• Journal of Life Science
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• v.24 no.11
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• pp.1168-1173
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• 2014

The homogentisate 1,2-dioxygenase (HGD) gene, which consists of 14 exons and spans approximately 42630bp on Bos taurus autosome 1 (BTA 1), is one of the six enzymes required for catabolism of the aromatic amino acids tyrosine and phenylalanine. It has been reported that BTA1 harbors quantitative trait loci that effect marbling score (MS), carcass weight (CW), and longissimus muscle area (LMA) in cattle. The aim of this study was to identify the single nucleotide polymorphisms (SNPs) in the HGD gene and to analyze their association with economic traits in Korean cattle (Hanwoo). Genetic polymorphisms were screened by direct sequencing, which detected 10 SNPs (T11187C, T11301A, T11398G, G29833A, G34256T, G34257C, T34284C, T42333G, T42348C, and T42468C). Six polymorphic sites were selected for genotyping, and economic traits were analyzed using a general linear model in Korean cattle (n=90). The observed genotype frequencies for G34256T were 0.5843(GG), 0.3708(GT), and 0.0449(TT). In addition, 0.3596(GG), 0.3708(GC), and 0.2697(CC) were observed for the G34257C mutation. Statistical association analysis revealed that G34256T polymorphisms were significantly associated with MS, and G34257C polymorphisms were significantly associated with MS and LMA (p<0.05). Further study is needed in order to use the genetic variant as a marker for marker-assisted selection in Korean cattle.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.11 no.2
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• pp.720-726
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• 2010

Haplotype-based research has become increasingly important in the field of personalized medicine since the haplotype reflects a set of SNPs (Single Nucleotide Polymorphisms) that are genetically associated and inherited together. Currently, the most widely used application softwares available for haplotype reconstruction, based on in silico method, include PL-EM, Haplotyper, PHASE and HAP. PL-EM, Haplotyper and PHASE are command-line application running on LINUX or Unix system and HAP is a web-based client-server application. This paper deals with an integrated haplotype reconstruction system that have been developed with PL-EM and Haplotyper selected from the accuracy test with experimentally verified data on public application softwares. This integrated system is a kind of client-sever one with user friendly web interface and can provide end-users with a high quality of haplotype analysis. SNPs genotype data with a length of 5 derived from 5 people and SNPs genotype data with a length of 13 derived from 15 people were used to test the analysis results of Haplotyper and PL-EM respectively. As a result, this system has been confirmed to provide the systematic and easy-to-understand analysis results that consist of two main parts, i.e. individual haplotype information and haplotype pool information. In this respect, the integration system will be utilized as a useful tool for the discovery of disease related genes and the development of personalized drugs through facilitating the reconstruction of haplotype maps.

• Korean Journal of Plant Resources
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• v.34 no.5
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• pp.478-490
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• 2021

We aimed to generate basic breeding data for melon (Cucumis melo L.). A total of 219 melon accessions conserved at the National Agrobiodiversity Center (NAC) in Rural Development Administration (RDA) were used in this study, of which 72 (33%) were collected from India. The majority of accessions showed orange (42%) and white (36%) flesh color. In addition to phenotypic evaluations, the accessions were genotyped using a molecular marker for the carotenoid biosynthesis gene CmOr. DNA fragments of the expected size were amplified in 205 out of 219 accessions. Digestion of the PCR products with HinfI restriction endonuclease showed 100% concordance between phenotype and genotype in green-fleshed accessions, but 98%, 97%, and 80% concordance in orange-, white-, and creamy-fleshed accessions, respectively. Sequence analysis revealed single nucleotide changes in the three positions of SNP1, SNP2 and SNP1int in the CmOr gene among accessions. These newly found alleles suggest that there are multiple mechanisms in determining fruit flesh color in melon. Also, the phenotype data of diverse accessions obtained in this study will be a valuable source for melon breeding.

