• Journal of Embryo Transfer
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• v.31 no.1
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• pp.61-64
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• 2016

We developed a polymerase chain reaction (PCR)-based molecular method for sexing and identification using sexual dimorphism between the Zinc Finger-X and -Y (ZFX-ZFY) gene and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) for mitochondrial DNA (mtDNA) cytochrome B (CYTB) gene in meat pieces and commercial sausages from animals of different origins. Sexual dimorphism based on the presence or absence of SINE-like sequence between ZFX and ZFY genes showed distinguishable band patterns between male and female DNA samples and were easily detected by PCR analyses. Male DNA had two PCR products appearing as distinct two bands (ZFX and ZFY), and female DNA had a single band (ZFX). Molecular identification was carried out using PCR-RFLP of CYTB gene, and showed clear species classification results. The results yielded identical information on the sexes and the species of the meat samples collected from providers without any records. The analyses for DNA isolated from commercial sausage showed that pig was the major source but several sausages originated from chicken and Atlantic cod. Applying this PCR-based molecular method was useful and yielded clear sex information and identified the species of various tissue samples originating from livestock.

• The Plant Pathology Journal
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• v.23 no.1
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• pp.13-21
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• 2007

Sweet potato feathery mottle virus(SPFMV) is one of the most prevalent viruses infecting sweet potatoes and occurs widely in sweet potato cultivating areas in Korea. To assess their genetic variation, a total of 28 samples infected with SPFMV were subjected to restriction fragment length polymorphism(RFLP) analysis using DNAs amplified by RT-PCR with specific primer sets corresponding to the coat protein(CP) region of the virus. The similarity matrix by UPGMA procedure indicated that 28 samples infected with SPFMV were classified into three groups based on the number and size of DNA fragments by digestion of CP-encoding regions with 7 enzymes including SalI, AluI, EcoRI, HindIII, FokI, Sau3AI, and DraI bands. Four primer combinations out of 5 designed sets were able to differentiate SPFMV and sweet potato virus G infection, suggesting that these specific primers could be used to differentiate inter-groups of SPFMV. Sequence analysis of the CP genes of 17 SPFMV samples were 97-99% and 91-93% identical at the intra-group and inter-groups of SPFMV, respectively. The N-terminal region of the CP is highly variable and examination of the multiple alignments of amino acid sequences revealed two residues(residues 31 and 32) that were consistently different between SPFMV-O and SPFMV-RC.

• The Plant Pathology Journal
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• v.32 no.5
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• pp.431-440
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• 2016

In 2004, bacterial spot-causing xanthomonads (BSX) were reclassified into 4 species-Xanthomonas euvesicatoria, X. vesicatoria, X. perforans, and X. gardneri. Bacterial spot disease on pepper plant in Korea is known to be caused by both X. axonopodis pv. vesicatoria and X. vesicatoria. Here, we reidentified the pathogen causing bacterial spots on pepper plant based on the new classification. Accordingly, 72 pathogenic isolates were obtained from the lesions on pepper plants at 42 different locations. All isolates were negative for pectolytic activity. Five isolates were positive for amylolytic activity. All of the Korean pepper isolates had a 32 kDa-protein unique to X. euvesicatoria and had the same band pattern of the rpoB gene as that of X. euvesicatoria and X. perforans as indicated by PCR-restriction fragment length polymorphism analysis. A phylogenetic tree of 16S rDNA sequences showed that all of the Korean pepper plant isolates fit into the same group as did all the reference strains of X. euvesicatoria and X. perforans. A phylogenetic tree of the nucleotide sequences of 3 housekeeping genes-gapA, gyrB, and lepA showed that all of the Korean pepper plant isolates fit into the same group as did all of the references strains of X. euvesicatoria. Based on the phenotypic and genotypic characteristics, we identified the pathogen as X. euvesicatoria. Neither X. vesicatoria, the known pathogen of pepper bacterial spot, nor X. perforans, the known pathogen of tomato plant, was isolated. Thus, we suggest that the pathogen causing bacterial spot disease of pepper plants in Korea is X. euvesicatoria.

