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

Tea plant breeding typically progresses through individual selection, line evaluation, regional adaptability testing, and cultivar registration. Despite its pivotal role in genetic improvement, line identification remains a major bottleneck. In this study, we integrated transcriptomic and biochemical profiling of one-bud-two-leaf samples from 15 tea accessions to improve the precision and molecular depth of elite clonal line evaluation. We identified the regulatory networks underlying key quality components. Elevated epigallocatechin gallate (EGCG) accumulation positively correlated with the up-regulation of core structural genes such as CHS , F3'H , LAR , ANS and specific transcription factors like CsMYB199 and CsMYB111 . Concurrently, enhanced caffeine biosynthesis was driven by the increased expression of TCS1/2 and CsMYB184 , coupled with the suppression of CsMYB14-like . Furthermore, to resolve the ambiguous parentage typical of open-pollinated elite lines, we mined 1,470 highly expressed, synonymous single nucleotide polymorphism (SNP) markers from the transcriptome. Using exclusion-based parentage analysis, 13 progeny lines exhibited zero triplet mismatches with their putative parents, confirming their true parentage. By contrast, unrelated lines showed mismatch counts ranging from 53 to 316. To further identify and protect these elite lines, we selected a core set of 150 SNP markers to develop DNA fingerprint profiles. The cumulative probability of identity (PI) for a core set of 150 SNPs reached 4.26×10 ^− 57 , providing unprecedented resolution for DNA fingerprinting and plant variety protection (PVP). Ultimately, this study establishes a robust transcriptomics-driven framework that bridges molecular trait mechanisms with precision tea breeding strategies.