• Journal of Animal Science and Technology
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• v.56 no.7
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• pp.23.1-23.7
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• 2014

Background: Scanning of the genome for selection signatures between breeds may play important role in understanding the underlie causes for observable phenotypic variations. The discovery of high density single nucleotide polymorphisms (SNPs) provide a useful starting point to perform genome-wide scan in pig populations in order to identify loci/candidate genes underlie phenotypic variation in pig breeds and facilitate genetic improvement programs. However, prior to this study genomic region under selection in commercially selected Berkshire and Korean native pig breeds has never been detected using high density SNP markers. To this end, we have genotyped 45 animals using Porcine SNP60 chip to detect selection signatures in the genome of the two breeds by using the $F_{ST}$ approach. Results: In the comparison of Berkshire and KNP breeds using the FDIST approach, a total of 1108 outlier loci (3.48%) were significantly different from zero at 99% confidence level with 870 of the outlier SNPs displaying high level of genetic differentiation ($F_{ST}{\geq}0.490$). The identified candidate genes were involved in a wide array of biological processes and molecular functions. Results revealed that 19 candidate genes were enriched in phosphate metabolism (GO: 0006796; ADCK1, ACYP1, CAMK2D, CDK13, CDK13, ERN1, GALK2, INPP1; MAK, MAP2K5, MAP3K1, MAPK14, P14KB, PIK3C3, PRKC1, PTPRK, RNASEL, THBS1, BRAF, VRK1). We have identified a set of candidate genes under selection and have known to be involved in growth, size and pork quality (CART, AGL, CF7L2, MAP2K5, DLK1, GLI3, CA3 and MC3R), ear morphology and size (HMGA2 and SOX5) stress response (ATF2, MSRB3, TMTC3 and SCAF8) and immune response (HCST and RYR1). Conclusions: Some of the genes may be used to facilitate genetic improvement programs. Our results also provide insights for better understanding of the process and influence of breed development on the pattern of genetic variations.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.35 no.6
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• pp.676-681
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• 2002

Different types of transcripts encoding growth hormone (GH) were identified from cDNA libraries constructed with pituitaries of a marine fish species, greenling (Hexagrammos otakii). GH-homologous cDNA clones were isolated using the high-density filter hybridization and the expressed sequence tag techniques. Of 39 full-length positive cDNA clones, 31 clones ($79\%$) displayed an identical sequence, however, remaining 8 clones exhibited several polymorphisms in their sequences including (1) the length and sequence variability in the 5' upstream region, (2) insertional sequences in open reading frame, and (3) deletion and/or single nucleotide polymorphism in the untranslated 3' region. Based on RT-PCT and RNA dot blot analyses, these transcripts were proven to be expressed in a pituitary-specific manner.

• Journal of Preventive Medicine and Public Health
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• v.42 no.1
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• pp.1-4
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• 2009

Objectives : Isolated cleft lip with or without cleft palate(CL/P) is among the most common human birth defects, with a prevalence of approximately 1 in 700 live births. The B-Cell Leukemia/lymphoma 3(BCL3) gene has been suggested as a candidate gene for CL/P based on association and linkage studies in some populations. This study tests for an association between markers in BCL3 and isolated, non-syndromic CL/P using a case-parent trio design, while considering parent-of-origin effects. Methods : Forty case-parent trios were genotyped for two single nucleotide polymorphisms(SNPs) in the BCL3 gene. We performed a transmission disequilibrium test(TDT) on individual SNPs, and the FAMHAP package was used to estimate haplotype frequencies and to test for excess transmission of multi-SNP haplotypes. Results : The odds ratio for transmission of the minor allele, OR(transmission), was significant for SNP rs8100239(OR=3.50, p=0.004) and rs2965169(OR=2.08, p=0.027) when parent-of-origin was not considered. Parentspecific TDT revealed that SNP rs8100239 showed excess maternal transmission. Analysis of haplotypes of rs2965169 and rs8100239 also suggested excess maternal transmission. Conclusions : BCL3 appears to influence risk of CL/P through a parent-of-origin effect with excess maternal transmission.

• Journal of Life Science
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• v.18 no.4
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• pp.572-579
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• 2008

Genome research in economic animals has progressed rapidly in recent years, transforming from primitive genome maps to quantitative/qualitative trait maps that are indispensable to gene discovery. These advances have been benefited from the result of animal genome sequencing projects and functional genomics that are being extensively applied in livestock animal research following the development of large expressed sequences tags (ESTs). Genome sequencing efforts will provide information to QTL study by larger scale single nucleotide polymorphisms (SNPs) association study. Comparative genomics which is applying the information from human genome research as well as rodents model has contributed to important discoveries in economic animal genome research. These efforts will speed up much denser QTL maps development for phenotypic traits which are not easy to measure and to be identified by quantitative genetics [20] and lead to development of convincing markers associated with economically important trait, which will be eventually applied to livestock industry. In addition to practical application, animal genome research will enrich the understanding of human physiology in terms of genome biology.

