Table 1_Rootstock genotype drives a metabolic trade-off between phenylpropanoids and terpenoids in Camellia sinensis.xlsx

In perennial crops, a metabolic trade-off between defense-related and aroma-related compounds fundamentally shapes quality, yet its regulation remains elusive. Grafting is a key horticultural technique that can alter this balance in tea plants (Camellia sinensis), but the underlying molecular mechanisms are unclear. To decipher this rootstock-driven trade-off, we employed an integrated multi-omics approach in Camellia sinensis cv. ‘Yashixiang Dancong’ and Camellia sinensis cv. ‘Lingtou Dancong’. Scions of the high-aroma cultivar ‘Yashixiang’ were grafted onto the vigorous ‘Lingtou’ rootstocks (hetero-grafting) and self-grafted (homo-grafting). We observed a pronounced metabolic trade-off: hetero-grafting significantly reduced phenylpropanoids (catechins) and caffeine (bitter-tasting compounds) while markedly enriching volatile terpenoids and fatty acid derivatives (aroma compounds). Transcriptome analysis revealed that this shift was orchestrated by a systematic transcriptional reprogramming mediating the trade-off: key gateway genes in the phenylpropanoid and caffeine pathways (CsPAL, Cs4CL, CsTCS) were downregulated, creating a bottleneck that limited flux toward non-volatile metabolites. Concurrently, genes encoding rate-limiting enzymes in the terpenoid backbone pathways (CsHMGR, CsDXS) were upregulated, enhancing precursor supply for volatile synthesis. This demonstrates that the rootstock genotype directs a precise metabolic trade-off in the scion, prioritizing aroma (terpenoids) production over defense (phenylpropanoids) accumulation. Our findings elucidate the molecular basis of grafting-modulated flavor quality and provide a framework for harnessing rootstock-scion interactions to fine-tune metabolic trade-offs in perennial crops.