Harnessing functional metabolite diversity in tea plant germplasm: from metabolic signatures to quality-oriented breeding

Tea plant (<italic>Camellia sinensis</italic>) exhibits remarkable metabolic diversity in their specialized secondary metabolites, such as catechins, theanine, caffeine, and volatile compounds, defining both ecological adaptability and therapeutic value. Environmental factors and phytohormonal regulation are proven as critical modulators of secondary metabolism, with certain signaling pathways coordinating stress-responsive metabolite production through transcriptional and post-transcriptional mechanisms. The development of chromosome-scale genome assemblies, pangenome, and 3D chromatin map resources has revealed extensive genomic variations that lead to metabolic distinctions. While metabolomics approaches including nuclear magnetic resonance, mass spectrometry, and emerging ion mobility techniques have enabled comprehensive profiling of flavor-related compounds, challenges persist in linking metabolic signatures to genetic determinants across diverse germplasms. Population genomics studies through metabolic genome-wide association have identified key quantitative trait loci and allelic variants governing metabolite accumulation. This review integrates recent metabolomic and genomic advancements to construct a roadmap for harnessing tea's functional metabolite diversity through germplasm resources, elucidating the biochemical and genetic foundations of quality traits to advance precision breeding applications.