• Korean Journal of Medicinal Crop Science
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• v.25 no.6
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• pp.411-417
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• 2017

Background: Adenophora triphylla var. japonica (Regel) H. Hara shows vegetative growth with radical leaves during the first year and shows reproductive growth with cauline leaves and bolting during the second year. In addition, the shape of the plant varies within the same species. For this reason, there are limitations to classifying the species by visual examination. However, there is not sufficient genetic information or molecular tools to analyze the genetic diversity of the plant. Methods and Results: Approximately 34.59 Gbp of raw data containing 342,487,502 reads was obtained from next generation sequencing (NGS) and these reads were assembled into 357,211 scaffolds. A total of 84,106 simple sequence repeat (SSR) regions were identified and 14,133 primer sets were designed. From the designed primer sets, 95 were randomly selected and were applied to the genomic DNA which was extracted from five plants and pooled. Thirty-nine primer sets showing more than two bands were finally selected as SSR markers, and were used for the genetic relationship analysis. Conclusions: The 39 novel SSR markers developed in this study could be used for the genetic diversity analysis, variety identification, new variety development and molecular breeding of A. triphylla.

• Journal of Microbiology and Biotechnology
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• v.19 no.5
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• pp.491-494
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• 2009

Within the secondary metabolite class of flavonoids, which consist of more than 10,000 known structures, flavones define one of the largest subgroups. The diverse function of flavones in plants as well as their various roles in the interaction with other organisms offers many potential applications including in human nutrition and pharmacology. We used two genes, flavone synthase (PFNS-l) that converts naringenin into apigenin and flavone 7-O-methyltransferase (POMT-7) that converts apigenin into 7-O-methyl apigenin, to synthesize 7-O-methyl apigenenin from naringenin. The PFNS-l gene was subcloned into the E. coli expression vector pGEX and POMT-7 was subcloned into the pRSF vector. Since both constructs contain different replication origins and selection markers, they were cotransformed into E. coli. Using E. coli transformants harboring both PFNS-l and POMT-7, naringenin could be converted into 7-O-methyl apigenin, genkwanin.

• Genomics & Informatics
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• v.12 no.1
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• pp.42-47
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• 2014

Asian populations contain a variety of ethnic groups that have ethnically specific genetic differences. Ethnic variants may be highly relevant in disease and human differentiation studies. Here, we identified ethnically specific variants and then investigated their distribution across Asian ethnic groups. We obtained 58,960 Pan-Asian single nucleotide polymorphisms of 1,953 individuals from 72 ethnic groups of 11 Asian countries. We selected 9,306 ethnic variant single nucleotide polymorphisms (ESNPs) and 5,167 ethnic variant copy number polymorphisms (ECNPs) using the nearest shrunken centroid method. We analyzed ESNPs and ECNPs in 3 hierarchical levels: superpopulation, subpopulation, and ethnic population. We also identified ESNP- and ECNP-related genes and their features. This study represents the first attempt to identify Asian ESNP and ECNP markers, which can be used to identify genetic differences and predict disease susceptibility and drug effectiveness in Asian ethnic populations.

• Journal of Physiology & Pathology in Korean Medicine
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• v.34 no.5
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• pp.245-254
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• 2020

The purpose of this study was to investigate the effects of natural herb mixture containing Laminaria japonica Areschoung (LAM) on fine dust-induced bronchitis in mice. Laminaria japonica Areschoung is main content of LAM, which is including fucoidan. Fucoidan extracted from phaophyta is known to prevent bronchitis and to defend against bacteria and virus infection. In this study, we experienced the effect of LAM on bronchitis and investigated gene expressions (e.g ; IL-8, COX-2, MCP-1) and bio-markers (e.g ; IL-8, PGE2, MUC5AC) associated with bronchitis by using A549 cells. Also, we investigated whether LAM can suppress the bronchitis in fine dust-induced animal models. We injected fine dust (50 ㎕) twice as INT (Intra-Nasal-Trachea) method. Then LAM (200 mg/kg and 400 mg/kg) were oral administered for 14 days. We analyzed the number of immune cells, immunoglobulin E, bio-markers level associated with bronchitis. LAM significantly decreased bio-marker (IL-1β, IL-6, IL-8, TNF-α, Histamine, PGE2), immune cells (white blood cell, neutrophil, lymphocyte, monocyte), and immunoglobulin E, that are increased by fine dust. Taken together, this study suggest that LAM can be used as effective herbal extract for bronchitis.

