Discrimination of Korean ginseng (Panax ginseng Meyer) cultivar Chunpoong and American ginseng (Panax quinquefolius) using the auxin repressed protein gene

Application of PLS-NN model based on mid-infrared spectroscopy in the origin identification of Cornus officinalis

Mid-infrared spectroscopy has been increasingly used as a nondestructive analytical technique in Chinese herbal medicine identification in recent years. In this study, a new chemometric model named as PLS-NN model was proposed based on the mid-infrared spectral data of Cornus officinalis samples from 11 origins. It was realized by combining the partial least squares and neural networks for the identification of the origin of Chinese herbal medicines. First, we extracted features from the spectral data in 3448 bands using the partial least squares method, and extracted 122 components that contained more than 95% of the information. Then, we trained the PLS-NN model by neural network using the extracted components as inputs and the corresponding origin classes as outputs. Finally, based on an external test set, we evaluated the generalization ability of the PLS-NN model using metrics such as accuracy, F1-Score and Kappa coefficient. The results show that the PLS-NN model performs well in all three metrics when compared to models such as Decision trees, Support vector machine, Partial least squares Discriminant analysis, and Naive bayes. The model not only realizes the dimensionality reduction of full-spectrum data and improves the training efficiency of the model, but also has higher accuracy compared with the full-spectrum data model. The PLS-NN model was applied to identify the origin of Cornus officinalis with an accuracy of 91.9%.

Origin identification of Cornus officinalis based on PCA-SVM combined model

Infrared spectroscopy can quickly and non-destructively extract analytical information from samples. It can be applied to the authenticity identification of various Chinese herbal medicines, the prediction of the mixing amount of defective products, and the analysis of the origin. In this paper, the spectral information of Cornus officinalis from 11 origins was used as the research object, and the origin identification model of Cornus officinalis based on mid-infrared spectroscopy was established. First, principal component analysis was used to extract the absorbance data of Cornus officinalis in the wavenumber range of 551~3998 cm-1. The extracted principal components contain more than 99.8% of the information of the original data. Second, the extracted principal component information was used as input, and the origin category was used as output, and the origin identification model was trained with the help of support vector machine. In this paper, this combined model is called PCA-SVM combined model. Finally, the generalization ability of the PCA-SVM model is evaluated through an external test set. The three indicators of Accuracy, F1-Score, and Kappa coefficient are used to compare this model with other commonly used classification models such as naive Bayes model, decision trees, linear discriminant analysis, radial basis function neural network and partial least square discriminant analysis. The results show that PCA-SVM model is superior to other commonly used models in accuracy, F1 score and Kappa coefficient. In addition, compared with the SVM model with full spectrum data, the PCA-SVM model not only reduces the redundant variables in the model, but also has higher accuracy. Using this model to identify the origin of Cornus officinalis, the accuracy rate is 84.8%.

Nucleic acid amplification test (NAAT) conducted in a microfluidic chip to differentiate between various ginseng species

Panax ginseng and Panax quinquefolius have different medicinal properties and market values; however, they can be difficult to distinguish from one another based on physical appearances alone. Therefore, a molecular test that can be performed in commercial settings is needed to overcome this difficulty. A locus that contains a single nucleotide polymorphism (SNP) site to differentiate between P. ginseng and P. quinquefolius has been selected. An isothermal nucleic acid amplification test (NAAT) has been developed for use in a microfluidic chip; this NAAT method, which is based on lesion-induced DNA amplification (LIDA), amplifies the extracted plant genomic samples and enhances the detection of specific SNPs. This NAAT method was used to authenticate five ginseng root samples which indicated that two of the five samples appear to be mislabeled. These authentication results were consistent with those obtained from next generation sequencing (NGS) although this molecular test is more affordable and faster than NGS.