• Journal of Animal Science and Technology
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• v.66 no.4
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• pp.702-716
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• 2024

The objective of this study was to identify genomic regions and candidate genes associated with productive traits using a total of 37,099 productive records and 6,683 single nucleotide polymorphism (SNP) data obtained from five Great-Grand-Parents (GGP) farms in Landrace. The estimated of heritabilities for days to 105 kg (AGE), average daily gain (ADG), backfat thickness (BF), and eye muscle area (EMA) were 0.49, 0.49, 0.56, and 0.23, respectively. We identified a genetic window that explained 2.05%-2.34% for each trait of the total genetic variance. We observed a clear partitioning of the four traits into two groups, and the most significant genomic region for AGE and ADG were located on the Sus scrofa chromosome (SSC) 1, while BF and EMA were located on SSC 2. We conducted Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), which revealed results in three biological processes, four cellular component, three molecular function, and six KEGG pathway. Significant SNPs can be used as markers for quantitative trait loci (QTL) investigation and genomic selection (GS) for productive traits in Landrace pig.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.12
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• pp.1689-1695
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• 2017

Objective: The cytokine inducible SH2-containing protein (CISH), which might play a role in porcine intestine immune responses, was one of the promising candidate genes for piglet anti-disease traits. An experiment was conducted to characterize the porcine CISH (pCISH) gene and to evaluate its genetic effects on pig anti-disease breeding. Methods: Both reverse transcription polymerase chain reaction (RT-PCR) and PCR were performed to obtain the sequence of pCISH gene. A pEGFP-C1-CISH vector was constructed and transfected into PK-15 cells to analysis the distribution of pCISH. The sequences of individuals were compared with each other to find the polymorphisms in pCISH gene. The association analysis was performed in Min pigs and Landrace pigs to evaluate the genetic effects on piglet diarrhea traits. Results: In the present research, the coding sequence and genomic sequence of pCISH gene was obtained. Porcine CISH was mainly localized in cytoplasm. TaqI and HaeIII PCR restriction fragment length polymorphism (RFLP) assays were established to detect single nucleotide polymorphisms (SNPs); A-1575G in promoter region and A2497C in Intron1, respectively. Association studies indicated that SNP A-1575G was significantly associated with diarrhea index of Min piglets (p<0.05) and SNP A2497C was significantly associated with the diarrhea trait of both Min pig and Landrace piglets (p<0.05). Conclusion: This study suggested that the pCISH gene might be a novel candidate gene for pig anti-disease traits, and further studies are needed to confirm the results of this preliminary research.

• Food Science of Animal Resources
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• v.32 no.1
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• pp.6-12
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• 2012

The association of three candidate genes, fatty acid synthase (FASN), microsomal triglyceride transfer protein (MTTP) and fatty acid binding protein 3 (FABP3), with fatty acid (FA) composition in Duroc pigs was investigated. Identified single nucleotide polymorphisms (SNPs) were used for polymerase chain reaction-restriction fragment length polymorphism genotyping. The c.265C>T SNP of FASN gene was significantly associated with high levels of palmitoleic acid (C16:1) (p<0.05), oleic acid (C18:1) (p<0.01), and mono-unsaturated fatty acid (MUFA) (p<0.01), but low levels of linoleic acid (C18:2) (p<0.01), alpha linolenic acid (C18:3) (p<0.05), and poly-unsaturated fatty acid (PUFA) (p<0.01) in animals having the CT genotype. The c.2573T>C SNP in the MTTP gene had a significant effect only in elevating the level of palmitoleic acid (C16:1) (p<0.05) in heterozygote animals. The polymorphism in FABP3 showed no significant effects on any fatty acid composition traits. These results suggest that the identified SNPs in the FASN and MTTP genes can be useful markers for selecting Duroc pigs having desirable healthy fatty acid composition.

• Journal of Acupuncture Research
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• v.23 no.2
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• pp.173-179
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• 2006

Objectives : In this study, we investigated the SNP (single-nucleotide polymorphism) of IL10 in patients with stroke. The present study was undertaken to see if specific genotypic and allelic variations are associated with stroke in the Korean population. Methods : Blood samples from all subjects were obtained for DNA extraction and collected in EDTA tube. Genomic DNA was extracted using DNA isolation kit for Mammalian Blood (Boehringer Mannheim, IN, USA). The extracted DNA was amplified by polymerase chain reaction (PCR). Pyrosequencing was performed according to manufacturer's standard protocol. Results : There was no statistically significant genotypic distribution difference between control and stroke group. The frequencies of A/A homozygotes and A/C heterozygotes among control subjects were 91 (87.5%) and 13 (12.5%). The frequencies of A/A and A/C among the stroke patients were 85 (89.5%) and 10 (10.5%). There was not statistically significant allelic frequency difference between control and stroke group. The allelic frequency of A and C was 195 (93.8%) and 13 (6.2%) among the control subjects and 180 (94.7%) and 10 (5.3%) in stroke patients, respectively. Conclusion : The cytokine IL10 may not be pathogenetic factors in stroke. But further studies including different cytokine gene can be a useful for predicting stroke. Establishment of more systemic approach and high quality of prospective cohorts will be necessary for the good prediction of genetic markers.

