• Journal of Animal Science and Technology
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• v.46 no.6
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• pp.917-924
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• 2004

Using PCR-RFLP haplotyping for the mitochondrial DNA(mtDNA) fragment containing the NADH dehydrogenase 2 gene(ND2) and three tRNA genes(tRNA-Met, tRNA-Trp and tRNA-Ala), we characterized the genetic diversity of five pig breeds including Jeju native pigs. mtDNA polymorphisms showing distinct cleavage patterns were found in the pig breeds. Two digestion patterns were detected when HaeIII- and Hinfl-RFLP, and four in the Tsp5091-RFLP analyses. Combining the three restriction enzyme digestion patterns found in five different pig breeds, four mtDNA haplotypes were observed and the haplotype frequencies were significantly different by the pig breeds. A monomorphic haplotype, mtWB, was observed in both Korean wild boars and Large White pigs. Both Duroc and Landrace pigs contained two haplotypes suggesting their multiple maternal lineages. Jeju native pig has two haplotypes(mtJN and mtJD). Of these, mtJN is identified as a Jeju native pig specific haplotype. This study suggested that more than two progenitor populations have been taken part in the domestication process of the Jeju native pig population, and/or probably subsequent crossing with other pig breeds from near east Asia. Unlike with our prediction, there was no direct evidence under molecular levels on the maternal introgression of Korean wild boar in the domestication of Jeju native pigs. In conclusion, specificity of mtDNA haplotypes related to pig breeds win be useful for identifying the maternal lineage as wen as constructing the genealogical pedigree in pigs.

• Research in Plant Disease
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• v.23 no.3
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• pp.241-248
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• 2017

The purpose of this study was to develop rapid methods for distinguishing between Heterodera schachtii and H. glycines detected from chinese cabbage fields of highland in Gangwon, Korea. To do this, we performed PCR-RFLP and PCR with the primers set developed in this study for GC147, GC408 and PM001 population, H. schachtii, and YS224, DA142 and BC115 population, H. glycines. Eight restriction enzymes generated RFLP profiles of mtDNA COI region for populations of H. schachtii and H. glycines, repectively. As a result, treatment of two restriction enzymes, RsaI and HinfI, were allowed to distinguish H. schachtii from H. glycines based on the differences of DNA band patterns. The primer set, #JBS1, #JBG1 and #JB3R, amplified specific fragments with 277 and 339 bp of H. schachtii, 339 bp of H. glycines, respectively, while it did not amplify fragments from three root-knot nematodes and two root-lesion nematodes. Thus, the primer set developed in this study could be a good method, which is used to distinguish between H. schachtii and H. glycines.

• Clinical and Experimental Reproductive Medicine
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• v.28 no.2
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• pp.141-145
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• 2001

Objective: We inversigated Small Heterodimer Partner (SHP) gene mutation in Korean Polycystic Ovarian Syndrome (PCOS) patients. SHP protein regulates the activity of nuclear receptors which regulate the cellular development and differentiation. Recently, the mutation of SHP gene was found in the obesity and diabetes patients in Japanese group, and suggested that its mutation may involved in pathogenic mechanism of PCOS. Methods: This study was performed in 20 PCOS patients and 20 normal women. The DNAs were extracted from the peripheral bloods, and amplified at each exon (1 and 2) of SHP gene by PCR method. Subsequently, each PCR product was digested with the restriction enzyme indicated below for studying restriction fragment length polymorphism (RFLP). After enzyme digestion, the results of RFLP were compared PCOS patients with control women to find any sequence variation. Results: We examined 9 regions of exon 1 with Msp I, Pvu II, Dde I and 3 regions of exon 2 with Pst I, Dde I. There is no heterozygous or homozygous mutation in patients and control women at these restriction sites. Conclusion: The genetic analysis at our restriction sites in the SHP gene did not show any genetic variation in Korean PCOS patients. Our PCR-RFLP analysis was not covered the entire SHP gene (68 bp/1,006 bp), we need to further analysis of the entire SHP gene.

