Journal of Tea Science Research, 2025, Vol.15, No.1, 1-11 http://hortherbpublisher.com/index.php/jtsr 5 4.2 Biotic stress responses Transcriptomic analysis revealed that when tea plants are infected by fungal diseases, a large number of defension-related genes are activated, including those involved in MAPK signal transduction, receptor kinase activity, and cell wall structure regulation. Genes containing the NB-ARC domain, were significantly enriched and positively correlated with both cold resistance and disease resistance traits, suggesting that these defense mechanisms may be shared (Hazra et al., 2023; Li et al., 2025). The PYL gene was also expressed in response after insect feeding, further supporting its role in biological stress (An et al., 2023). The flavonoid synthesis pathway is significantly enriched in the cold and disease resistance of tea plants, among which secondary metabolites play a role as key defense compounds. Under stress conditions, GSTs and other enzymes involved in secondary metabolism, were differentially expressed, enhancing the resistance of plants to pathogenic bacteria (Cao et al., 2022; Hazra et al., 2023; Li et al., 2025). 4.3 Epigenetic regulation of stress responses Although research on the methylation and histone modification of tea plants under stress conditions is currently insufficient, the expansion and structural variation of gene families related to stress resistance suggest that epigenetic mechanisms may play an important role in regulating stress responsive genes (Tong et al., 2024; Tariq et al., 2024). Regulatory RNAs, especially miRNAs and long chain non coding RNAs (lncRNAs), are important post transcriptional regulators in stress response. MiRNAs such as csn-miR398aa-3p-1 and csn-miR166 target SOD and HD Zip III genes, respectively, to regulate tolerance to drought and cold stress (Qian et al., 2023; Li et al., 2025). The csn-miR171b-3p_2-CsSCL6-4 module can promote the expression of drought tolerance related genes. LncRNAs can also interact with transcription factors and miRNAs, participating in the regulation of response responses to salt and drought stress (Cao et al., 2015). By integrating RNA Seq and small RNA sequencing (sRNA Seq) data, researchers have identified a large number of miRNA mRNA regulators involved in response to low temperature, freezing, and drought stress (Wang et al., 2022; Xu et al., 2023). 5 Case Studies in Functional Genomics of Tea 5.1 Functional gene discovery in Longjing 43 Longjing 43 is a widely cultivated high-quality green tea variety, and its outstanding aroma characteristics have long attracted attention. In recent years, researchers have discovered through high-quality reference genome assembly and pan-genome analysis that genes related to terpene synthesis in Longjing 43 and other dominant varieties have been amplified. This amplification is usually achieved through tandem duplication and the formation of gene clusters (Xia et al., 2020a; Chen et al., 2023) (Figure 2). Transcriptome analysis indicated that, the expression of these aroma-related genes, especially those involved in the monoterpene and sesquiterpene synthesis pathways, was elevated in young leaves and buds, which are the main raw materials of high-end tea products (Xu et al., 2018; Xia et al., 2020a). These results emphasize the significance of gene copy number variations and tissue-specific expression in the formation of the unique aroma of Longjing 43. Genome-wide association studies (GWAS) and SNP variation studies conducted in Longjing 43 also revealed a strong correlation between allelic differences and the accumulation of key flavor metabolites (such as catechins, theanine, caffeine) (Yamashita et al., 2020; Fang et al., 2021; Chen et al., 2023). e.g., SNP loci in genes encoding flavonoid biosynthases (FLS, UGT, MYB, WD40, etc.), and their transporter genes have been shown to be significantly associated with catechin content and overall tea quality (Xu et al., 2018; Fang et al., 2021). Currently, these genetic markers are being used to guide the genome-assisted breeding of Longjing 43 and related varieties, enhancing superior traits. 5.2 Regulatory network modeling in purple tea Purple tea varieties (like Zijuan and Zikui), have a distinct purple appearance and potential health benefits due to their high content of anthocyanins. Pan-genome and transcriptome studies have found that anthocyanin
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