Development of short tandem repeat (STR) and derived cleaved amplified polymorphic (dCAPS) markers for distinguishing species and varieties of the genus Panax in Vietnam

Abstract

In this study, we developed a protocol for the authentication of P. vietnamensis var. vietnamensis (Ngoc Linh ginseng) by combining two molecular markers: short tandem repeat (STR) and derived cleaved amplified polymorphic sequences (dCAPS). STR markers: Pvm30 and Pvm31 were found in the chloroplast genome of P. vietnamensis var. vietnamensis. These markers were able to accurately identify P. stipuleanatus, P. vietnamensis var. fuscidiscus, and P. ginseng. P. vietnamensis var. vietnamensis and P. vietnamensis var. langbianensishad a high similarity of chloroplast genomic sequence (99.96%) leading to STR markers could not distinguish these two ginseng varieties. Therefore, dCAPS marker: PvmdCAPS was applied to compensate for the defect of the STR markers. From the alignment result of the matK coding sequences of these two varieties, PvmdCAPS primers were designed at the position of single nucleotide polymorphisms (SNP) at the 248th nucleotide and had the ability to discriminate between these two Panax varieties. In summary, the combination of STR and dCAPS was used to distinct Panax species in Vietnam, especially P. vietnamensis var. vietnamensis.