• Journal of Plant Biotechnology
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• v.44 no.3
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• pp.235-242
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• 2017

Cudrania tricuspidata Bureau is a widely-used, medicinal, perennial and woody plant. Obtaining information about the genetic diversity of plant populations is highly important with regard toconservation and germplasm utilization. Although C. tricuspidata is an important medicinal plant species registered in South Korea, no molecular markers are currently available to distinguish Korean-specific ecotypes from other ecotypes from different countries. In this study, we developed single nucleotide polymorphism (SNP) markers derived from the chloroplast and nuclear genomic sequences, which serve to to identify distinct Korean-specific ecotypes of C. tricuspidata via amplification refractory mutation system (ARMS)-PCR and high resolution melting (HRM) curve analyses. We performed molecular authentication of twelve C. tricuspidata ecotypes from different regions using DNA sequences in the maturaseK (MatK) chloroplast intergenic region and nuclear ribosomal DNA internal transcribed spacer (ITS) regions. The SNP markers developed in this study are useful for rapidly identifying specific C. tricuspidata ecotypes from different regions.

• Journal of Korean Society of Forest Science
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• v.98 no.5
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• pp.568-575
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• 2009

Korean wild and forest cultivated ginseng has long been accepted as high medicinal values compared to field cultivated ginseng. Owing to the high price of Korean wild ginseng, Chinese wild and forest cultivated ginseng were smuggled and sold as Korean wild and forest cultivated ginseng. Therefore, an efficient method is required to distinguish Korean ginseng from Chinese ginseng. Microsatellites, simple sequence repeats (SSRs), are highly polymorphic loci present in DNA that consist of repeating units of base pairs. Thus SSR markers are highly advantageous for detection of small genetic variances of intra-species. In the present study, we constructed a microsatellite-enriched genomic library from South Korean wild Panax ginseng. After sequence analysis of 992 randomly picked positive colonies, 126 (12.7%) of the colonies were found to contain microsatellite sequences, and 38 primer pairs were designed. By polymorphism assessment using 36 primer pairs, 4 primers (PG409, PG450, PG491, and PG582) were shown to be polymorphic to distinguish the South Korean ginseng from the Chinese ginseng. These 4 microsatellite markers will provide powerful tools to authenticate South Korean ginseng from Chinese ginseng.

• Journal of Ginseng Research
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• v.44 no.1
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• pp.135-144
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• 2020

Background: Panax species are important herbal medicinal plants in the Araliaceae family. Recently, we reported the complete chloroplast genomes and 45S nuclear ribosomal DNA sequences from seven Panax species, two (P. quinquefolius and P. trifolius) from North America and five (P. ginseng, P. notoginseng, P. japonicus, P. vietnamensis, and P. stipuleanatus) from Asia. Methods: We conducted phylogenetic analysis of these chloroplast sequences with 12 other Araliaceae species and comprehensive comparative analysis among the seven Panax whole chloroplast genomes. Results: We identified 1,128 single nucleotide polymorphisms (SNP) in coding gene sequences, distributed among 72 of the 79 protein-coding genes in the chloroplast genomes of the seven Panax species. The other seven genes (including psaJ, psbN, rpl23, psbF, psbL, rps18, and rps7) were identical among the Panax species. We also discovered that 12 large chloroplast genome fragments were transferred into the mitochondrial genome based on sharing of more than 90% sequence similarity. The total size of transferred fragments was 60,331 bp, corresponding to approximately 38.6% of chloroplast genome. We developed 18 SNP markers from the chloroplast genic coding sequence regions that were not similar to regions in the mitochondrial genome. These markers included two or three species-specific markers for each species and can be used to authenticate all the seven Panax species from the others. Conclusion: The comparative analysis of chloroplast genomes from seven Panax species elucidated their genetic diversity and evolutionary relationships, and 18 species-specific markers were able to discriminate among these species, thereby furthering efforts to protect the ginseng industry from economically motivated adulteration.

