Tree Genetics and Molecular Breeding 2024, Vol.14, No.6, 277-285 http://genbreedpublisher.com/index.php/tgmb 279 Figure 1 Landscape of the tea plant genome: transcription factors (Adopted from Xia et al., 2020) Image caption: (a), Gene density (b), intact LTR-RTs from the copia (c) and gypsy families (d), GC content (e), SSR density (f), and differentially expressed genes between leaf and root tissues (g) are shown. The inner circle represents the collinear blocks identified in the tea plant genome. (B) LAI evaluation of the genome assemblies of two tea plant varieties and seven other plant species, CSS, Camellia sinensis var. sinensis; CSA, C. sinensis var. assamica; OSA, Oryza sativa ssp. japonica; ZMA, Zea mays; CCA, Coffea canephora; TCA, Theobroma cacao;ACH, Actinidia chinensis;ATH, Arabidopsis thaliana; VVI, Vitis vinifera. * CSS indicates the previous assembly of C. sinensis var. sinensis (Wei et al., 2018). (C) Estimated times of insertion for intact LTR-RTs (≤4 MYA) of the tea plant, rice, and maize. (D) Distribution of the distance of tea plant LTR-RTs to protein-coding genes. Only distances≤10 kb are plotted. (E) Repeat content in introns of the tea plant and other three representative plants. (F) Expression levels of duplicated genes with (orange color) or without (green color) intronic TE insertions in eight tissues of tea plant: roots (RT), stems (ST), apical buds (BD), young leaves (YL), mature leaves (ML), old leaves (OL), flowers (FL) and fruits (FR). P**<0.01; P*<0.05. (G) Proportion of TEs in intronic regions of protein-coding genes and pseudogenes of the tea plant (Adopted from Xia et al., 2020) 4 Tools and Technologies for Utilizing Wild Tea Species in Breeding 4.1 Advances in genomic sequencing and annotation for tea Recent advancements in genomic sequencing have significantly enhanced our understanding of tea plant genetics. The assembly of high-quality reference genomes for wild tea species, such as the ancient tea tree, has provided valuable insights into the genetic makeup and evolutionary history of tea plants (Zhang et al., 2020). These genomic resources facilitate the identification of candidate genes associated with important traits like flavonoid biosynthesis, which are crucial for tea quality. Additionally, the development of comprehensive transcriptome datasets for wild relatives of tea, such as Camellia taliensis, has enabled the identification of genes involved in stress response and tea quality, further supporting breeding efforts (Zhang et al., 2015). 4.2 Application of genome-wide association studies (GWAS) Genome-wide association studies (GWAS) have become a pivotal tool in tea breeding, allowing researchers to link specific genetic variations with desirable traits. For instance, GWAS has been employed to identify SNPs associated with quality-related metabolites in tea, such as catechins and caffeine, which are essential for
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