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In order to develop a novel system for the discrimination of five ginseng cultivars (Panax ginseng Meyer), single nucleotide polymorphism (SNP) genotyping assays with real-time polymerase chain reaction were conducted. Nucleotide substitution in gDNA library clones of P. ginseng cv. Yunpoong was targeted for the SNP genotyping assay. From these SNP sites, a set of modified SNP specific fluorescence probes (PGP74, PGP110, and PGP130) and novel primer sets have been developed to distinguish among five ginseng cultivars. The combination of the SNP type of the five cultivars, Chungpoong, Yunpoong, Gopoong, Kumpoong, and Sunpoong, was identified as 'ATA', 'GCC', 'GTA', 'GCA', and 'ACC', respectively. This study represents the first report of the identification of ginseng cultivars by fluorescence probes. An SNP genotyping assay using fluorescence probes could prove useful for the identification of ginseng cultivars and ginseng seed management systems and guarantee the purity of ginseng seed.

Recently, new ginseng cultivars having superior agricultural traits have been developed in Korea. For newly developed plant cultivars, the identifi cation of distinctiveness is very important factors not only in plant cultivar management but also in breeding programs. Thus, eighty-fi ve inter simple sequence repeat (ISSR) primers were applied to detect polymorphisms among six major Korean ginseng cultivars and two foreign ginsengs. A total of 197 polymorphic bands with an average 5.8 polymorphic bands and 2.9 banding patterns per assay unit across six Korean ginseng cultivars and foreign ginsengs from 236 amplifi ed ISSR loci with an average 6.9 loci per assay unit were generated by 34 out of 85 ISSR primers. Three species of Panax ginseng including the Korean ginseng cultivars, P. quinquefolius, and P. notoginseng, could be readily discriminated using most tested primers. UBC-821, UBC-868, and UBC-878 generated polymorphic bands among the six Korean ginseng cultivars, and could distinguish them from foreign ginsengs. Sequence characterized amplifi ed region (SCAR) marker system was introduced in order to increase the reproducibility of the polymorphism. One SCAR marker, PgI821C650, was successfully converted from the randomly amplifi ed polymorphism by UBC-821. It showed the expected dominant polymorphism among ginseng samples. In addition, the specifi c polymorphism for Sunwon was generated by treating Taq I restriction enzyme to polymerase chain reaction products of PgI821C650. These results will serve as useful DNA markers for identifi cation of Korean ginseng, especially Sunwon cultivar, seed management, and molecular breeding program supplemented with marker-assisted selection.