• Korean Journal of Plant Resources
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• v.20 no.1
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• pp.79-85
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• 2007

The species in genus Saxifiraga distributed in circumpolar arctic are taxonomically difficult to study. RAPD analyses were performed to compare the genetic diversity of the 16 Saxifrages originated from the Norwegian Arctic Svalbard and Korea. The 12 accessions of URP primers were tested and 4 of which showed polymorphism were selected. Total 79 (44.8%) DNA bands were scored and analyzed by UPGMA cluster analysis. The results indicated that all of the 9 Saxifraga species from Svalbard showed high genetic diversity than those from Korea. The Similarity matrix and cluster analyses indicated that the Saxifraga species from Svalbard and Korea can be divided into two different subgroups. RAPDs of the Saxifraga species of Korea showed higher homologous patterns than those of Arctic Saxifrage. Among the Saxifraga species, we found that the morphological similarity reflects the genetic similarity. The geographic distance, clonal reproduction, and environmental condition may contribute the high level of genetic diversity between Saxifraga species from the two isolated regions.

• Horticultural Science & Technology
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• v.32 no.4
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• pp.525-534
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• 2014

Microsatellite markers were used to identify 58 major commercial melon cultivars, and to assess hybrid seed purity of a melon breeding line known as '10H08'. A set of 412 microsatellite primer pairs were utilized for fingerprinting of the melon cultivars. Twenty-nine markers showed hyper-variability and could discriminate all cultivars on the basis of marker genotypes, representing the genetic variation within varietal groups. Cluster analysis based on Jaccard's distance coefficients using the UPGMA algorithm categorized 2 major groups, which were in accordance to morphological traits. The DNA bulks of female and male parents of breeding line '10H08' were tested with 29 primer pairs based on microsatellites to investigate purity testing of $F_1$ hybrid seeds, and 5 primer pairs exhibited polymorphism. One microsatellite primer pair (CMGAN12) produced unambiguous polymorphic bands among the parents. Among 192 seeds tested with CMGAN12, progeny possibly generated by self-pollination of the female parent were clearly distinguished from the hybrid progeny. These markers will be useful for fingerprinting melon cultivars and can help private seed companies to improve melon seed purity.

• Parasites, Hosts and Diseases
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• v.35 no.2
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• pp.119-126
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• 1997

Acanthnmoebn sp. YM-4 is simitar to A. culbertsoni based upon morphological characteristics of trophozoites and cysts. However, based on other characteristics, pathogenicity to mice, in uitro cytotoxicity and isoenzyme patterns, Acanthomoebo sp. YM- 4 was quite different from A. culbertsoni. Restriction fragment length polymorphism (RFLP) analysis of mtDNA is useful in the classification of members belonging to the genus Acanthcmoebn. Therefore, in this study, RFLP analysis of Acnnthcmoeba mtDNAs was accomplished using five restriction enzymes: Hnelll, Hinull, Clcl, Pudl and ScE. Each restriction enzyme produced approximately 3-15 fragments (range: from 0:6 kip to 34.4 kbp) . The mtDNA genome size, calculated by the summation of restriction fragments, averaged 46.4 kbp in Acnnthamoeba sp. YM-4,48.3 kbp in A. culbertsoni and 48.8 kbp in A. polyphaic, respectively. Digested mtDNA fragments of Accnthcmoeba sp. YM-4 contained nine and seven same size fragments, respectively, from a total of 67 and 69 fragments observed in A. culbertsoni and A. polyphcgn. An estimate of the genetic divergence was 10.1% between Acanthamoebc sp. YM-4 and A. culbertsoni, and 9.9% between Acanthamoebn sp. YM-4 and A. polyphcga.

• The Korea Journal of Herbology
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• v.30 no.3
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• pp.41-47
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• 2015

