A qPCR-based method based on a chloroplast atpF gene SNP for the accurate authentication of Salvia miltiorrhiza and Salvia yunnanensis in herbal products.

UNLABELLED: Salvia miltiorrhiza is a widely used Asian medicinal plant valued for its bioactive compounds and therapeutic benefits. However, it is often adulterated with the closely related species S. yunnanensis, complicating identification by conventional PCR and HPLC because of overlapping genetic and chemical profiles. To address this issue, we developed a qPCR assay using SNP-specific primers targeting chloroplast atpF variation between the two species. The assay showed high sensitivity and specificity, detecting S. yunnanensis adulteration at 0.1% in binary mixtures. HPLC analysis provided complementary chemical profiling data and supported the molecular results. Overall, the atpF SNP-based qPCR assay enables accurate identification of S. miltiorrhiza and detection of potential adulteration in herbal products. Compared with conventional PCR and HPLC-based approaches, this method offers a rapid, sensitive, and species-specific authentication strategy applicable to processed commercial herbal products. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10068-026-02234-5.