• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.186-186
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• 2022

Phytophthora root and stem rot (PRSR) and wildfire disease (WFD) of soybean are frequently observed in the field of South Korea. The most environmentally friendly way to control PRSR and WFD is to use soybean varieties with resistance to Phytophthora sojae (P. sojae) and Pseudomonas amygdali pv. tabaci. Plant germplasm is an important gene pool for soybean breeding and improvement. In this study, hundreds of soybean accessions were evaluated for the two pathogens, and genome-wide association analyses were conducted using 104,955 SNPs to identify resistance loci for the two pathogens. Of 193 accessions, 46 genotypes showed resistance reaction, while 143 did susceptibility for PRSP. Twenty SNPs were significantly associated with resistance to P. sojae on chromosomes (Chr.) 3 and 4. Significant SNPs on Chr.3 were located within the known Rps gene region. A region on Chr. 4 is considered as a new candidate resistance loci. For evalation of resistance to WFD, 18, 31,74,36 and 34 genotypes were counted by a scale of 1-5, respectively. Five SNP markers on Chrs 9,11,12,17 and 18 were significantly associated with resistance to P. amygdali pv. tabaci. The identified SNPs and genomic regions will provide a useful information for further researches and breeding for resistance to P. sojae and P. amygdali pv. tabaci.

• Animal cells and systems
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• v.9 no.2
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• pp.95-100
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• 2005

Essential hypertension results from the complex interaction between genetic and environmental factors. A C825T polymorphism of the gene encoding G-protein ${\beta}3$ subunit (GNB3), associated with enhanced G-protein coupled signaling and increased $Na^+-H^+$ exchanger, has been implicated in the development of essential hypertension in several human populations, especially in Caucasian population. We examined the disease relevance of this candidate gene by performing an association study in a study group of Korean heritage. Participants comprised 109 essential hypertensives and 109 normotensives, respectively. Genotyping was performed with PCR-BsaJI restriction digestion method. Observed genotype frequencies were in Hardy-Weinberg equilibrium in all groups. Genotype and allele frequencies did not differ significantly between normotensives and essential hypertensives (P>0.05). However, the serum total cholesterol (TC) and LDL-cholesterol levels were significantly higher in subjects with the TT genotype compared to those with the CC or CT genotypes in normotensives of our study subjects (P<0.05). Thus, these results suggest that GNB3/C825T polymorphism might be significantly associated with abnormality in serum lipid metabolism.

• Genomics & Informatics
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• v.8 no.3
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• pp.108-115
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• 2010

Hypertension is the most prevalent disease worldwide and is itself a risk factor for cerebral, cardiac, and renal diseases. The inconsistency of candidate genes suggested by previous genomewide association studies (GWASs) may be due to not only differences in study design and genetic or environmental background but also the difference in the power of analysis between continuous traits and discrete traits. We analyzed 352,228 single nucleotide polymorphisms (SNPs) in 8842 unrelated Koreans obtained from Ansan and Ansung cohorts. We performed a series of GWA analyses using three different phenotype models; young hypertensive cases (278 subjects) versus elderly normotensive controls (680 subjects); the upper 25% (2211 hypertensive cases) versus the lower 25% of the SBP distribution (2211 hypotensive controls); and finally SBP and DBP as continuous traits (8842 subjects). The numbers of young hypertensive cases and elderly normotensive controls were not large enough to achieve genomewide significance. The model comparing the upper 25% subjects to the lower 25% of subjects showed a power that was approximate to that of QTL analysis. Two neighboring SNPs of the ATP2B1 gene, rs17249754 (SBP, p=$2.53^{-10}$; DBP, p=$1.28{\times}10^{-8}$) and rs7136259 (SBP, p=$1.30{\times}10^{-9}$; DBP, p=$6.41{\times}10^{-8}$), were associated with both SBP and DBP. Interestingly, a SNP of the RPL6 gene, rs11066280, revealed a significant genomewide association with SBP in men only (p=$3.85{\times}10^{-8}$), and four SNPs located near the MAN2A1 gene showed a strong association with DBP only in elderly men aged 60-70 years (e.g., rs6421827, p=$4.86{\times}10^{-8}$). However, we did not observe any gene variant attaining genomewide significance consistently in the three phenotype models except for the ATP2B1 gene variants. In general, the association signal with blood pressure was stronger in women than in men. Genes identified in GWASs are expected to open the way for prevention, early diagnosis, and personalized treatment of hypertension.

