Whole genome sequencing analysis of two sinensis tea (Camellia sinensis var. sinensis) clones: Assessment of molecular variations to search for breeding markers

Tea (Camellia sinensis (L.) Kuntze) is a globally important crop valued for its flavour diversity and health benefits. Whole-genome sequencing (WGS) was performed to compare genomic variation and functional potential between clone Yabukita and locally adapted clone I.1.93. Using next-generation sequencing, approximately 10× genome coverage was achieved for both clones, with high mapping efficiency (98.24% for Yabukita and 97.88% for clone I.1.93), ensuring reliable downstream analyses. Single nucleotide polymorphism (SNP) analysis revealed distinct genomic patterns, with Yabukita showing a more uniform chromosomal SNP distribution, while clone I.1.93 exhibited higher SNP densities on specific chromosomes, particularly chromosomes 5 and 13. Silent mutations predominated in Yabukita (48.21%), whereas missense mutations were more frequent in clone I.1.93 (57.97%), suggesting greater functional divergence. Most SNPs occurred in non-coding regions, indicating potential regulatory roles. GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed highly similar shared pathways, including photosynthesis and protein interactions, alongside clone-specific enrichment related to photosynthesis in Yabukita and stress responses in clone I.1.93. miRNA profiling identified distinct regulatory patterns, including the clone-specific miR530 in clone I.1.93. Biosynthetic gene cluster analysis further predicted secondary metabolite pathways associated with terpenoid, polyketide, and saccharide biosynthesis. These findings provide valuable genomic insights for tea improvement and breeding programs.