• Biomedical Science Letters
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• v.22 no.3
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• pp.107-114
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• 2016

Maintenance of fasting blood glucose levels is important for glucose homeostasis. Disruption of feedback mechanisms are a major reason for elevations of glucose level in blood, which is a risk factor for type 2 diabetes mellitus that is mainly caused by malfunction of pancreatic beta-cell and insulin. The fasting blood glucose level has been known to be influenced by genetic and environmental factors. Mitochondria have many functions for cell survival and death: glucose metabolism, fatty acid oxidation, ATP generation, reactive oxygen species (ROS) metabolism, calcium handling, and apoptosis regulation. In addition to these functions, mitochondria change their morphology dynamically in response to multiple signals resulting in fusion and fission. In this study, we aimed to examine association between fasting blood glucose levels and variants of the genes that are reported to have functions in mitochondrial dynamics, fusion and fission, using a cohort study. A total 416 SNPs from 36 mitochondrial dynamics genes were selected to analyze the quantitative association with fasting glucose level. Among the 416 SNPs, 4 SNPs of PRKACB, 13 SNPs of PPP3CA, 6 SNPs of PARK2, and 3 SNPs of GDAP1 were significantly associated. In this study, we were able to confirm an association of mitochondrial dynamics genes with glucose levels. To our knowledge our study is the first to identify specific SNPs related to fasting blood glucose level.

• Asian-Australasian Journal of Animal Sciences
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• v.23 no.4
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• pp.417-424
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• 2010

The purpose of this study was to detect significant SNPs for carcass quality traits using DNA chips of high SNP density in Hanwoo populations. Carcass data of two hundred and eighty nine steers sired by 30 Korean proven sires were collected from two regions; the Hanwoo Improvement Center of National Agricultural Cooperative Federation in Seosan, Chungnam province and the commercial farms in Gyeongbuk province. The steers in Seosan were born between spring and fall of 2006 and those in Gyeonbuk between falls of 2004 and 2005. The former steers were slaughtered at approximately 24 months, while the latter steers were fed six months longer before slaughter. Among the 55,074 SNPs in the Illumina bovine 50K chip, a total of 32,756 available SNPs were selected for whole genome association study. After adjusting for the effects of sire, region and slaughter age, phenotypes were regressed on each SNP using a simple linear regression model. For the significance threshold, 0.1% point-wise p value from F distribution was used for each SNP test. Among the significant SNPs for a trait, the best set of SNP markers were selected using a stepwise regression procedure, and inclusion and exclusion of each SNP out of the model was determined at the p<0.001 level. A total of 118 SNPs were detected; 15, 20, 22, 28, 20, and 13 SNPs for final weight before slaughter, carcass weight, backfat thickness, weight index, longissimus dorsi muscle area, and marbling score, respectively. Among the significant SNPs, the best set of 44 SNPs was determined by stepwise regression procedures with 7, 9, 6, 9, 7, and 6 SNPs for the respective traits. Each set of SNPs per trait explained 20-40% of phenotypic variance. The number of detected SNPs per trait was not great in whole genome association tests, suggesting additional phenotype and genotype data are required to get more power to detect the trait-related SNPs with high accuracy for estimation of the SNP effect. These SNP markers could be applied to commercial Hanwoo populations via marker-assisted selection to verify the SNP effects and to improve genetic potentials in successive generations of the Hanwoo populations.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.256-259
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• 2005

Among non-synonymous SNPs that cause amino acid change in the protein product, the selection of disease-causing SNPs has been of great interest. We present the comparison between the evolutionary (SIFT score) and structural information (binding pocket) to show that the incorporation between them provides an advantage of sorting disease-causing SNPs from normal SNPs. To set up the procedure, we apply the machine learning method to the test data set from the laboratory experiments.