• Korean Journal of Biological Psychiatry
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• v.14 no.4
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• pp.262-267
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• 2007

The serotonin 6(5-HT6) receptor gene is a candidate gene for influencing the clinical response to treatment with antidepressants. The purpose of this study was to determine the relationship between the C267T polymorphism in the 5-HT6 receptor gene and the treatment response to citalopram in a Korean population with major depressive disorder(MDD). Methods : Citalopram was administered for 8 weeks to the 90 patients who completed study. 21-item Hamilton depression rating scale(HAMD-21) was used as a outcome measure. Results : We found that the genotype, allele, and allele-carrier distributions did not differ significantly between MDD patients and normal controls. A main effect of an interaction of genotype with time on the decrease in the HAMD-21 score during the 8 weeks study period was not found. ANOVA revealed no significant effects of the C825T polymorphism on the decrease in the HAMD-21 score at each time period. Conclusions : These results suggest that the C267T polymorphism in the 5-HT6 receptor gene is not associated with the treatment response to citalopram.

• Journal of Animal Science and Technology
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• v.65 no.1
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• pp.57-68
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• 2023

Flavor is an important sensory trait of chicken meat. The free amino acid (FAA) and nucleotide (NT) components of meat are major factors affecting meat flavor during the cooking process. As a genetic approach to improve meat flavor, we performed a genome-wide association study (GWAS) to identify the potential candidate genes related to the FAA and NT components of chicken breast meat. Measurements of FAA and NT components were recorded at the age of 10 weeks from 764 and 767 birds, respectively, using a White leghorn and Yeonsan ogye crossbred F2 chicken population. For genotyping, we used 60K Illumina single-nucleotide polymorphism (SNP) chips. We found a total of nine significant SNPs for five FAA traits (arginine, glycine, lysine, threonine content, and the essential FAAs and one NT trait (inosine content), and six significant genomic regions were identified, including three regions shared among the essential FAAs, arginine, and inosine content traits. A list of potential candidate genes in significant genomic regions was detected, including the KCNRG, KCNIP4, HOXA3, THSD7B, and MMUT genes. The essential FAAs had significant gene regions the same as arginine. The genes related to arginine content were involved in nitric oxide metabolism, while the inosine content was possibly affected by insulin activity. Moreover, the threonine content could be related to methylmalonyl-CoA mutase. The genes and SNPs identified in this study might be useful markers in chicken selection and breeding for chicken meat flavor.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.5
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• pp.2499-2506
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• 2016

Background: Gastric cancer (GC) is the second leading cause of cancer-related death worldwide. Several environmental, genetic and epigenetic factors have been suggested to have a role in GC development. Epigenetic mechanisms like histone changes and promoter hyper-methylation are now being increasingly studied. Associations between methylation of many gene promoters with the risk of gastric cancer have been investigated worldwide. Such aberrant methylation may result in silencing of specific genes related to cell cycling, cell adhesion, apoptosis and DNA repair. Thus this molecular mechanism might have a key role in proliferation and migration of cancerous cells. Materials and Methods: In this review article we included studies conducted on DNA methylation and gastric cancer in Iranian populations. Using Science direct, Pubmed/PMC, Springer, Wiley online library and SciELO databases, all published data until 31 January 2016 were gathered. We also searched Science direct data base for similar investigations around the world to make a comparison between Iran and other countries. Results: By searching these databases, we found that the association between methylation of seven gene promoters and gastric cancer had been studied in Iran until 31 January 2016. These genes were p16, hLMH1, E-cadherin, CTLA4, $THR{\beta}$, mir9 and APC. Searching in science direct database also showed that 92 articles had been published around the world till January 2016. Our investigation revealed that despite the importance of GC and its high prevalence in Iran, the methylation status of only a few gene promoters has been studied so far. More studies with higher sample numbers are needed to reveal the relation of methylation status of gene promoters to gastric cancer in Iran. Conclusions: Further studies will be helpful in identifying associations of DNA methylation in candidate genes with gastric cancer risk in Iranian populations.

• Journal of the Korea Organic Resources Recycling Association
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• v.11 no.3
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• pp.67-74
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• 2003

Starvation promoters can be utilized for in situ bioremediation and for the efficient bioprocessing. Previously we have cloned and characterized strong starvation promoters from envrionmentally relevant bacteria, Pseudomonas putida strains (Y. Kim, and A. Matin, J. Bacteriol. 177:1850-1859, 1995). Here we report the construction of the plasmid pYKS101 using one of the starvation promoters from P. putida MK1. The pYKS101 was found to be useful for a novel starvation promoter-driven gene expression system. Under this system, the target reporter gene, lacZ, was stably integrated into the chromosomal DNA of P. putida MK1. ${\beta}$-galactosidase activity was found to be four-fold higher upon carbon starvation than during exponential growth. The resultant recombinant strain is indigenous to the environment contaminated with various toxic materials, hence can be a good candidate for in situ bioremediation.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.2
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• pp.183-188
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• 2012

