SNP identification of Alisma orientale, Alisma plantago-aquatica and Alismatis Rhizoma in the market based on DNA barcoding / 中国药学杂志

ABSTRACT

OBJECTIVE: To establish a method for the rapid identification of Alismatis Rhizoma based on single nucleotide polymorphism (SNP) molecular marker. METHODS: Total genomic DNA was extracted using improved DNA extraction kit, and the internal tran scribed spacer 2 (ITS2) regions were amplified and annotated by using the hidden Markov model (HMM). In addition, the ITS2 sequences of Alisma orientale and Alisma plantago-aquatica were aligned through Clustal-W, and then SNP was detected to identify Alismatis Rhizoma. RESULTS: The length of A. orientale and A. plantago-aquatica ITS2 sequences was 311 bp. No intra-specific variation was found among the samples of two species, respectively. One stable SNP (A/T) was detected at 165 bp in ITS2 region which was useful for identification of the two species. The result was confirmed by NJ tree method. Furthermore, authentication of commercial Alismatis Rhizoma by SNP molecular marker and NJ tree method indicated that only two medicinal samples (7%) were A. orientale and the others (93%) were A. plantago-aquatica which was not recorded in the Chinese Pharmacopoeia. CONCLUSION: SNP molecular marker can stably and accurately distinguish Alismatis Rhizoma in the market and can offer scientific basis for protection of germplasm resources and cultivation of Alisma.