Objectives : Due to the morphological similarity of the pericarp and description of multi-species in National Pharmacopoeia of Korea and China, the Zanthoxylum Pericarpium is difficult to authenticate adulterant in species levels. Therefore, we introduced the sequence analysis of DNA barcode and identification of single nucleotide polymorphism(SNP) to establish a reliable tool for the distinction of Zanthoxylum Pericarpium from its adulterants. Methods : To analyze DNA barcode region, genomic DNA was extracted from twenty-four specimens of authentic Zanthoxylum species and inauthentic adulterant and the individual internal transcribed spacer regions (rDNA-ITS and ITS2) of nuclear ribosomal RNA gene were amplified using ITS1, ITS2-S2F, and ITS4 primer. For identification of species-specific sequences, a comparative analysis was performed using entire DNA barcode sequences. Results : In comparison of four Zanthoxylum ITS2 sequences, we identified 16, 4, 6, and 4 distinct species-specific nucleotides enough to distinguish Z. schinifolium, Z. bungeanum, Z. piperitum, and Z. simulans, respectively. The sequence differences were available genetic marker to discriminate four species. Futhermore, phylogenetic relationship revealed a clear classification between different Zanthoxylum species showing 4 different clusters. These results indicated that comparative analysis of ITS2 DNA barcode was an useful genetic marker to authenticate Zanthoxylum Pericarpium in species levels. Conclusions : The marker nucleotides, enough to distinguish Z. schinifolium, Z. piperitum, Z. bungeanum, and Z. simulans, were obtained at 30 SNP marker nucleotides from ITS2 sequences. These differences could be used to authenticate official Zanthoxylum Pericarpium from its adulterants as well as discriminating each four species.

• Horticultural Science & Technology
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• v.32 no.6
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• pp.853-863
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• 2014

This study was carried out to construct a DNA profile database of 100 strawberry cultivars using microsatellite markers. Two hundred seventy four microsatellite primer pairs were screened with a set of 21 strawberry cultivars with different morphological traits. Twenty five primer pairs were selected because they produced reliable and reproducible fingerprints. These primer pairs were used to develop DNA profiles of 100 strawberry cultivars. Three to thirteen alleles were detected by each marker with an average of 7.50. The average polymorphism information content varied from 0.331 to 841 (average 0.706). Cluster analysis showed that the 100 cultivars were divided into 7 major groups reflecting geographic origin and pedigree information. Moreover, most of the cultivars could be discriminated by marker genotypes. These markers will be useful as a tool for the protection of plant breeders' intellectual property rights in addition to providing the means to intervene seed disputes relating to variety authentication.

• Horticultural Science & Technology
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• v.35 no.1
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• pp.98-107
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• 2017

A DNA profile database was constructed to investigate the genetic relatedness of 72 germplasm samples of Pyrus and related cultivars using microsatellite markers. Three P. pyrifolia, four P. commus, and one P. betulifolia cultivars with different morphological traits were screened using 387 pairs of microsatellite primers. A core set of 11 primer pairs was selected to obtain 133 polymorphic amplified fragments meeting three criteria: high polymorphism information contents (PIC), high repeatability, and distinct allele patterns. The number of alleles per locus ranged between 4 and 22. Average PIC was 0.743 (range: 0.557 - 0.879). Cluster analysis using the unweighted pair - group method with arithmetical average (UPGMA) separated the 72 pear cultivars and germplasm samples into four major groups: Chinese, European pears, and a cluster of 55 Asian pears that could be reclassify into two subcluster, I - $1^{st}$ and II - $2^{nd}$, according to pedigree information. Almost all of the cultivars were discriminated by 11 microsatellite marker genotypes. The microsatellite DNA profile database may be utilized as tool to verify distinctness, uniformity, and stability between candidate cultivar, and to verify in the distinctness of existing cultivars.

• 한국균학회소식:학술대회논문집
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• 2015.11a
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• pp.41-41
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• 2015

Oomycetes belong to the kingdom Straminipila, a remarkably diverse group which includes brown algae and planktonic diatoms, although they have previously been classified under the kingdom Fungi. These organisms have evolved both saprophytic and pathogenic lifestyles, and more than 60% of the known species are pathogens on plants, the majority of which are classified into the order Peronosporales (includes downy mildews, Phytophthora, and Pythium). Recent phylogenetic investigations based on DNA sequences have revealed that the diversity of oomycetes has been largely underestimated. Although morphology is the most valuable criterion for their identification and diversity, morphological species identification is time-consuming and in some groups very difficult, especially for non-taxonomists. DNA barcoding is a fast and reliable tool for identification of species, enabling us to unravel the diversity and distribution of oomycetes. Accurate species determination of plant pathogens is a prerequisite for their control and quarantine, and further for assessing their potential threat to crops. The mitochondrial cox2 gene has been widely used for identification, taxonomy and phylogeny of various oomycete groups. However, recently the cox1 gene was proposed as a DNA barcode marker instead, together with ITS rDNA. To determine which out of cox1 or cox2 is best suited as universal oomycete barcode, we compared these two genes in terms of (1) PCR efficiency for 31 representative genera, as well as for historic herbarium specimens, and (2) in terms of sequence polymorphism, intra- and interspecific divergence. The primer sets for cox2 successfully amplified all oomycete genera tested, while cox1 failed to amplify three genera. In addition, cox2 exhibited higher PCR efficiency for historic herbarium specimens, providing easier access to barcoding type material. In addition, cox2 yielded higher species identification success, with higher interspecific and lower intraspecific divergences than cox1. Therefore, cox2 is suggested as a partner DNA barcode along with ITS rDNA instead of cox1. Including the two barcoding markers, ITS rDNA and cox2 mtDNA, the multi-locus phylogenetic analyses were performed to resolve two complex clades, Bremia lactucae (lettuce downy mildew) and Peronospora effuse (spinach downy mildew) at the species level and to infer evolutionary relationships within them. The approaches discriminated all currently accepted species and revealed several previously unrecognized lineages, which are specific to a host genus or species. The sequence polymorphisms were useful to develop a real-time quantitative PCR (qPCR) assay for detection of airborne inoculum of B. lactucae and P. effusa. Specificity tests revealed that the qPCR assay is specific for detection of each species. This assay is sensitive, enabling detection of very low levels of inoculum that may be present in the field. Early detection of the pathogen, coupled with knowledge of other factors that favor downy mildew outbreaks, may enable disease forecasting for judicious timing of fungicide applications.