• Nutrition Research and Practice
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• v.13 no.6
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• pp.498-508
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• 2019

BACKGROUND/OBJECTIVES: Lower circulating 25-hydroxyvitamin D [25(OH)D] levels are associated with a higher risk of hypertension (HTN); however, it remains unclear whether the relationship is causal. We aimed to evaluate the causal effects of circulating 25(OH)D levels on the prevalence of HTN in the Korean population using the Mendelian randomization (MR) approach. SUBJECTS/METHODS: Epidemiological data, serum 25(OH)D data, and genomic DNA biospecimens were obtained from 2,591 participants, a subset of the study population in the Korea National Health and Nutrition Survey 2011-2012. Five 25(OH)D-related single nucleotide polymorphisms (SNPs; DHCR7 rs12785878, CYP2R1 rs10741657, CYP2R1 rs12794714, CYP24A1 rs6013897, and GC rs2282679), identified a priori from genome-wide association studies, were used as instrument variables (IVs) for serum 25(OH)D levels. In the MR analysis, we performed IV analyses using the two-stage least squares method. RESULTS: In the observational analysis, circulating 25(OH)D levels were found to be inversely associated with the HTN prevalence in ordinary least squares models (odds ratio: 0.97, 95% confidence interval: 0.96, 0.99) after adjusting for the potential confounders. There were differences in the circulating 25(OH)D levels across genotypes of individual SNPs. In the MR analysis, using individual SNPs as IVs, 25(OH)D levels were not associated with the HTN prevalence. CONCLUSIONS: We found no association between genetically determined circulating 25(OH)D levels and HTN in Korean adults. Our results are listed owing to the relatively small sample size and possible weak instrument bias; therefore, further studies are needed to confirm these results.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.12
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• pp.1816-1825
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• 2019

Objective: We tried to analyze allele-specific expression in the pig neocortex using bioinformatic analysis of high-throughput sequencing results from the parental genomes and offspring transcriptomes from reciprocal crosses between Korean Native and Landrace pigs. Methods: We carried out sequencing of parental genomes and offspring transcriptomes using next generation sequencing. We subsequently carried out genome scale identification of single nucleotide polymorphisms (SNPs) in two different ways using either individual genome mapping or joint genome mapping of the same breed parents that were used for the reciprocal crosses. Using parent-specific SNPs, allele-specifically expressed genes were analyzed. Results: Because of the low genome coverage (${\sim}4{\times}$) of the sequencing results, most SNPs were non-informative for parental lineage determination of the expressed alleles in the offspring and were thus excluded from our analysis. Consequently, 436 SNPs covering 336 genes were applicable to measure the imbalanced expression of paternal alleles in the offspring. By calculating the read ratios of parental alleles in the offspring, we identified seven genes showing allele-biased expression (p<0.05) including three previously reported and four newly identified genes in this study. Conclusion: The newly identified allele-specifically expressing genes in the neocortex of pigs should contribute to improving our knowledge on genomic imprinting in pigs. To our knowledge, this is the first study of allelic imbalance using high throughput analysis of both parental genomes and offspring transcriptomes of the reciprocal cross in outbred animals. Our study also showed the effect of the number of informative animals on the genome level investigation of allele-specific expression using RNA-seq analysis in livestock species.

• Journal of Korean Medicine for Obesity Research
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• v.12 no.2
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• pp.28-43
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• 2012

Objectives: The aim of the study was to investigate the efficacy of Boiogito for obesity. We examined the efficacy of Boiogito for obese patients and we expected the reaction of Boiogito would vary according to the single nucleotide polymorphism(SNPs). Methods: 111 subjects(body mass index${\geq}25m/kg^2$) were recruited and randomized to receive Boiogito(n=55) or Placebo(n=56) for 8weeks. Anthropometric factors, serum lipid profile, glucose, blood pressure(BP), pulse rate, resting metabolic rate and Korean version of obesity-related quality of life(KOQOL) scale measured at baseline and 8weeks. SNPs(${\beta}3$-adrenergic receptor(ADRB3), G protein ${\beta}3$(GNB3), peroxisome proliferator activated receptor gamma 2 gene(PPAR-${\gamma}2$), uncoupling protein(UCP2)) were conducted at baseline. Adverse reactions and safety outcome variables were also checked during trials. Results: Both groups showed significant improvement on obesity after treatment. Boiogito group decreased triglyceride than did control group and improved KOQOL. Boiogito showed a significant higher efficacy in C/T and T/T genotype of GNB3 gene / in Trp64 and Arg64 genotype of ADRB3 gene / in D/D genotype of UCP2 gene / in Pro/Pro genotype of PPAR-${\gamma}$ gene. Conclusions: Boiogito promoted obesity indexes without severe adverse reactions and proved its safety. Pharmacogenetical studies of Boiogito on obesity could be a effective method for the individualized treatment and prevention of obesity.

