Journal of Tea Science Research, 2024, Vol.14, No.2, 79-91 http://hortherbpublisher.com/index.php/jtsr 88 8 Applications in Agriculture and Breeding 8.1 Genomic applications in tea breeding Recent advancements in tea plant genomics have significantly enhanced the breeding programs for tea plants. The integration of genomic predictions (GPs) and genome-wide association studies (GWASs) has shown potential in improving the genetic breeding of tea quality-related metabolites. For instance, the use of genome-wide single nucleotide polymorphisms (SNPs) detected from restriction site-associated DNA sequencing has facilitated the identification of candidate genes for key metabolites such as catechins and caffeine, thereby contributing to genomics-assisted tea breeding (Yamashita et al., 2020). Additionally, the high-quality genome assembly of Camellia sinensis var. sinensis has provided insights into the evolution of the tea genome and the biosynthesis of key tea metabolites, providing references for future research aimed at improving tea quality and diversity within tea germplasm (Wei et al., 2018). 8.2 Genetic modifications and their acceptance The application of genetic modifications in tea plants, such as CRISPR-based genome editing, has the potential to accelerate breeding programs by enabling precise modifications of the genome. This approach has been exemplified in other crops like wheat, where genome editing has been used to modify traits such as flowering time and stress resistance (Appels et al., 2018). However, the acceptance of genetically modified tea plants may face challenges due to consumer perceptions and regulatory hurdles. It is crucial to engage with stakeholders, including consumers, policymakers, and industry players, to address concerns and highlight the benefits of genetic modifications in enhancing tea quality and sustainability. 8.3 Future potentials in agricultural applications The future of tea plant breeding lies in the continued application of high-quality sequencing and annotation technologies. The reference genome of the tea plant and the resequencing of diverse accessions have provided valuable resources for understanding genome evolution and adaptation, which can be leveraged to develop improved tea varieties with enhanced quality and stress resistance (Xia et al., 2020a). Moreover, the phased genome based on single sperm sequencing has revealed complex relatedness and genetic signatures among tea accessions, offering insights into the regulation of gene expression and the evolution of tea plants (Zhang et al., 2020a). These genomic resources will play a pivotal role in future breeding efforts, enabling the development of tea varieties that are better adapted to changing environmental conditions and consumer preferences. The advancements in tea plant genomics have opened new avenues for improving tea breeding programs. By leveraging genomic predictions, genome-wide association studies, and genetic modifications, researchers can accelerate the development of high-quality tea varieties. The continued application of high-quality sequencing and annotation techniques will further enhance our understanding of the tea plant genome, aiding in future innovations in tea agriculture and breeding. 9 Concluding Remarks Recent advancements in high-quality sequencing and annotation have significantly enhanced our understanding of the tea plant genome. The sequencing of the Camellia sinensis var. sinensis genome has provided insights into the evolution of tea quality traits and the molecular mechanisms underlying these traits. The identification of specific gene families responsible for the biosynthesis of key metabolites such as catechins, theanine, and caffeine has been a major breakthrough. Additionally, the reference genome and resequencing of diverse tea plant accessions have shed light on the genome evolution and adaptation of tea plants, revealing the critical roles of LTR retrotransposons in genome size expansion and gene diversification. These studies have laid a solid foundation for future research aimed at improving tea quality and stress resistance through targeted breeding programs. Despite the significant progress, several challenges remain in the field of tea genomics. One of the primary challenges is the complexity of the tea plant genome, which is characterized by a high percentage of repetitive sequences and multiple rounds of whole-genome duplications. This complexity makes it difficult to achieve complete and accurate genome assemblies. The functional annotation of genes, particularly those involved in
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