• Journal of the Korean Data and Information Science Society
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• v.22 no.3
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• pp.515-521
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• 2011

There are increasing demands for the producing and breeding new domestic riding horses for the vitalizations of horse riding industry in Korea, according as 'Horse Industry Support Act' became. In this study, we were to develop the functional relation through the conformation comparison & body composition analysis. 76 heads of 5 breeds utilized for riding horses in Korea were used and their body measurements on 12 items were measured and cluster analysis was conducted to determine the correlation relation among them. The measurements were standardized that (height, croup height, pelvis length), and (hip width, width of pelvis) were highly correlated. In these results of the decision tree, we confirmed to classify the breed type determination by their body measurements (hip height, hip width, head length, croup height). This result can be used as basic data for the development of horse type determination (racing, riding, Riding for the Disabled, Working, or fattening) through the analysis of body composition, and be utilized as the basic data for the producing and breeding new domestic riding horses through the 3D Stereosocpic image system analyze.

• Korean Journal of Animal Reproduction
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• v.25 no.4
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• pp.359-369
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• 2001

Polymerase chain reaction (PCR) amplification of DNA as 30 different arbitrary primers and random amplified polymorphic DNAs (RAPD) analysis were performed on genomic DNA extracted from the blood of the marine rockfish (Sebastes schlegeli) from the Yellow Sea and the Southern Sea. The unique properties of the genomic DNA were used to investigate the features of the population dynamics and origins of the species. Out of 30 primers, seven generated 207 highly reproducible RAPD polymorphic products, producing approximately 2.7 polymorphic bands per primer. About 67.4% of total amplified products (307) were either polymorphic (207) to rockfish. The degree of similarity varied from 0.22 to 0.63 as calculated by bandsharing analysis. Also, the average level of bandsharing was 0.39$\pm$0.02 within the rockfish strains. The electrophoretic analysis of RAPD-PCR products showed the relatively high levels if variation between different individuals in rockfish from the Yellow Sea. However, the RAPD outlines obtained with DNA of different rockfish strains from the Yellow Sea and the Southern Sea in Korea were very similar. Also, a small number of polymorphic bands were identified. Even if further analyses or more rockfish populations are required, this result implies RAPD analysis reflects genetic differences between the geographical strains of the rockfish.

• Korean Journal of Poultry Science
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• v.40 no.2
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• pp.83-89
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• 2013

iNOS (Inducible nitric oxide synthase) and TLR-4 (Toll-like Receptor-4) play crucial roles in innate immunity of poultry. iNOS has been mapped to chicken chromosome 14 and implicated in a variety of chicken diseases. iNOS possesses potent antimicrobial activity, including the inhibition of microbes replication in vitro. TLR-4 is a pathogen associated molecular-pattern receptor for bacterial product, such as LPS (lipopolysaccharides) found in Gram negative bacteria, that triggers pro-inflammatory cytokine expression after engagement with ligands. In the previous studies, genetic analysis of iNOS and TLR-4 revealed the possible association of mutation in these genes with the intestinal microflora of cecum when infected with Salmonella spp. This study was aimed to augment previous findings, which show the association of iNOS (C14513T) and TLR-4 (G4409T) polymorphisms with economic traits in Korean Native Black (KNB), Rhode Island Red (RIR) and Cornish chickens. Investigation in the effect of SNPs on economic traits (layday, layw, layno, bw150, bw270, layw270) was conducted. iNOS (C14513T) had a significant effect on the average body weight at 270 days of age (p<0.05) in both KNB and RIR, whereas TLR-4 (G4409T) showed no significant correlation with all traits (p>0.05). The results obtained from using the candidate genes can be useful for the genetic improvement of body weight in both KNB and RIR breeds.

• Reproductive and Developmental Biology
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• v.29 no.1
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• pp.9-13
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• 2005

This study was performed to analyze the sequence variation in mtDNA D-loop and their effects on milk and milk fat production in Holstein cows. The analyzed sequences were compared with previously published sequences from other cattle breeds (GenBank J01394). PCR was performed to amplify a total of 964 bp between nucleotide 15758 and 383 within D-loop region of mtDNA using specific primers. Thirty five polymorphic sites by nucleotide substitution were found in mtDNA. The frequencies of positions at 106, 169, 16057, 16231 and 16255 nt with high levels of sequence polymorphism were 0.090, 0.555, 0.055, 0.090 and 0.050, respectively. The substitution effect at 169 nt was found significant on milk production, and substitution effect at 16118, 16139 and 16302 nt was highly significant (p<0.1) on milk fat production. Polymorphism of mtDNA sequence in D-loop region might be useful for the analysis of cytoplasmic genetic variation and associations with the other economically important traits and maternal lineage analysis in Holstein cows.

• Journal of Animal Science and Technology
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• v.46 no.5
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• pp.729-734
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• 2004

This study was performed to analyze the sequence variations of mtDNA D-loop and their effects on milk in Hanwoo(Korean cattle). The resulting sequences were compared with previously published sequences for other cattle breeds (GenBank JOI394). The Polymerase Chain Reaction was performed to amplify a total of 964 bp between nucleotide 15758 and 383 within D-loop region of mtDNA using specific primers. Twenty polymorphic sites by nucleotide substitution were found in mtDNA D-loop region of Hanwoo. The frequencies of positions at 8, 169, 16042, 16051, 16057, 16093, 16119, 16122, 16209, 16255 and 16302 nt with high levels of sequence polymorphism were 0.150, 0.950, 0.085, 0.138, 0.106, 0.085, 0.138, 0.212, 0.085, 0.148 and 0.180, respectively. The substitution effect at 16119(p<0.1) and 16185(p< 0.05) nt was found significant on milk production. Polymorphism of mtDNA sequence in D-Ioop region could be useful for the analysis of cytoplasmic genetic variation and associations with the other economically important traits and maternal lineage analysis in Hanwoo.