• Journal of Plant Biotechnology
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• v.47 no.3
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• pp.218-226
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• 2020

This report describes methods for selecting informative single nucleotide polymorphisms (SNPs), and the development of an online Solanaceae genome database, using 234 tomato resequencing data entries deposited in the NCBI SRA database. The 126 accessions of Solanum lycopersicum, 68 accessions of Solanum lycopersicum var. cerasiforme, and 33 accessions of Solanum pimpinellifolium, which are frequently used for breeding, and some wild-species tomato accessions were included in the analysis. To select tag-SNPs, we identified 29,504,960 SNPs in 234 tomatoes and then separated the SNPs in the genic and intergenic regions according to gene annotation. All tag-SNP were selected from non-synonymous SNPs among the SNPs present in the gene region and, as a result, we obtained tag-SNP from 13,845 genes. When there were no non-synonymous SNPs in the gene, the genes were selected from synonymous SNPs. The total number of tag-SNPs selected was 27,539. To increase the usefulness of the information, a Solanaceae genome database website, TGsol (http://tgsol. seeders.co.kr/), was constructed to allow users to search for detailed information on resources, SNPs, haplotype, and tag-SNPs. The user can search the tag-SNP and flanking sequences for each gene by searching for a gene name or gene position through the genome browser. This website can be used to efficiently search for genes related to traits or to develop molecular markers.

• Journal of Embryo Transfer
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• v.23 no.3
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• pp.197-201
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• 2008

In order to provide information of genetic variants for Haptoglobin (Hp) gene, which may be related to weight traits in pig, a total of 235 animals from National Institute of Animal Science (NIAS) were screened with 3 primers. The primer sequences were selected using the porcine cDNA sequences based on NM_214000, and the exon boundaries were estimated. Genetic variants were observed using direct sequencing analysis, and there were 9 SNPs detected at nucleotide positions 503 (A/G), 509 (A/G), 709 (C/T), 734 (C/A), 742 (G/A), 769 (A/G), 840 (C/T), 876 (C/T) and 882 (C/A). All the SNPs were located in coding regions, and mutations caused amino acid changes at nucleotide positions 503, 509, 734, 742 and 769. Allele frequencies of SNPs were estimated for all segments. The SNPs at nucleotide position 509 (p<0.0001) and 734 (p<0.05) were significantly associated with average daily gain, but no significance was observed with other SNPs. From the results, the identified SNPs may be a useful candidate marker for the porcine weight gain traits.

• Korean Journal of Poultry Science
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• v.45 no.3
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• pp.209-217
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• 2018

The innate immune recognition is based on the detection of microbial products. Toll-like receptors (TLRs) located on the cell surface and the endosome senses microbial components and nucleic acids, respectively. Chicken TLRs mediate immune responses by sensing ligands from pathogens, have been studied as immune adjuvants to increase the efficacy of vaccines. Single nucleotide polymorphisms (SNPs) of TLR3 and TLR4 genes in chicken were associated with resistance and susceptibility to viral infection. In this study, SNPs of chTLR3 and chTLR4 genes were retrieved from public database and annotated with chicken reference genome. Three-dimensional models of the chTLR3 and chTLR4 proteins were built using a Swiss modeler. We identified 35 and 13 nsSNPs in chTLR3 and chTLR4 genes respectively. Sorting Intolerant from Tolerant (SIFT) and Polymorphism Phenotyping v2 (Polyphen-2) analyses, suggested that, out of 35 and 13 nsSNPs, 4 and 2 SNPs were identified to be deleterious in chTLR3 and chTLR4 gene respectively. In chTLR3, 1 deleterious SNP was located in ectodomain and 3 were located in the Toll / IL-1 receptor (TIR) domain. Further structural model of chTLR3-TIR domain suggested that 1 deleterious SNP be present in the B-B loop region, which is important for TIR-TIR domain interactions in the downstream signaling. In chTLR4, the deleterious SNPs were located both in the ectodomain and TIR domain. SNPs predicted for chTLR3 and chTLR4 in this study, might be related to resistance or susceptible to viral infection in chickens. Results from this study will be useful to develop the effective measures in chicken against infectious diseases.

• Biomolecules & Therapeutics
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• v.15 no.3
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• pp.156-161
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• 2007

Rapid advances in pharmacogenomic research have provided important information to improve drug selection, to maximize drug efficacy, and to minimize drug adverse reaction. The SNPs that are the most abundant type of genetic variants have been proven as valid biomarkers to give information on the prediction of pharmacokinetic/pharmacodynamic properties of drugs based on genotype. In order to elucidate a correlation between SNPs of calcium channel encoding gene and adverse reactions of calcium channel blockers, we investigated SNPs in CACNA1C gene known as a binding site of calcium channel blocker. 96 patients with hypertension who had taken or are taking an antihypertensive drug, 1,4-dihydropyridine (DHP) were included for analysis. These patients were composed of 47 patients with adverse drug reactions (ADR) such as edema from calcium channel blockers and 49 patients without ADR as a control group. The exons encoding the drug binding sites were amplified by PCR using specific primers, and SNPs were analyzed by direct sequencing. We found that there was no SNP in the exons encoding DHP binding site, but four novel SNPs in the exon-intron junction region. However, four novel SNPs were not associated with the ADR of calcium channel blockers. In conclusion, this study showed that ADR from calcium channel blockers may not be caused by SNPs of the binding sites of calcium channel blockers in CACNA1C gene.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.8
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• pp.1150-1159
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• 2018