• Journal of Radiation Industry
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• v.5 no.4
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• pp.347-352
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• 2011

In order to identify the genetic relationship analysis by acute and chronic gamma irradiation, Arabidopsis (Arabidopsis thaliana L.) were irradiated with 200 Gy of gamma-rays using gamma-irradiator (3,000 Ci; Nordion, Canada) and gamma-phytotron (400 Ci; Nordion, Canada) for acute and chronic irradiation, respectively. Genetic relationship among two acute gamma-irradiated plants (A1 and A24) and three chronic gamma-irradiated plants (C1W, C2W, C3W) were analyzed using the amplified fragment length polymorphism (AFLP) technique compared with each non-irradiated plant. A total of 28 EcoRI and MseI primer combinations were used to screen 8 treatments by the ABI3130 capillary electrophoresis system. Amplified products by 28 primer sets showed 1,679 bands with an average of 51 bands per primer combination. Out of the total bands scored, 1,164 fragments were polymorphic bands, with different alleles existing among the treatments. The cluster analysis was performed using the UPGMA (Unweighted Pair Group Method using Arithmetic) in the computer program NTSYS-pc. In clustery analysis, acute gamma-irradiation showed higher genetic variation compared with chronic gamma-irradiation.

• Korean journal of applied entomology
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• v.57 no.4
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• pp.317-322
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• 2018

In Vollenhovia emeryi (Hymenoptera: Myrmicinae), the queen and the male are known to be clonally reproduced. Its colonies can be classified into the two morphs with the wing length of the queen caste. The morph with normal wings is called the long-winged and the other the short-winged that is brachypterous. Even though the two morphs are considered a species, investigation on the species status of the two morphs was suggested with natural separation in nature and the distinctive wing morphology. It has yet to be determined whether the clonally reproduced queen caste is haploid or diploid. Our data clearly show that the two morphs are the same species and the queen caste is diploid on the basis of the genome size data comparison.

• Korean Journal of Medicinal Crop Science
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• v.27 no.1
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• pp.17-23
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• 2019

Background: Cnidium officinale Makino and Ligusticum chuanxiong Hort. are important medicinal crops in Korea. However, there is insufficient information on the identification of thrips, which attack these plants. Until now, one species of thrips has been recorded as a main pest. Methods and Results: To identify the thrips emerging in C. officinale Makino and L. chuanxiong Hort., these plants were independently cultivated in two local areas. Thirty individuals of each plant species were selected randomly and surveyed for the presence of thrips. After confirming the existence of thrips, 100 thrips individuals were collected from each crop using the beating method. To identify thrips species, we performed PCR-restriction fragment length polymorphism (RFLP)-based analysis using ITS2 primer sets. Six thrips species were identified: western flower thrips (Frankliniella occidentalis), flower thrips (F. intonsa), onion thrips (Thrips tabaci), chrysanthemum thrips (T. nigropilosus), chilli thrips (Scirtothrips dorsalis), and grass thrips (Anaphothrips obscurus). The proportion of these species differed between the host plant species. Conclusions: Six thrips species were major pests of two medicinal crops. Integrated pest management is required to control these thrips species, and will enhance the yield and quality of C. officinale and L. chuanxiong.

• The Plant Pathology Journal
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• v.38 no.6
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• pp.629-636
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• 2022

Colletotrichum species is known as the major causal pathogen of red pepper anthracnose in Korea and various groups of fungicides are registered for the management of the disease. However, the consistent use of fungicides has resulted in the development of resistance in many red pepper-growing areas of Korea. Effective management of the occurrence of fungicide resistance depends on constant monitoring and early detection. Thus, in this study, various methods such as agar dilution method (ADM), gene sequencing, allele-specific polymerase chain reaction (PCR), and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) were applied for the detection of benzimidazole resistance among 24 isolates of Colletotrichum acutatum s. lat. and Colletotrichum gloeosporioides s. lat. The result of the ADM showed that C. gloeosporioides s. lat. was classified into sensitive and resistant isolates to benomyl while C. acutatum s. lat. was insensitive at ≥1 ㎍/ml of benomyl. The sequence analysis of the β-tubulin gene showed the presence of a single nucleotide mutation at the 198th amino acid position of five isolates (16CACY14, 16CAYY19, 15HN5, 15KJ1, and 16CAYY7) of C. gloeosporioides s. lat. Allele-specific PCR and PCR-RFLP were used to detect point mutation at 198th amino acid position and this was done within a day unlike ADM which usually takes more than one week and thus saving time and resources that are essential in the fungicide resistance management in the field. Therefore, the molecular techniques established in this study can warrant early detection of benzimidazole fungicide resistance for the adoption of management strategies that can prevent yield losses among farmers.