Discrimination of Panax ginseng from counterfeits using single nucleotide polymorphism: A focused review

Discrimination of plant species, cultivars, and landraces is challenging because plants have high phenotypic and genotypic resemblance. Panax ginseng is commonly referred to as Korean ginseng, which contains saponins with high efficacy on cells, and has been reported to be worth billions in agroeconomic value. Korean ginseng's increasing global agroeconomic value includes additional species and cultivars that are not Korean ginseng but have physical characteristics close to it. This almost unidentifiable physical characteristic of Korean ginseng-like species is discriminated via molecular markers. Single nucleotide polymorphism (SNP), found across the plant species in abundance, is a valuable tool in the molecular mapping of genes and distinguishing a plant species from adulterants. Differentiating the composition of genes in species is quite evident, but the varieties and landraces have fewer differences in addition to single nucleotide mismatch. Especially in the exon region, there exist both favorable and adverse effects on species. With the aforementioned ideas in discriminating ginseng based on molecular markers, SNP has proven reliable and convenient, with advanced markers available. This article provides the simplest cost-effective guidelines for experiments in a traditional laboratory setting to get hands-on SNP marker analysis. Hence, the current review provides detailed up-to-date information about the discrimination of Panax ginseng exclusively based on SNP adding with a straightforward method explained which can be followed to perform the analysis.

The genetic authentication of Panax ginseng and Panax quinquefolius based on using single nucleotide polymorphism (SNP) conducted in a nucleic acid test chip

Panax ginseng and Panax quinquefolius, which are commonly called Chinese ginseng and American ginseng respectively, have different medicinal properties and market values; however, these samples can be difficult to differentiate from one another based on physical appearances of the samples especially when they are in powdery or granular forms. A molecular technique is thus needed to overcome this difficulty; this technique is based on the nucleic acid test (NAT) conducted on the microfluidic chip surface. Three single nucleotide polymorphism (SNP) sites (i.e. N1, N2, N3) on the Panax genome that differ between P. ginseng (G) and P. quinquefolius (Q) have been selected to design probes for the NAT. Primers were designed to amplify the antisense strands by asymmetric PCR. We have developed three different NAT methodologies involving surface immobilization and subsequent (stop flow or dynamic) hybridization of probes (i.e. N1G, N1Q, N2G, N2Q, N3Q) to the antisense strands. These NAT methods consist of two steps, namely immobilization and hybridization, and each method is distinguished by what is immobilized on the microfluidic chip surface in the first step (i.e. probe, target or capture strand). These three NATs developed are called probe-target method 1, target-probe method 2 and three-strand complex method 3. Out of the three methods, it was found that the capture strand-target-probe method 3 provided the best differentiation of the ginseng species, in which a 3' NH₂ capture strand is first immobilized and the antisense PCR strand is then bound, while N2G and N3Q probes are used for detection of P. ginseng (G) and P. quinquefolius (Q) respectively.

Bar-HRM: a reliable and fast method for species identification of ginseng (Panax ginseng, Panax notoginseng, Talinum paniculatum and Phytolacca Americana)

Background

Korean ginseng has long been famous and is one of the most well known forms of ginseng. The root of plants in the genus Panax is commonly recognized as ginseng. Different Panax species of ginseng root have been used as treatments. Although many other herbs are called ginseng, they do not contain the active compounds of ginsenosides. In Thailand, we have Thai ginseng which is of course not one of Panax species. Thai ginseng is the root from Talinum paniculatum and, due to its morphological root similarity, it is almost impossible to differentiate between them. Also, another plant species, Phytollacca americana, has significantly similar root morphology to real ginseng but its seeds and root are poisonous. Misunderstanding what true ginseng is compared to others could endanger lives and cause financial loss by buying inferior products.

Methods

DNA barcoding combination with High Resolution Melting (called Bar-HRM) was used for species discrimination of the Panax ginseng and others. Five regions included ITS2, matK, psbA-trnH and rbcL were evaluated in the analyses.

Results

The ITS2 region was found to be the most suitable primers for the analysis. The melting profile from the HRM analyses using the chosen ITS2 primers showed that Korean ginseng (Panax ginseng) could be discriminated from other Penax species. Also, other ginseng species with morphological similarity could be easily distinguished from the true ginseng. The developed Bar-HRM method poses a great potential in ginseng species discrimination and thus could be also useful in ginseng authentication.