• Research in Plant Disease
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• v.17 no.2
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• pp.211-215
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• 2011

Cucumber mosaic virus (CMV)-like isolate was collected from Raphanus sativus (cv. Choon-hyang), which showed mosaic symptoms. The isolate was confirmed to a strain of CMV by host responses in Vigna unguiculata, Chenopodium amaranticolor and Gomphrena globosa, by viral genome composition with RT-PCR and PCR-RFLP, and by serological analysis. Symptom developed by the strain of CMV was severe in Nicotiana benthamiana, N. glutinosa, N. tabacum (cv. Samsun, cv. Xanthi), Cucumis melo (cv. Early hanover), Cucumis sativus (cv. White wonder), Capsicum annuum (cv. Chung-yang and cv. Geum-top), but mild symptom was developed in Raphanus sativus (cv. Choon-hyang), Brassica rapa ssp. pekinensis (cv. Bul-Am No. 3), and B. juncea (cv. Daenong Jukgot). Newly isolated strain of CMV could infect diverse crops including Solanaceae, Cucurbitaceae and Brassicaceae. We designated the new strain of CMV as Gn-CMV based on the novel infectivity of Brassicaceae. In double-stranded (ds) RNA analysis, Gn-CMV consisted of 3.3, 3.0, and 2.2 kb genomes likewise other strains of CMV. SDS-polyacrylamide gel electrophoresis (SDS-PAGE) showed 28 kDa of the CMV coat protein. By restriction enzyme mapping using Cac8I, ClaI and MspI of RT-PCR products indicated that Gn-CMV belongs to CMV subgroup I.

• Korean Journal of Microbiology
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• v.37 no.1
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• pp.72-79
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• 2001

The effect of phenol on the change of bacterial community in the effluent water from a wastewater treatment plant was analyzed by PCR and terminal restriction fragment length polymorphism (T-RFLP). The fragments of 16S rDNA were amplified by PCR with bacterial primers, where one of the primers was biotinylated at the 5'-end. After digestion with restriction enzymes, HaeIII and AluI, the biotinylated terminal restriction tragments (T-RFs) of the digested products were selectively isolated by using streptavidin paramagnetic particles. The single-stranded DNA of T-RFs was separated by electrophoresis on a polyacrylamide gel and detected by silver staining technique. When 10 standard strains were analyzed by our method, each strain had a unique T-RF which corresponded to the calculated size from the known sequences of RDP database. The T-RFLP fingerprint generated from the effluent water was very complex, and the predominant T-RFs corresponded to members of the genus Acinetobacter, Bacillus and Pseudomonas. In addition, the perturbation of bacterial community was observed when phenol was added to the sample at the final concentration of 250 $l^{-1}$. The number of T-RFs increased and the major bacterial population could be assigned to the genus Acinetobacter, Comamonas, Cytophaga and Pseudomonas. A intense band assigned to the putative genera of Acinetobacter and Cytophaga was eluted, amplified, and sequenced. The nucleotide sequence of the T-RF showed close relationship with the sequence of Acinetobacter junii.

• Korean Journal of Microbiology
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• v.40 no.3
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• pp.244-247
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• 2004

To investigate the effects of elevated $CO_2$ on the denitrifying bacterial community structure in a wetland soil, dynamics of bacterial community structure was explored in an artificial wetland ecosystem with one of three plant species (T. latifolia, S. lacustris, and 1. effusus) under two levels of $CO_2$(370 ppm or 740 ppm) after 110day incubation. For the analysis of bacterial community structure, functional genes such as nitrite reductase genes (nirS) were PCR-amplified followed by cloning of PCR products and screening by restriction fragment length polymorphism (RFLP). nirS gene fragments were amplified in all analyzed soil samples. Species richness estimated by the number of distinct phylotypes were 83 and 95 in the ambient $CO_2$ treatment and the elevated treatment, respectively. Two phylotypes (type 1 and type 2) were dominant in both of the treatments. Elevated $CO_2$ treatment increased species richness of denitrifying as well as changed a large proportion of denitrifier phylotypes compared to those of the ambient treatment. Overall, the data in this study suggested that the denitrifying communities in the wetland soil are diverse and that the richness of denitrifying bacterial community might be affected by elevated $CO_2$ treatment.

• Journal of Life Science
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• v.17 no.11
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• pp.1505-1510
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• 2007

We found 8 single nucleotide polymorphisms (SNPs) in adipocyte fatty acid bonding protein (FABP4) gene as candidate gene of FAT1 locus on pig chromosome 4. With over 800 heads of major commercial pig breeds including Duroc, Landrace, Berkshire and Yorkshire, we analyzed SNPs of FABP4 gene to determine possible effects of FABP4 genotype to economically important traits. $400{\sim}800\;bp$ amplicons in FABP4 gene were used PCR-RFLP for each SNPs and we found that the frequency of some SNPs of this gene was different among the breeds. According to the statistical analyses to determine possible associations of each genotype with economic traits, it was found that subgroup with different genotypes showed significant differences in daily gain, backfat thickness, lean percentage and feed conversion ratio (P<0.05). Thus, as a Part of enhancing the selection competence related to swine growth rate and lean percentage, it is expected that FABP4 gene markers verified in this study will be useful to use for Korean commercial pig industry.