To investigate the influence of the prolactin receptor 3 (PRLR3) gene and the retinol-binding protein 4 (RBP4) gene on the production traits of swine, genotyping was performed on 156 and 141 Berkshire pigs, respectively, that were carefully selected for economic traits. The frequencies of allele A in the PRLR3 locus and allele B in the RBP4 locus were 0.50 and 0.42, respectively. Neither locus was in the Hardy-Weinberg equilibrium. After a genotype was assigned to the individuals whose parents had the homozygous genotype, a statistical analysis was conducted for 291 pigs. The animals with the PRLR3 and RBP4 genotypes included 182 and 227 head, respectively. Even though the genotypic effects of PRLR3 (p<0.05) and RBP4 (p<0.01) had a significant influence on the pigs' back fat thickness, the interaction of both genes was not highly significant in terms of the back fat thickness (p = 0.1235). While the estimated epistasis effects of aaBB and aaBb decreased the back fat thickness and reduced the growth rate, the effects of AAbb and aabb increased the growth rate. Despite the insignificant difference in the PRLR genotypes in terms of the days to 90 kg and the average daily gain, the back fat thickness showed a significant difference (p<0.05), and the additive effect of allele A and the dominant effect of the hetero-genotype were -0.377 and 1.206 mm, respectively. The RBP4 genotypes had a very significant effect (p<0.01) on the back fat thickness, the days to 90 kg, and the average daily gain. The additive effects of allele B of the RBP4 locus on the back fat thickness, the days to 90 kg, and the average daily gain were 0.70 mm, -1.3 days and 6.2 g, respectively. Moreover, the dominant effects of the heterozygote for those traits were 0.63 mm, 9.9 days and -45.0 g, respectively. Allele A of the PRLR3 locus favorably influenced the back fat thickness, the days to 90 kg of the body weight, and the average daily gain and its dominant effect unfavorably influenced those traits. Allele B of RBP4 showed an incremental growth rate and back fat thickness, which could lower the lean meat percentage in the carcass. The RBP4 hetero-genotype negatively affected the pork production. These results strongly imply that the selection of allele A of PRLR3 and allele B of RBP4 would produce highly productive pigs in the Berkshire breed. Careful selection of allele B of RBP4 is required because of the increase in the back fat thickness.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.6
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• pp.893-899
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• 2009

Few studies have reported the existence of imprinted genes in cattle compared to the human and mouse. Genomic imprinting is expressed in monoallelic form and it depends on a single parent-specific form of the allele. Comparative analysis of mammals other than the human is a valuable tool for explaining the genomic basis of imprinted genes. In this study, we investigated 34 common imprinted genes in the human and mouse as well as 35 known non-imprinted genes in the human. We found short interspersed nuclear elements (SINEs), long interspersed nuclear elements (LINEs), and long terminal repeats (LTRs) in imprinted (human and mouse) and control (cattle) genes. Pair-wise comparisons for the three species were conducted using SINEs, LINEs, and LTRs. We also calculated 95% confidence intervals of frequencies of repetitive sequences for the three species. As a result, most genes had a similar interval between species. We found 11 genes with conserved SINEs, LINEs, and LTRs in the human, mouse, and cattle. In conclusion, eleven genes (CALCR, Grb10, HTR2A, KCNK9, Kcnq1, MEST, OSBPL5, PPP1R9A, Sgce, SLC22A18, and UBE3A) were identified as candidate imprinted genes in cattle.

• Animal Bioscience
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• v.36 no.3
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• pp.429-440
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• 2023

Objective: 12-oxo-5Z,8Z,10E,14Z-eicosatetraenoic acid (12-KETE), a metabolite of arachidonic acid, is a strong candidate signal for placenta separation following calf discharge at delivery. In the present study, the effects of 12-KETE on bovine trophoblast cells were investigated to determine its function in the placentome at delivery. Methods: Bovine trophoblast cells derived from blastocysts were used. They were cocultured with or without fibroblasts derived from bovine placentome and/or bovine uterine epithelial cells. 12-KETE was added to the culture medium. Results: Bovine trophoblast cells contained binucleate cells and strongly expressed caudal type homeobox 2 (CDX-2) genes. Addition of 12-KETE to the trophoblast cell colony without feeder cells or that on a fibroblast monolayer induced rapid exfoliation of the colony. After 12-KETE addition, trophoblast cells emitted strong fluorescence caused by the degradation of dye-quenched collagen, indicating that 12-KETE activated matrix metalloproteinase of the trophoblast cells. Exfoliated cell colonies were stained with YOPRO-1, but not propidium iodide (PI). Moreover, DNA fragmentation and Bcl-2 associated X protein (Bax) gene (apoptosis stimulator) upregulation were observed in exfoliated cells, indicating that 12- KETE induced trophoblast cell apoptosis. These results were consistent with previous in vivo observations; however, even a lower concentration of 12-KETE activated trophoblast protease. Meanwhile, fibroblasts derived from the bovine placentome converted arachidonic acid to 12-KETE. Conclusion: These observations indicate that 12-KETE may serve as a signal for placenta separation at delivery.