• Horticultural Science & Technology
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• v.33 no.5
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• pp.737-750
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• 2015

This study was carried out to construct a DNA profile database for 102 watermelon cultivars through the comparison of polymorphism level and genetic relatedness using genomic microsatellite (gMS) and expressed sequence tag (EST)-microsatellite (eMS) markers. Sixteen gMS and 10 eMS primers showed hyper-variability and were able to represent the genetic variation within 102 watermelon cultivars. With gMS markers, an average of 3.63 alleles per marker were detected with a polymorphism information content (PIC) value of 0.479, whereas with eMS markers, the average number of alleles per marker was 2.50 and the PIC value was 0.425, indicating that eMS detects a lower polymorphism level compared to gMS. Cluster analysis and Jaccard's genetic distance coefficients using the unweighted pair group method with arithmetic average (UPGMA) based on the gMS, eMS, and combined data sets showed that 102 commercial watermelon cultivars could be categorized into 6 to 8 major groups corresponding to phenotypic traits. Moreover, this method was sufficient to identify 78 out of 102 cultivars. Correlation analysis with Mantel tests for those clusters using 3 data sets showed high correlation ($r{\geq}0.80$). Therefore, the microsatellite markers used in this study may serve as a useful tool for germplasm evaluation, genetic purity assessment, and fingerprinting of watermelon cultivars.

• Journal of Microbiology and Biotechnology
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• v.27 no.11
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• pp.1983-1993
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• 2017

Salmonella enterica subsp. enterica serovar Typhimurium, one of the most common foodborne pathogens, is transmitted mainly through contaminated food derived from infected animals. In this study, S. Typhimurium ST1120, an isolate from pig feces in Korea, was subjected to whole-genome analysis to understand its genomic features associated with virulence. The genome of ST1120 was found to have a circular chromosome of 4,855,001 bp (GC content 52.2%) and a plasmid of 6,863 bp (GC content 46.0%). This chromosome was predicted to have 4,558 open reading frames (ORFs), 17 pseudogenes, 22 rRNA genes, and 86 tRNA genes. Its plasmid was predicted to have three ORFs. Comparative genome analysis revealed that ST1120 was phylogenetically close to S. Typhimurium U288, a critical isolate in piggery farms and food chains in Europe. In silico functional analysis predicted that the ST1120 genome harbored multiple genes associated with virulence and stress resistance, including Salmonella pathogenicity islands (SPIs containing SPI-1 to SPI-5, SPI-13, and SPI-14), C63PI locus, ST104 prophage locus, and various antibiotic resistance genes. In accordance with these analysis results, ST1120 showed competence in invasion and survival abilities when it was added to host cells. It also exhibited robust resistance against antibiotics in comparison with other S. Typhimurium strains. This is the first report of the complete genome sequence of S. Typhimurium isolated from swine in Korea. Comparative genome analysis between ST1120 and other Salmonella strains would provide fruitful information toward understanding Salmonella host specificity and developing control measures against S. Typhimurium infection.

• Korean Journal of Environmental Biology
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• v.40 no.2
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• pp.199-205
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• 2022

Two tree frogs, Dryophytes suweonensis and Dryophytes japonicus, inhabiting Korea, are morphologically similar and share the same habitats. Therefore, they are identified mainly through their calls, especially for males. Dryophytes suweonensis is registered as an endangered (IUCN: EN grade) and protected species in South Korea. Thus, it is necessary to develop a method to rapidly identify and discriminate the two species and establish efficient protection and restoration plans. We identified significant genetic variation between them by sequencing a maternally-inherited mitochondrial 12S ribosomal DNA region. Based on the sequence data, we designed a pair of primers containing 7bp differences for high resolution melting(HRM) analysis to rapidly and accurately characterize their genotypes. The HRM analysis using genomic DNA showed that the melting peak for D. suweonensis was 76.4±0.06℃, whereas that of D. japonicus was 75.0±0.05℃. The differential melt curve plot further showed a distinct difference between them. We also carried out a pilot test for the application of HRM analysis based on immersing D. suweonensis in distilled water for 30 min to generate artificial environmental DNA(eDNA). The results showed 1.10-1.31℃ differences in the melting peaks between the two tree frog samples. Therefore, this HRM analysis is rapid and accurate in identifying two tree frogs not only using their genomic DNA but also using highly non-invasive eDNA.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.41-44
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• 2000

With the advent of DNA microarray and "chip" technologies, gene expression in an organism can be monitored on a genomic scale, allowing the transcription levels of many genes to be measured simultaneously. Functional interpretation of massive expression data and linking such data to DNA sequences have become the new challenges to bioinformatics. I will us yeast cell cycle expression data analysis as an example to demonstrate how special database and computational methods may be used for extracting functional information, I will also briefly describe a novel clustering algorithm which has been applied to the cell cycle data.

• Genomics & Informatics
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• v.5 no.3
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• pp.137-139
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• 2007

RAN-aCGH is an R GUI tool for the analysis and visualization of array comparative genomic hybridization (array-CGH) experiments. The tool consists of data-loading, preprocessing for missing data, several methods for statistical identification of DNA copy number aberration, and visualization of the copy number change. RAN-aCGH requires a single input format, provides various visualizations, and allows the addition of a new statistical method, all in a user-friendly graphic user interface (GUI).