TEA012477 and TEA029928 were shown to influence chlorophyll synthesis and plant morphology, respectively (Figure 2). The study also highlighted differences in linkage disequilibrium (LD) decay rates among populations, suggesting that the accumulation of structural variations varies across groups. These findings provide strong evidence for the connection between structural genome variation and phenotypic diversity in tea. 6.2 SVs Related to catechin and theanine biosynthesis Catechins and theanine are key compounds that determine both the flavor and health benefits of tea. Wei et al. (2018) used the cultivated tea variety Camellia sinensis var. sinensis (CSS) to build a high-quality draft genome, laying the groundwork for exploring the molecular basis of tea quality. Their study revealed that the CSS genome underwent two rounds of whole-genome duplication (WGD), which occurred around 30-40 million years ago and 90-100 million years ago. These events greatly increased the copy number of metabolic genes. Extensive tandem duplications led to species-specific expansion of the SCPL1A family of acyltransferases. Many of these genes are highly expressed in young buds and leaves and are strongly correlated with high levels of monomeric catechins. Another key structural variation involves the origin of the CsTSI gene. This gene evolved through functional divergence from the GSI-type glutamine synthetase family and acquired the ability to synthesize theanine (Figure 3). Its function has been validated in transgenic Arabidopsis, confirming that the new function brought by this structural change contributed to the formation of a tea-specific metabolic pathway. The study also found clear structural differences between the genomes of CSS and CSA, including disrupted collinearity and partial gene rearrangements. These findings further support the central role of structural variations in the evolutionary trajectory of tea plants.
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