Journal of Tea Science Research, 2024, Vol.14, No.5, 293-303 http://hortherbpublisher.com/index.php/jtsr 296 In the tea genome, large-scale structural variations (SVs) and presence/absence variations (PAVs) are not evenly distributed. Instead, they tend to cluster in specific regions or "hotspots". These areas often harbor genes related to agronomic traits, such as stress resistance and quality-related genes, forming the genetic foundation for functional diversity across tea germplasms (Tong et al., 2024; Tariq et al., 2024). 3.2 Identified SVs in cultivated and wild tea accessions A large number of insertion and deletion variations (indels) have been identified across different cultivated tea varieties. So far, more than 217,000 large structural variations (SVs) and over 56,000 presence/absence variations (PAVs) have been detected. Some of these are directly linked to key traits, such as cold tolerance, and help explain phenotypic differences between CSS and CSA (Tong et al., 2024). Copy number variations (CNVs) are widespread in wild and ancient tea populations. These affect many gene families involved in secondary metabolism and stress responses. Such variations not only enrich the functional genome of tea plants but also provide a genetic basis for the broad adaptability and trait diversity seen in wild resources (Lu et al., 2021; Tariq et al., 2024). In wild and ancient tea accessions, many chromosomal structural changes, such as inversions and translocations, have also been observed. These SVs are strongly associated with adaptive traits like leaf shape and plant architecture. Despite natural or artificial selection pressures, these structures have remained intact, suggesting their crucial role in the evolutionary history of tea (Tong et al., 2024). 3.3 Evolutionary implications of SVs in tea Structural variations have played a key role in the domestication of tea plants. They helped shape population structure and drove the divergence between CSS and CSA. Some SVs are linked to important domestication traits, such as leaf development, metabolite biosynthesis, and stress tolerance. These variations have contributed to the selection and fixation of functional genes (Duan et al., 2024; Tong et al., 2024). Many SVs and PAVs can serve as genetic markers of both natural and artificial selection. The genomic regions where they are located often reflect selection under specific environmental pressures or human cultivation preferences. These variations are closely associated with a wide range of agronomic and quality-related traits, highlighting their important role in the ongoing evolution and breeding improvement of tea plants (Lu et al., 2021; Tong et al., 2024). 4 Functional Roles of Structural Variations 4.1 Gene expression changes driven by SVs Structural variations (SVs), such as insertions and deletions, often occur in regulatory regions like promoters and enhancers. These changes can alter gene expression levels. In the high-quality reference genome of tea, studies have shown that about 70.38% of the genome consists of long terminal repeat retrotransposons (LTR-RTs). These LTR-RTs tend to insert near promoters and introns, playing a key role in diversifying gene expression. They particularly affect genes related to tea aroma—such as those involved in terpene biosynthesis—and stress resistance (Xia et al., 2020). Therefore, SVs can regulate the expression of important functional genes and contribute to quality traits and environmental adaptability. SVs can also rearrange genomic regions, introducing new regulatory elements or forming chimeric gene structures. This may lead to the creation of fusion genes or novel transcripts. Tong et al. (2024) resequenced 363 tea accessions from around the world and constructed a population structure map covering eight subgroups. They identified 730 Mb of new sequences—regions not annotated in existing reference genomes—and discovered 6,058 full-length protein-coding new genes. In addition, they detected 217,376 large SVs and 56,583 PAVs. These findings suggest that SVs help shape transcriptomic diversity and may drive the emergence of new functional genes, promoting trait differentiation and evolutionary change.
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