• Plant Breeding and Biotechnology
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• v.5 no.3
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• pp.243-251
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• 2017

Rhus chinensis is a shrub widely distributed in Asia. It has been used for traditional medicine and ecological restoration. Here, we report the complete chloroplast genome sequence of two R. chinensis genotypes collected from China and Korea. The assembled chloroplast genome of Chinese R. chinensis is 149,094 bp long, consisting of a large single copy (97,246 bp), a small single copy (18,644 bp) and a pair of inverted repeats (16,602 bp). Gene annotation revealed 77 protein coding genes, 30 tRNA genes, and 4 rRNA genes. A phylogenomic analysis of the chloroplast genomes with 11 known complete chloroplast genomes clarified the relationship of R. chinensis with the other plant species in the Sapindales order. A comparative chloroplast genome analysis identified 170 SNPs and 85 InDels at intra-species level of R. chinensis between Chinese and Korean collections. Based on the sequence diversity between Korea and Chinese R. chinensis plants, we developed three DNA markers useful for genetic diversity and authentication system. The chloroplast genome information obtained in this study will contribute to enriching genetic resources and conservation of endemic Rhus species.

• Journal of Plant Biotechnology
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• v.44 no.2
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• pp.135-141
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• 2017

Cudrania tricuspidata Bureau is a widely used medicinal perennial woody plant. For conservation and germplasm utilization of the plant, it is imperative to obtaining information regarding the genetic diversity of the plant populations. Although C. tricuspidata is an important medicinal plant registered in South Korea, no molecular markers are currently available to distinguish Korean-specific ecotypes from other ecotypes of different countries. In this study, we developed single nucleotide polymorphism (SNP) markers derived from chloroplast genomic sequences to identify distinct Korean-specific ecotypes of C. tricuspidata via the amplification refractory mutation system (ARMS)-PCR analyses. Molecular authentication of twelve C. tricuspidata ecotypes from different regions was performed, using DNA sequences in the trnL-F chloroplast intergenic region. The SNP markers developed in this study are useful for rapidly identifying specific C. tricuspidata ecotypes from different regions.

• Journal of Plant Biotechnology
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• v.45 no.2
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• pp.102-109
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• 2018

Thistle is a perennial plant that is widely used for medicinal purposes. Information on the genetic diversity of thistle populations are great important for their conservation and germ plasmic utilization. Although thistle is an important medicinal plant species registered in South Korea, no molecular markers are currently available to distinguish them from other similar species from different countries. In this study, we developed single nucleotide polymorphism (SNP) markers derived from the nuclear ribosomal DNA internal transcribed spacer (ITS) regions of genomic sequences to identify distinct Korean-specific thistle species via an amplification refractory mutation system (ARMS)-PCR and high resolution melting (HRM) curve analyses. We performed molecular authentication of four different kinds of thistle species from different regions using DNA sequences in the ITS intergenic region. We also developed a quantitative PCR assay using species-specific ITS primers, which allowed us to estimate the ratio of Korean-specific thistle species using varying ratios of mixed genomic DNA templates from the two species. The SNP markers developed in this study are useful for rapidly identifying specific thistle species from different countries.

• The Korea Journal of Herbology
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• v.31 no.5
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• pp.15-23
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• 2016

Objectives : Araliae Continentalis Radix and Angelicae Pubescentis Radix have been used as the same medicinal name Korean and Chinese traditional medicines, respectively. The authentic Araliae Continentalis Radix is described only the root of Aralia continentalis in the Korean Pharmarcopoeia. However, the dried root of Angelica biserrata, Levisticum officinale, or Heracleum moellendorffii also has been distributed adulterants of Araliae Continentalis Radix. To develop a reliable method for identifying Araliae Continentalis Radix from adulterants, we carried out the analyses of universal DNA barcode sequences.Methods : Four plants species were collected from different habitate and nucleotide sequences of matK and rbcL were analyzed. The species-specific sequences and phylogenetic relationship were estimated using entire sequences of two DNA barcodes, respectively.Results : In comparative analysis of matK sequences, we were identified 104 positions of marker nucleotide for Ar. continentalis, 3 for An. biserrata, 4 for L. officinale and 8 for H. moellendorffii enough to distinguish individual species, respectively. Furthermore, we obtained marker nucleotides in rbcL at 42 positions for Ar. continentalis, 5 for An. biserrata and 2 for H. moellendorffii, but not for L. officinale. The phylogenetic tree of matK and rbcL were showed that all samples were clustered into four groups constituting homogeneous clades within the species.Conclusions : We confirmed that species-specific marker nucleotides of matK sequence provides distinct genetic information enough to identify four species. Therefore, we suggest that matK gene is useful DNA barcode for discriminating authentic Araliae Continentalis Radix from inauthentic adulterants.

