Genomics and Applied Biology 2024, Vol.15, No.4, 191-199 http://bioscipublisher.com/index.php/gab 196 Figure 2 Analyses of simple sequence repeat (SSR) in four chloroplast genomes (Adopted from Li et al., 2021a) Image caption: a Number different SSRs types detected by MISA. b Number of simple sequence repeats (SSRs) in the four chloroplast genomes by Venn diagram. c Location of the all SSRs from four species. CWN: ‘Wuyi narcissus’ cultivar of C. sinensis var. sinensis (natural triploid Chinary type tea); CSS: C. sinensis var. sinensis (diploid Chinary type tea); CSA: C. sinensis var. assamica (diploid Chinese Assamica type tea); CIA: C. sinensis var. assamica (diploid Indian Assamica type tea) (Adopted from Li et al., 2021a) 6.2 Correlation between chloroplast variation and phenotypic traits Chloroplast genome variations in Camellia sinensis are closely linked to phenotypic traits such as catechin and caffeine content. Studies have identified numerous single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) within genes related to catechin and caffeine biosynthesis, which differ significantly between various tea cultivars. For instance, the catechin/caffeine contents between 'Shuchazao' and 'Yunkang 10' cultivars were found to be significantly different, correlating with the genetic variations identified in their chloroplast genomes (Liu et al., 2019). Furthermore, the ycf1 gene has been highlighted as the most variable gene in cultivated tea, with significant nucleotide substitutions and sequence insertions, suggesting its potential role in phenotypic variation (Peng et al., 2021). 6.3 Potential markers for tea breeding and conservation The identification of genetic markers within the chloroplast genome is crucial for tea breeding and conservation efforts. Simple sequence repeats (SSRs) and indel markers have been developed to assess genetic diversity and phylogenetic relationships among tea cultivars (Liu et al., 2018; Chen et al., 2022). These markers have shown high polymorphism and transferability, making them valuable tools for genetic studies and marker-assisted selection (MAS) in tea breeding programs (Liu et al., 2018; 2019). Additionally, specific SNP allelic variations associated with important traits such as the timing of spring bud flush have been identified, providing a basis for MAS in early breeding of tea plants (Wang et al., 2019). The development of these markers not only aids in the selection of desirable traits but also contributes to the conservation of genetic resources by identifying and preserving genetically diverse tea cultivars. 7 Challenges and Future Directions 7.1 Limitations of current research methods Current research on the chloroplast genome of Camellia sinensis has provided significant insights into the evolutionary dynamics and phylogenetic relationships within the genus. However, several limitations persist. One major challenge is the frequent occurrence of hybridization and polyploidization events, which complicate the phylogenetic analysis and taxonomic classification of Camelliaspecies (Li et al., 2019; Lin et al., 2022; Liang et al., 2023). Additionally, the reliance on chloroplast DNA alone may not capture the full genetic diversity and evolutionary history of the species, as nuclear and mitochondrial genomes also play crucial roles (Shang et al., 2022). The current methods also face difficulties in resolving the phylogenetic relationships due to the limited number of informative markers and the high similarity among chloroplast genomes of different Camelliaspecies (Li et al., 2021a; Chen et al., 2022).
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