• Journal of Plant Biotechnology
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• v.43 no.2
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• pp.181-188
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• 2016

In this study, we developed 15 novel polymorphic simple sequence repeat (SSR) markers by SSR-enriched genomic library construction from Codonopsis lanceolata. We obtained a total of 226 non-redundant contig sequences from the assembly process and designed primer sets. These markers were applied to 53 accessions representing the cultivated C. lanceolata in South Korea. Fifteen markers were sufficiently polymorphic, and were used to analyze the genetic relationships between the cultivated C. lanceolata. One hundred three alleles of the 15 SSR markers ranged from 3 to 19 alleles at each locus, with an average of 6.87. By cluster analysis, we detected clear genetic differences in most of the accessions, with genetic distance varying from 0.73 to 0.93. Phylogenic analysis indicated that the accessions that were collected from the same area were distributed evenly in the phylogenetic tree. These results indicate that there is no correlative genetic relationship between geographic areas. These markers will be useful in differentiating C. lanceolata genetic resources and in selecting suitable lines for a systemic breeding program.

• The Korean Journal of Mycology
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• v.49 no.1
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• pp.33-44
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• 2021

Lentinula edodes (Berk.) Pegler, the most produced mushroom in the world, is an edible mushroom with very high nutritional and pharmacological value. Currently, interest in the protection of genetic resources is increasing worldwide, and securing the distinction between new cultivars is very important. Therefore, the development of efficient molecular markers that can discriminate between L. edodes cultivars is required. In this study, we developed cleaved amplified polymorphic sequence (CAPS) markers for the identification of L. edodes cultivars (Sanbaekhyang and Sulbaekhyang). These markers were developed from whole genome sequencing data from L. edodes monokaryon strain B17 and resequencing data from 40 cultivars. A nucleotide deletion existed in scaffold 19 POS 214449 in Sanbaekhyang (GT→G), and a single nucleotide polymorphism changed in scaffold 7 POS 215801 in Sulbaekhyang (G→A). The restriction enzymes Hha I and HpyCH4IV distinguished Sanbaekhyang and Sulbaekhyang, respectively, from other cultivars. Thus, we developed two CAPS markers for the identification of the L. edodes cultivars Sanbaekhyang and Sulbaekhyang.

• Journal of Life Science
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• v.33 no.11
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• pp.897-904
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• 2023

This study was done to develope genetic markers with the unique characteristics of genes according to the genomic information of Bacillus velezensis K10. B. velezensis K10 maintained a total of 4,159,835 bps, which was found to encode 5,136 open reading frames (orfs). B. velezensis K10 was found to have much more gene migration due to external factors overall compared to standard strain B. velezensis JS25R. In order to discover genetic selection markers, orfs on the genome to be easily induced to gene mutation were surveyed such as recombinase, integrase, transposase, and phage-related genes. As a result of the investigation, 9 candidate markers were isolated with high possibility as genetic selection markers. Although a part in the various origin's areas showed specificities in comparison with homology, the selected markers were all existed in phage-related areas because they were relatively lower homologies in phage-related genes. PCR analysis was done on B. licheniformis K12, B. velezensis K10, B. subtilis, and B. cereus to establish them as inter-species candidate selection markers. As a result, it was confirmed that B. velezensis K10-specific PCR products were formed in a total of 6 primer sets such as BV3 and BV5 to 9. On the other hand, analysis at the subspecies level observed the formation of B. velezensis K10-specific PCR products in 4 primer sets such as BV3, 5, 8, and 9. Among them, since BV5 and BV8 were detected by very specific results, we suggest that BV5 and 8 can be used as B. velezensis K10 gene selection markers at the species and sub-species level.