• Journal of Ginseng Research
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• v.41 no.1
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• pp.31-35
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• 2017

Background: Korean ginseng (Panax ginseng) is a well-known medicinal plant of Oriental medicine that is still in practice today. Until now, a total of 11 Korean ginseng cultivars with unique features to Korean ginseng have been developed based on the pure-line-selection method. Among them, a new cultivar namely G-1 with different agricultural traits related to yield and content of ginsenosides, was developed in 2012. Methods: The aim of this study was to distinguish the new ginseng cultivar G-1 by identifying the unique single-nucleotide polymorphism (SNP) at its 45S ribosomal DNA and Panax quinquefolius region than other Korean ginseng cultivars using multiplex amplification-refractory mutation system-polymerase chain reaction (ARMS-PCR). Results: A SNP at position of 45S ribosomal DNA region between G-1, P. quinquefolius, and the other Korean ginseng cultivars was identified. By designing modified allele-specific primers based on this site, we could specifically identified G-1 and P. quinquefolius via multiplex PCR. The unique primer for the SNP yielded an amplicon of size 449 bp in G-1 cultivar and P. quinquefolius. This study presents an effective method for the genetic identification of the G-1 cultivar and P. quinquefolius. Conclusion: The results from our study shows that this SNP-based approach to identify the G-1 cultivar will be a good way to distinguish accurately the G-1 cultivar and P. quinquefolius from other Korean ginseng cultivars using a SNP at 45S ribosomal DNA region.

• Journal of Plant Biotechnology
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• v.48 no.1
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• pp.26-33
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• 2021

Angelica is a widely used medicinal and perennial plant. Information on the genetic diversity of Angelica populations is essential for their conservation and germ plasmic utilization. Although Angelica is an important medicinal plant species registered in South Korea, no molecular markers are currently available to distinguish it from other similar species from different countries. This developed single nucleotide polymorphism (SNP) markers derived from nuclear ribosomal DNA internal transcribed spacer regions genomic sequences to identify distinct Korean-specific Angelica species via amplification refractory mutation system (ARMS)-PCR curve analyses. We performed molecular authentication of different kinds of Korean-specific Angelica species such as A. gigas Nakai and A. gigas Jiri using DNA sequences in the ITS intergenic region. The SNP markers developed in this study are useful for rapidly identifying specific Angelica species from different countr.

• The Korea Journal of Herbology
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• v.37 no.4
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• pp.9-16
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• 2022

Objectives : In the Korean Pharmacopoeia 12th edition (KP 12) and the Korean Herbal Pharmacopoeia (KHP), two authentic herbal medicines are described, namely Bang-gi (Cheong-pung-deung) and Mok-bang-gi, respectively. In China, Bun-bang-gi is also used as herbal medicine. This study was conducted to develop a molecular authentication tool for distinguishing the three herbal medicine used as Bang-gi, which are Sinomeni Caulis et Rhizoma (Rhizome of Sinomenium acutum), Stephaniae Tetrandrae Radix (Root of Stephania terandra), and Cocculi Radix (Root of Cocculus trilobus). Methods : Twelve samples of three species (four samples of S. acutum, five samples of S. tetrandra, and three samples of C. trilobus) were collected from different habitats. The sequences of internal transcribed spacer (ITS) regions were obtained and comparatively analyzed to design the species-specific sequence characterized amplified region (SCAR) primers. The specificity of each pair of SCAR primers that amplified species-specific amplicon was evaluated for establishing the singleplex and multiplex PCR assay tools. Results : The singleplex SCAR markers show discriminability in C. acutum, S. tetrandra, and C. trilobus. These SCAR markers were also efficiently authenticated three species in the multiplex SCAR amplification using single PCR reaction. Furthermore, these PCR assay methods were applicable to authenticate dried herbal medicines distributed in the markets. Conclusions : The SCAR markers and PCR assay tools help discriminate the three herbal medicines used as Bang-gi at the species levels and provide a reliable genetic method to prevent the inauthentic distribution of these herbal medicines.