Molecular Plant Breeding 2025, Vol.16, No.5, 278-286 http://genbreedpublisher.com/index.php/mpb 280 Haplotype resolution is helpful for analyzing allele-specific expression and its influence on aroma and flavor traits, as well as promoting targeted gene improvement and precision breeding (Zhang et al., 2021; Chen et al., 2023). The development of pan-genome resources also provides more genetic diversity support for GS and haplotype breeding. 4 Role of Functional Genomics and Omics Technologies 4.1 Transcriptomics and metabolomics for candidate gene discovery Researchers can analyze the relationship between gene expression and metabolite accumulation at different developmental stages, in different tissues or under different treatment conditions through high-throughput transcriptome sequencing (RNA-seq) and metabolite profiling. The combined analysis of the transcriptome and metabolome has discovered many key genes related to the synthesis of flavor substances such as amino acids, flavanols, and caffeine. Candidate genes regulating these metabolic pathways have also been identified through the gene-metabolite network (Wei et al., 2018; Zhang et al., 2018). In specific varieties, haplotype assembly and allele-specific expression analysis are helpful for identifying structural genes such as CsMCT, CsGGPPS2, and CsTPS10 that play key roles in aroma formation (Gu et al., 2023). These results provide valuable genetic resources and molecular markers for molecular breeding. 4.2 Epigenomic regulation of aroma-related genes Epigenomics (such as DNA methylation and histone modification) is also important in regulating the expression of genes related to the aroma of tea plants. Although there are not many direct studies on the epigenetic regulation of aroma genes in tea plants, existing studies have found through haplotype assembly and allele-specific expression analysis that the expression of key genes in the aroma synthesis pathway varies in different tissues and developmental stages, which may be related to epigenetic regulation (Gu et al., 2023). Population genomics and selection signal analysis also revealed that metabolic pathway genes related to aroma and flavor were subjected to intense selection pressure, suggesting that epigenetic regulation may play an important role in the evolution and domestication of aroma traits in tea plants (Zhang et al., 2021). 4.3 Integration of multi-omics for systems-level understanding Integrating multi-omics data provides new ideas for understanding the molecular mechanisms of tea tree aroma and flavor at the systematic level. The construction of the pan-genome revealed the structural variations and functional diversity of aroma and flavor-related genes in tea plants, and also provided a scientific basis for genome-wide association analysis and molecular design breeding (Chen et al., 2023; Tariq et al., 2024). Researchers can comprehensively analyze the genetic basis of aroma and flavor traits from gene variation, expression regulation to metabolite accumulation by integrating different omics data (Wei et al., 2018; Zhang et al., 2018). The combined analysis of the pan-genome and multi-omics revealed the functional differentiation of the core genome and the variable genome, providing theoretical support and technical tools for precise molecular breeding of aroma and flavor traits (Tariq et al., 2024). 5 Genome Editing and Synthetic Biology Applications 5.1 CRISPR/Cas-based gene editing for trait improvement CRISPR/Cas9 is an efficient gene editing tool. The research identified 248 million potential editing sites in tea plants, covering all gene structural elements. Many of these sites are concentrated in regions related to secondary metabolites and amino acid biosynthesis, providing a basis for the precise regulation of aroma and flavor traits. Theoretically, by targeting and regulating the genes of key metabolic pathways, the aroma and flavor of tea can be improved in a targeted manner. However, due to the fact that the highly hybrid and transformation system of tea plants is still not perfect, there are still technical difficulties in practical application. However, the discovery of these gene editing sites has provided important resources for subsequent molecular breeding (Figure 1) (Li et al., 2023).
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