• Biomedical Science Letters
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• v.18 no.1
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• pp.1-9
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• 2012

Differentially expressed genes by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) were identified in order to evaluate them as dioxin-sensitive markers and crucial signaling molecules to understand dioxin-induced toxic mechanisms in human bronchial cells. Gene expression profiling was analyzed by cDNA microarray and ten genes were selected for further study. They were cytochrome P450, family 1, subfamily B, polypeptide 1 (CYP1B1), S100 calcium binding protein A8 (calgranulin A), S100 calcium binding protein A9 (calgranulin B), aldehyde dehydrogenase 1 family, member A3 (ALDH6) and peroxiredoxin 5 (PRDX5) in up-regulated group. Among them, CYP1B1 was used as a hallmark for dioxin and sharply increased by TCDD exposure. Down-regulated genes were IK cytokine, interferon-induced protein with tetratricopeptide repeats 1 (IFIT1), nuclease sensitive element binding protein 1 (NSEP1), protein tyrosine phosphatase type VI A, member 1 (PTP4A1), ras oncogene family 32 (RAB32). Although up-regulated 4 genes in microarray were coincided with northern hybridization, down-regulated 5 genes showed U-shaped expression pattern which is sharply decreased at lower doses and gradually increased at higher doses. These results introduce some of TCDD-responsive genes can be sensitive markers against TCDD exposure and used as signaling cues to understand toxicity initiated by TCDD inhalation in pulmonary tissues.

• Journal of Plant Biotechnology
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• v.35 no.4
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• pp.299-306
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• 2008

A modified method of Agrobacterium-mediated perilla transformation was developed using two selection markers of an antibiotics (either hpt or nptll) and an herbicidal (bar) gene. Perilla hypocotyl explants were cocultured with Agrobacterium tumefaciens EHA 105 strain harboring plasmid vector (either pMOG6-Bar or pCK-Bar) for three days, respectively. Primary shoots were selected with antibiotics of hygromycin (15 mg/L) or kanamycin (125 mg/L) and regenerated shoots were further selected with herbicide phosphinothricin (ppt,1.2 mg/L) to obtain authentic transformants. Roots were induced for the regenerated shoots on the MS medium without hormone and 80 putative transgenic plants were obtained. Transgene integration into perilla genome was confirmed by Southern blot and their expression was analyzed by Northern blot. T1 perilla seeds drived from To plants were tested 0.3% basta spray for identification of stable gene delivery to next generation.

• Korean Journal of Plant Resources
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• v.23 no.3
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• pp.214-222
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• 2010

Many research results have indicated that many kinds of useful ingredients are rich in buckwheat, which have high nutritional values and medicinal properties, so, buckwheat has been cultivated around Asia and Europe. In this paper, genetic diversity of common and tartary buckwheat germplasms were studied based on morphological and molecular markers in order to provide useful information for conservation and utilization of buckwheat genetic resources. The length, width, thick, value and weight of the seed of the common and tartary buckwheat were measured and analyzed by the statistics methods. The result has shown that there are morphological variation both in common buckwheat and tartary buckwheat seeds collected from different regions. It also has shown that the morphological variation of tartary seeds was significantly correlated to geographical regions. The nuclear ribosomal internal transcribed spacers (ITS) of the tartary buckwheat collected from different countries were cloned, sequenced and statistically analyzed. The data showed that ITS sequences were informative to analyze the phylogeny of the tartary buckwheat and the data also showed that the genetic distances varied among different tartary buckwheat seeds collected from different countries.