Objective: Non-synonymous single nucleotide polymorphisms (nsSNPs) were identified in Berkshire selective sweep regions and then were investigated to discover genetic nsSNP mechanisms that were potentially associated with Berkshire domestication and meat quality. We further used bioinformatics tools to predict damaging amino-acid substitutions in Berkshire-related nsSNPs. Methods: nsSNPs were examined in whole genome resequencing data of 110 pigs, including 14 Berkshire pigs, generated using the Illumina Hiseq2000 platform to identify variations that might affect meat quality in Berkshire pigs. Results: Total 65,550 nsSNPs were identified in the mapped regions; among these, 319 were found in Berkshire selective-sweep regions reported in a previous study. Genes encompassing these nsSNPs were involved in lipid metabolism, intramuscular fatty-acid deposition, and muscle development. The effects of amino acid change by nsSNPs on protein functions were predicted using sorting intolerant from tolerant and polymorphism phenotyping V2 to reveal their potential roles in biological processes that may correlate with the unique Berkshire meat-quality traits. Conclusion: Our nsSNP findings confirmed the history of Berkshire pigs and illustrated the effects of domestication on generic-variation patterns. Our novel findings, which are generally consistent with those of previous studies, facilitated a better understanding of Berkshire domestication. In summary, we extensively investigated the relationship between genomic composition and phenotypic traits by scanning for nsSNPs in large-scale whole-genome sequencing data.

• Journal of Life Science
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• v.23 no.7
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• pp.919-925
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• 2013

Human thymic stromal lymphopoietin receptor (TSLPR) might play an important role in the development of inflammatory and allergic responses. We previously identified eleven single nucleotide polymorphisms (SNPs) and two variation sites in the TSLPR gene and showed that all the SNPs of the TSLPR gene are associated with susceptibility to atopic asthma. The present study aimed to investigate whether the TSLPR gene SNPs are associated with susceptibility to rheumatoid arthritis (RA). We compared the genotype and the allele frequencies of the TSLPR SNPs in 457 RA patients and 570 healthy controls. The genotype and the allele frequencies of the TSLPR gene SNPs in the RA patients were not significantly different from the respective frequencies of the healthy controls. Additional analysis showed that the genotype and the allele frequencies of the TSLPR gene SNPs did not appear to be associated with RA in female RA patients. The TSLPR gene SNPs in the RA patients did not affect the production of rheumatoid factor (RF) and antisynthetic cyclic citrullinated peptide (CCP). Our results suggest that the TSLPR gene SNPs are not associated with susceptibility to RA in the Korean population.

• Genomics & Informatics
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• v.3 no.4
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• pp.149-153
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• 2005

Asthma is an inflammatory airways disease characterized by bronchial hyperresponsiveness and airways obstruction, which results from a complex interaction of genetic and environmental factors. Interleukin (IL)-13 and IL-4 are important in IgE synthesis and allergic inflammation, therefore genes encoding IL-13 and IL-4 are candidates for predisposition to asthma. In the present study, we screened single-nucleotide polymorphisms (SNPs) in IL-13 and IL-4 and examined whether they are risk factors for asthma. We resequenced all exons and the promoter region in 12 asthma patients and 12 normal controls, and identified 18 SNPs including 2 novel SNPs. The linkage disequilibrium(LD) pattern was evaluated with 16 common SNPs, and haplotypes were also estimated within the block. Although IL-13 and IL-4 are localized within 27 kb on chromosome 5q31 and share many biological profiles, this region was partitioned into 2 blocks. One SNP and three SNPs were determined as haplotype-taggingSNPs (htSNPs) within IL-13 and IL-4 haplotype-block, respectively. No significant associations were observed between any of the SNPs or haplotypes and development of asthma in small number of Korean subjects. However, the genetic variants of IL-13 and IL-4 would provide valuable strategies for the genotyping studies in large population.