• Journal of the Korean Chemical Society
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• v.50 no.2
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• pp.116-122
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• 2006

In this study we extracted DNA from 100 tissues of breast cancer patients and 103 normals. Then we confirmed single-nucleotide polymorphism(SNP) using PCR-DHPLC(polymerase chain reaction-denaturing high performance liquid chromatogrphy).Also, we studied SNP of samples using several columns to identify relation between packing materials of column and resolution.As a result, we identified 4 C/A, C/G genotypes(4%) in exon 5 and 37 T del genotypes(37%) in exon 8 among 100 breast cancer tissues and 2 in exon 5, 9 in exon 8 among 103 normal samples.In resolution test, we confirmed that PS-DVB(poly styrene-divinylbenzen) column is more efficient than C18 column.

• Genomics & Informatics
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• v.7 no.4
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• pp.187-194
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• 2009

Cytochrome P450 2E1 (CYP2E1) is a member of the cytochrome P450 superfamily, and it is a key enzyme responsible for the metabolic activation of many smallmolecular-weight compounds such as alcohol, which is classified as a human carcinogen. In this study, we identified 19 single nucleotide polymorphisms (SNPs) in CYP2E1 in Korean population. In these SNPs, we examined possible genetic association of CYP2E1 polymorphisms with HBV clearance and the risk of hepatocellular carcinoma (HCC). Five common polymorphic sites were selected, CYP2E1 polymorphisms at rs381-3867, rs3813870, rs2070673, rs2515641 and rs2480257, considering their allele frequencies, haplotype-tagging status and LDs for genotyping in larger-scale subjects (n=1,092). Statistical analysis demonstrated that CYP2E1 polymorphisms and haplotypes show no significant association with HBV clearance, HCC occurrence and onset age of HCC (p>0.05). Previous studies, however, have shown contradictory findings on associations of CYP2E1 polymorphisms with CYP2E1 activities and HCC risk. Comparing the contrasting results of previous researches suggest that CYP2E1 polymorphism is associated with CYP2E1 activity induced by ethanol, but is not directly associated with HCC risk. CYP2E1 variation/haploype information identified in this study will provide valuable information for future studies on CYP2E1.

• Mycobiology
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• v.51 no.3
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• pp.139-147
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• 2023

Aspergillus sojae has long been considered a domesticated strain of Aspergillus parasiticus. This study delineated relationships among the two species and an Aspergillus PWE36 isolate. Of 25 examined clustered aflatoxin genes of PWE36, 20 gene sequences were identical to those of A. sojae, but all had variations to those of A. parasiticus. Additionally, PWE36 developmental genes of conidiation and sclerotial formation, overall, shared higher degrees of nucleotide sequence identity with A. sojae genes than with A. parasiticus genes. Examination of defective cyclopiazonic acid gene clusters revealed that the PWE36 deletion pattern was identical only to those of A. sojae. Using A. sojae SMF134 genome sequence as a reference, visualization of locally collinear blocks indicated that PWE36 shared higher genome sequence homologies with A. sojae than with A. parasiticus. Phylogenetic inference based on genome-wide single nucleotide polymorphisms (SNPs) and total SNP counts showed that A. sojae strains formed a monophyletic clade and were clonal. Two (Argentinian and Ugandan) A. parasiticus isolates but not including an Ethiopian isolate formed a monophyletic clade, which showed that A. parasiticus population is genetically diverse and distant to A. sojae. PWE36 and A. sojae shared a most recent common ancestor (MRCA). The estimated divergence time for PWE36 and A. sojae was about 0.4 mya. Unlike Aspergillus oryzae, another koji mold that includes genetically diverse populations, the findings that current A. sojae strains formed a monophyletic group and shared the MRCA with PWE36 allow A. sojae to be continuously treated as a species for food safety reasons.