Czech J. Genet. Plant Breed., X:X | DOI: 10.17221/116/2025-CJGPB

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

Dwinita Wikan Utami^1*, Adhityo Wicaksono², M. Khais Prayoga³, Heri Syahrian³, Vitria P. Rahadi³, Erdiansyah Rezamela³, Budi Martono⁴, Tri Joko Santoso¹, Nur Kholilatul Izzah⁴, Haris Maulana¹, Ady Daryanto¹, Rerenstradika Tizar Terryana⁵, Imas Rita Saadah¹, David Virya Chen²

¹ Research Center for Horticulture, Research Organization for Agriculture and Food, National Research and Innovation Agency (BRIN), Bogor, West Java Province, Indonesia

² Scientific Department, Genomik Solidaritas Indonesia (GSI Lab), Jakarta, Indonesia

³ Research Institute for Tea and Cinchona, Bandung, Indonesia

⁴ Research Center for Estate Crops, Research Organization for Agriculture and Food, National Research and Innovation Agency (BRIN), Bogor, West Java Province, Indonesia

⁵ Research Center for Applied Botany, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Bogor, West Java Province, Indonesia

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.

Keywords: comparative genomics; next-generation sequencing; single-nucleotide polymorphism; tea breeding

Received: November 24, 2025; Revised: January 20, 2026; Accepted: February 6, 2026; Prepublished online: February 23, 2026