• Korean Journal of Plant Taxonomy
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• v.41 no.2
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• pp.119-129
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• 2011

Phylogenetic studies were conducted to evaluate the taxonomic relationships among 27 taxa, including 2 outgroups of Korean Campanulaceae, using PCR-RFLP analysis and ITS sequences. In the PCR-RFLP analysis, 15 restriction endonucleases produced 244 restriction sites and size variations from the chloroplast DNA, and 59 restriction sites (24%) showed polymorphism. The length of the ITS regions ranged from 588 bp to 797 bp. The sequence divergence including the outgroups is 0-39.36%. Phylogenetic analyses based on PCR-RFLP and ITS data suggest that Campanulaceae is monophyletic; Codonopsis and Platycodon forms an independent clade; the Peracarpa and Asyneuma clade is a sister to the Adenophora-Hanabusaya clade; Campanula is monophyletic; and Wahlenbergia basally branches within the ITS tree, whereas they are placed between Campanula and the Codonopsis-Platycodon clade in the PCR-RFLP tree; Hanabusaya is placed within the Adenophora clade; and Adenophora is paraphyletic and shows discordance to the infrageneric classifications based on morphological data. The present results show two data sets, largely congruent at the generic level, but their phylogenetic positions, in particular the Wahlenbergia and Hanabusaya and the infrageneric classifications in Adenophora, show some incongruence.

• Korean journal of applied entomology
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• v.46 no.2
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• pp.175-182
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• 2007

Two fruit moths of the oriental fruit moth, Grapholita molesta (Busck), and the peach fruit moth, Carposina sasakii (Matsumura), infest apples in Korea by internally feeding behavior. C. sasakii is a quarantine insect pest from some other countries importing Korean apples. G. molesta is not a quarantine insect pest, but can be incorrectly identified as C. sasakii especially when it is found inside apple fruits at its larval stages because it is not easy to identify the two species by morphological characters alone. This incomplete identification results in massive economical loss by fruits needlessly destroyed or turned away at border inspection stations of the importing nations. This difficulty can be overcome by molecular DNA markers. Several polymorphic regions of mitochondrial DNA of both species were sequenced and used for developing specific striction sites and polymerase chain reaction (PCR) primers. Based on these sequences, three diagnostic PCR-restriction fragment length polymorphism (RFLP) sites were detected and validated for their practical uses. Also, species-specific PCR primers were devised to develop diagnostic PCR method for identifying the internal feeders.

• Applied Biological Chemistry
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• v.47 no.2
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• pp.182-186
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• 2004

Morphological observation of roots and molecular technique were used to investigate the symbiotic relationships between arbuscular mycorrhizal (AM) fungi and ginseng roots. Korean ginseng, Panax ginseng, was collected from 8 sites in Korea. Colonization pattern of AM fungi in ginseng roots was determined as an Arum type under light microscopes. Nested PCR using AM fungal specific primers was employed to amplify a partial region on 18s rDNA of AM fungi from the root extracted mixed DNA. The amplified DNA was cloned and analyzed by random fragment length polymorphism (RFLP) with restriction enzymes, AluI, HinfI and AsuC21. One from each RFLP pattern was selected for sequencing. A total 16 clones were sequenced and identified as 2 species of AM fungi; Paraglomus brasilianum and Glomus spurcum. Paramglomus brasilianum was found from most of the ginseng roots, in this syudy suggesting that this species of AM fungi could have specific relationship with the ginseng root. Possible roles of AM fungal species in ginseng roots are discussed.