• The Korea Journal of Herbology
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• v.34 no.6
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• pp.91-97
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• 2019

Objective : To establish a reliable tool between for the distinction of original plants of Sanguisorbae Radix, we analyzed the complete chloroplast genome sequence of Sanguisorbae Radix and identified single nucleotide polymorphisms (SNPs). Materials and methods : The chloroplast genome sequence of Sanguisorba officinalis, Sanguisorba tenuifolia f. alba (Trautv. & Mey.) Kitam and Sanguisorba tenuifolia Fisch. ex Link obtained using next-generation sequencing technology were described and compared with those of other species to develop specific markers. Candidate genetic markers were identified to distinguish species from the chloroplast sequences of each species using Modified Phred Phrap Consed and CLC Genomics Workbench programs. Results : The structure of the chloroplast genome of each sample that had been assembled and verified was circular, and the length was about 155 kbp. Through comparative analysis of the chloroplast sequences, we found 220 nucleotides, 158 SNPs, and 62 Indel (insertion and/or deletion), to distinguish Sanguisorba officinalis, Sanguisorba tenuifolia f. alba (Trautv. & Mey.) Kitam and Sanguisorba tenuifolia Fisch. ex Link. Finally, 15 specific SNP genetic markers were selected for the verification at positions. Avaliable primers for the dried herb, which is used as medicine, were used to develop the PCR amplification product of Sanguisorbae Radix to assess the applicability of PCR analysis. Conclusion : In this study, we found that Fendel-qPCR analysis based on the chloroplast DNA sequences can be an efficient tool for discrimination of Sanguisorba officinalis, Sanguisorba tenuifolia f. alba (Trautv. & Mey.) Kitam and Sanguisorba tenuifolia Fisch. ex Link.

• Journal of Practical Agriculture & Fisheries Research
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• v.24 no.3
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• pp.5-14
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• 2022

Trichoderma is known as pathogen caused serious green mold disease on commercial production. T. pleuroti and T. pleuroticola were common species in various mushroom media. Many strains of T. pleuroti, known as aggressive species causing major economic losses in Korea, showed benomyl resistance. Accurate identification and detection of Trichoderma species associated with oyster mushrooms is very important for disease control. We developed species-specific primers for T. pleuroticola, T. pleuroti, T. harzianum, and T. atroviride based on species-specific fragments isolated from amplified fragment length polymorphism analysis. PCR products corresponding to the predicted fragment of 500bp, 230bp, 180bp, and 410bp were amplified from T. pleuroticola, T. pleuroti, T. harzianum, and T. atroviride, respectively. Multiplex PCR assay using species-specific primers quickly and accurately identified and detected T. pleuroti from mushroom media in which various species co-exist. Our results can be useful for the effective control of mushroom disease.

• Animal Bioscience
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• v.36 no.4
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• pp.671-678
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• 2023

Objective: Previous studies isolated the thermophilic ammonium-tolerant (TAT) bacterium Bacillus sp. TAT105 that grew in composting swine manure with the assimilation of ammonium nitrogen and reduced ammonia emissions during composting. Those studies also investigated the potential for applications of TAT105 to composting. It was observed that the concentration of TAT bacteria, phylogenetically close to TAT105, increased during composting. The objectives of this study were to identify the phylogenetic placement of these TAT bacteria and investigate their distribution in various composts. Methods: The phylogenetic placement of TAT105 was examined based on the sequence of 16S ribosomal RNA gene. The genomic DNA homology between TAT105 and the type strains of bacterial species that were phylogenetically close to TAT105 were examined by DNA-DNA hybridization. Moreover, the tolerances of these strains to NH₄Cl and NaCl were analyzed using a cultivation method. Concentrations of TAT bacteria in various composts were evaluated using an agar medium specific to TAT bacteria and polymerase chain reaction followed by restriction fragment length polymorphism analysis. Results: TAT105 was most closely related to Bacillus thermolactis and Bacillus kokeshiiformis. Many variants of these species have been detected in various environments, including composts. The type strains of these species displayed TAT characteristics that were similar to those of TAT105. Among the composts examined in this study, TAT bacteria were detected at high concentrations (10⁵ to 10⁹ colony forming units per gram of dry matter) in most of the composts made from cattle manure, swine manure, bark, and excess sludge. Conclusion: TAT bacteria comprised B. thermolactis, B. kokeshiiformis, and their phylogenetically close relatives. They were considered to be adaptable to composting of some certain materials, and a favorable target for searching for strains with some useful function that could be applied to composting of these materials.