Identification of plant materials containing ephedrine alkaloids based on DNA barcoding and TaqMan real-time PCR assay

An intentional or inadvertent mixing of plant materials containing ephedrine alkaloids, especially Ephedra, is illegal. In order to better detect plant materials containing ephedrine alkaloids in export and smuggling, DNA barcoding combined with a TaqMan real-time PCR-based assay were used in this study. We collected 201 samples from 18 species belonging to four genera distributed in three families to amplify two barcoding markers, internal transcribed spacer 2 (ITS2) and psbA-trnH. 175 ITS2 sequences and 136 psbA-trnH sequences were obtained. Alignments and the neighbor-joining tree indicated that ITS2 showed a better discrimination of species than psbA-trnH. In addition, based on the sequence comparison of the ITS2 region from 18 species, three sets of primer/probes were designed using the real-time PCR assay platform. A sensitivity test showed the above primer/probe sets were specific and sensitive (as little as 0.0050 ng/mu L target DNA) to identify species containing ephedrine alkaloids. Hence, the combination of novel DNA barcoding and the TaqMan real-time PCR-based technique are promising tools for the identification of plant materials containing ephedrine alkaloids. It is beneficial to standardize market circulation and detection of plant materials containing ephedrine alkaloids.