CAPS markers using mitochondrial consensus primers for molecular identification of Panax species and Korean ginseng cultivars (Panax ginseng C. A. Meyer)

Abstract

Cleaved amplified polymorphic sequence (CAPS) marker system using mitochondrial consensus primers was applied for molecular identification of Korean ginseng cultivars (Panax ginseng). Initially, a total of 34 primers were tested to six Korean ginseng cultivars and two foreign Panax species, P. quinquefolius and P. notoginseng. In the polymerase chain reaction (PCR) amplification results, four primers (mt7, mt11, mt13, and mt18) generated co-dominant polymorphic banding patterns discriminating the Korean ginseng cultivars from P. quinquefolius and P. notoginseng. In the CAPS analysis results, the majority of the cleaved PCR products also yielded additional latent polymorphisms between the Korean ginseng cultivars and two foreign Panax species. Specific latent CAPS polymorphisms for cultivar Gopoong and Chunpoong were detected from internal region amplified with mt9 primer by treating HinfI and Tsp509I endonucleases, respectively. Sequencing analysis revealed that the length of amplified region of Korean ginseng cultivars was 2,179 bp, and those of P. quinquefolius and P. notoginseng were 2,178 and 2,185 bp, respectively. Blast search revealed that the amplified region was a mitochondrial cytochrome oxidase subunit 2 (cox2) gene intron II region. Nineteen single nucleotide polymorphisms (SNP) including each specific SNP for Gopoong and Chunpoong, and three insertion and deletion (InDel) polymorphisms were detected by sequence alignment. The CAPS markers developed in this study, which are specific to Gopoong and Chunpoong, and between the Korean ginseng cultivars and two foreign Panax species, will serve as a practical and reliable tool for their identification, purity maintenance, and selection of candidate lines and cultivars.

Identification of orchardgrass (Dactylis glomerata L.) cultivars by using simple sequence repeat markers

“…This finding supports the study by Delgado-Martinez et al (2012), which successfully used 4 SSR markers to construct fingerprints for 77 olive accessions, corresponding to 25 cultivars from the Extremadura region of Spain. These results were also similar to Lee et al (2012), who used 4 CAPS primers to generate co-dominant polymorphic banding patterns discriminating the Korean ginseng (Panax ginseng C. A. Meyer) cultivars from P. quinquefolius and P. notoginseng. In addition, Weng et al (2005) used 3 out of 120 operon RAPD primers for the fingerprints of 27 Porphyra lines in China.…”

EST-SSR Marker Sets for Practical Authentication of All Nine Registered Ginseng Cultivars in Korea

“…However, for ginseng there have not been sufficient molecular markers or a systematic authentication system available. Recently, some molecular markers have been developed for identification of individual ginseng cultivars which include sequence tagged site markers for ‘Chunpoong’ and ‘Gumpoong’ [31], a cleaved amplified polymorphic sequence marker for ‘Gopoong’ [32], molecular authentication of ‘Gopoong’ and ‘Gumpoong’ through internal transcribed spacer and 5.8S rDNA sequencing [33], and a single nucleotide polymorphism genotyping assay for five cultivars, ‘Chunpoong’, ‘Yunpoong’, ‘Gopoong’, ‘Gumpoong’, and ‘Sunpoong’ [34]. However, these studies were each performed based on one region of the genome and cannot discriminate each cultivar from the others, so they are difficult to utilize for practical and systematic authentication of the cultivars.…”

Recent Methodology in Ginseng Analysis

“…Genetic markers for ginseng include simple sequence repeats (also called microsatellites) [127,128], randomly amplified polymorphic DNA [129], restriction fragment length polymorphisms [130,131], insertion/deletion markers [132], single nucleotide polymorphisms (SNPs) [132], amplified fragment length polymorphisms (AFLPs) [133], AFLP-derived sequence characterized amplified regions [134], and cleaved amplified polymorphic sequence markers [135]. Novel genetic tools to discover markers have also been developed including loop-mediated isothermal amplification [136] and DNA microarray-based fingerprinting [137,138].…”