• Reproductive and Developmental Biology
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• v.28 no.1
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• pp.37-43
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• 2004

This study was carried out to investigate PSS (Porcine Stress Syndrome) with the PSE (Pale, Soft, Exudative) in 319 different pigs(Yorkshire 150; Landrace 89 and Duroc 80). The PCR-RFLP method was adapted to detect the ryanodine receptor (RYR 1) gene mutation and to estimate the genotype frequency of the RYR1 gene in breeding pig population. The DNA samples were collected from hair follicles of pigs of Yorkshire, Landrace and Duroc. After DNA amplification by PCR, the PCR products were digested by restriction enzyme, Cfo I. Primary PCR products of ryanodine receptor gene were length of 659 bp in hair follicle and their second PCR products were length of 522 bp in hair follicle. The exon region (522 bp) including point mutation ($C \arrow T; Arg \arrow Cys$) in the porcine ryanodine receptor gene, which is a causal mutation for PSS, was digested with Cfo I restriction enzyme. The RYR1 gene was classifed into three genotypes by agarose gel electrophoresis. The normal homozygous (NN) individuals showed two DNA fragments consisted of 439 and 83 bp. The mutant homozygous (nn) individuals showed only one DNA fragment 522 bp. In addition, all three fragments (522, 439 and 83 bp) were showed in heterozygous (Nn) carrier animals. The normal homozygous (NN), heterozygous (Nn) and mutant homozygous (nn) were 98.00, 2.00 and 0.00% in Yorkshire pigs, 87.64, 11.24 and 1.12% in Landrace, 100.00, 0.00 and 0.00% in Duroc, respectively. The gene frequencies of N and n were 0.990 and 0.010 in Yorkshire pigs, 0.933 and 0.067 in Landrace, 1.000 and 0.000 in Duroc, respectively.

• Korean Journal of Microbiology
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• v.42 no.2
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• pp.103-110
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• 2006

T-RFLP analysis and clone sequencing analysis based on bacterial 16S rDNA were conducted to assess bacterial community structure and diversity in Zoysia japonica soil treated with liquid fertilizer containing amino acids(LFcAA) after spray with herbicide. The results of T-RFLP (terminal restriction fragment length poly-morphism) analysis using restriction enzyme Hae III showed that the T-RFs of various size appeared evenly in the 32 clones of KD3 and 38 clones of KD4 respectively that had been treated with liquid fertilizer containing amino acid(LFcAA) compared to 23 clones of KD2 hat had not been treated with LFcAA. The microbial com- munity structure in KD2 appeared less diverse than those in KD3 and KD4. Analysis of partial sequences for 110 clones from KDI (control), KD2 (non-treated), KD3 (LFcAA 1X), KD4 (LFcAA 2X), respectively, revealed that most bacteria were related with uncultured bacteria in a 16S rDNA sequence similarity range of 91-99% through blast search. Otherwise, the other clones were members of proteobacteria, Acidobacteria, Act-inobacteria, Sphingobacteria and Planctomyces groups. Especially in KD4, members of Alpha Proteobacteria, Rhizobiales, Sphigomonadales, Caulobacterales, Gamma Proteobacteria, the genus Pseudomonas, Betapro-teobacteria, Nitrosomonadales and genus Nitrosospira appeared to be dominant. In addition, Acidobacteria group, Actinobacteria group, Planctomycetacia and Sphingobacteria were also shown. The microbial com-munity structure in Z. japonica soil sprayed with herbicide was affected by LFcAA.

• Korean Journal of Food Science and Technology
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• v.34 no.6
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• pp.1134-1139
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• 2002

Campylobacter, Arcobacter, and Helicobacter, classified into the same rRNA superfamily VI by taxonomy, cause food-borne diseases, stomach ulcer, and gastric cancer. To detect each strain selectively from contaminated foods, PCR, multiplex-PCR, and restricion fragment length polymorphism (RFLP) were applied on Campylobacter, Arcobacter, and Helicobacter. The same PCR products could be detected using CHA primer targeted for 16S rRNA of Campylobacter, Arcobacter, and Helicobacter. To detect C. jejuni and C. coli from A. butzleri and H. pylori, pg50/pg3 primer targeted for fla A gene was used, and for A. butzleri, Arco2/Butz primer targeted for 23S rRNA was utilized. For H. pylori detection, icd1/icd2 primer targeted for isocitrate dehydrogenase gene was employed, and JEJ1/JEJ2 primer targeted for ceuE gene was effective for C. jejuni detection from the three strains. C. jejuni, C. coli could be separated from A. butzleri and H. pylori through PCR-RFLP using restriction enzyme Dde I. Such primers would be effective for detecting each strain selectively through PCR when C. jejuni, C. coli, A butzleri and H. pylori are contaminated together.