Transcriptomics in identifying tea plant breeding lines: a case study on the elite progenies of Camellia sinensis ‘Emei Wenchun’

Tea breeding typically proceeds through individual selection, line identification, regional testing, and cultivar registration. Despite its important role in genetic improvement, line identification often lacks a systematic molecular methodology. In this study, we integrated transcriptomic and biochemical profiling of one-bud-two-leaf samples from 15 tea accessions to enhance the molecular characterization and evaluation of elite clonal lines. Exploratory candidate-gene analyses revealed expression patterns of genes involved in flavonoid and caffeine biosynthesis, including CsCHS (TGY079101), CsF3 ′ H (TGY125466), CsLAR (TGY051808), CsANS (TGY116873), CsTCS1 (TGY127107), and CsTCS2 (TGY127102), which may partially explain the biochemical compositional characteristics of these lines. Furthermore, to assess parentage compatibility in open-pollinated elite lines, we identified 1,470 highly expressed synonymous transcriptome-derived SNP markers. Exclusion-based parentage analysis revealed zero mismatches across the parent-progeny trios for all 13 progeny lines, supporting genetic compatibility between the proposed parents and progenies. By contrast, alternative control combinations showed mismatch counts ranging from 53 to 316. To further facilitate the identification of these elite lines, we selected a core set of 150 SNP markers to develop a candidate transcriptome-derived SNP fingerprint panel. The theoretical cumulative probability of identity (PI) for the 150-SNP panel reached 4.255 × 10 − 57 under the assumption of independent loci. The integrated transcriptomic, biochemical, and SNP analyses provide complementary molecular information for characterizing elite tea breeding lines. The transcript-trait associations should be considered exploratory, and the 150-SNP panel represents a proof-of-concept within the studied genetic context. The analytical methods used here can guide line identification in tea plant breeding. Future work should validate these findings across broader and more genetically diverse tea germplasms.