• Genes and Genomics
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• v.40 no.12
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• pp.1331-1338
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• 2018

Although there have been plenty of dominance deviation analysis, few studies have dealt with multiple phenotypes. Because researchers focused on multiple phenotypes (final weight and backfat thickness) of Landrace pigs, the classification of the genes was possible. With genome-wide association studies (GWASs), we analyzed the additive and dominance effects of the single nucleotide polymorphisms (SNPs). The classification of the pig genes into four categories (overdominance in final weight, overdominance in backfat thickness and overdominance in final weight, underdominance in backfat thickness, etc.) can enable us not only to analyze each phenotype's dominant effects, but also to illustrate the gene ontology (GO) analysis with different aspects. We aimed to determine the additive and dominant effect in backfat thickness and final weight and performed GO analysis. Using additive model and dominance deviation analysis in GWASs, Landrace pigs' overdominant and underdominant SNP effects in final weight and backfat thickness were surveyed. Then through GO analysis, we investigated the genes that were classified in the GWASs. The major GO terms of the underdominant effects in final weight and overdominant effects in backfat thickness were ion transport with the SLC8A3, KCNJ16, P2RX7 and TRPC3 genes. Interestingly, the major GO terms in the underdominant effects in the final weight and the underdominant effects in the backfat thickness were the regulation of ion transport with the STAC, GCK, TRPC6, UBASH3B, CAMK2D, CACNG4 and SCN4B genes. These results demonstrate that ion transport and ion transport regulation genes have distinct dominant effects. Through GWASs using the mode of linear additive model and dominance deviation, overdominant effects and underdominant effects in backfat thickness was contrary to each other in GO terms (ion transport and ion transport regulation, respectively). Additionally, because ion transport and ion transport regulation genes are associative with adipose tissue accumulation, we could infer that these two groups of genes had to do with unique fat accumulation mechanisms in Landrace pigs.

• Genes and Genomics
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• v.40 no.12
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• pp.1279-1285
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• 2018

Interdigitating dendritic cell sarcoma (IDCS) is an aggressive neoplasm and is an extremely rare disease, with a challenging diagnosis. Etiology of IDCS is also unknown and most studies with only case reports. In our case, immunohistochemistry showed that the tumor cells were positive for S100, CD45, and CD68, but negative for CD1a and CD21. This study aimed to investigate the causative factors of IDCS by sequencing the protein-coding regions of IDCS. We performed whole-exome sequencing with genomic DNA from blood and sarcoma tissue of the IDCS patient using the Illumina Hiseq 2500 platform. After that, we conducted Sanger sequencing for validation of sarcoma-specific variants and gene ontology analysis using DAVID bioinformatics resources. Through comparing sequencing data of sarcoma with normal blood, we obtained 15 nonsynonymous single nucleotide polymorphisms (SNPs) as sarcoma-specific variants. Although the 15 SNPs were not validated by Sanger sequencing due to tumor heterogeneity and low sensitivity of Sanger sequencing, we examined the function of the genes in which each SNP is located. Based on previous studies and gene ontology database, we found that POLQ encoding DNA polymerase theta enzyme and FNIP1 encoding tumor suppressor folliculin-interacting protein might have contributed to the IDCS. Our study provides potential causative genetic factors of IDCS and plays a role in advancing the understanding of IDCS pathogenesis.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.12
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• pp.1863-1870
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• 2018

Objective: The Bayesian first-order antedependence models, which specified single nucleotide polymorphisms (SNP) effects as being spatially correlated in the conventional BayesA/B, had more accurate genomic prediction than their corresponding classical counterparts. Given advantages of $BayesC{\pi}$ over BayesA/B, we have developed hyper-$BayesC{\pi}$, ante-$BayesC{\pi}$, and ante-hyper-$BayesC{\pi}$ to evaluate influences of the antedependence model and hyperparameters for $v_g$ and $s_g^2$ on $BayesC{\pi}$.Methods: Three public data (two simulated data and one mouse data) were used to validate our proposed methods. Genomic prediction performance of proposed methods was compared to traditional $BayesC{\pi}$, ante-BayesA and ante-BayesB. Results: Through both simulation and real data analyses, we found that hyper-$BayesC{\pi}$, ante-$BayesC{\pi}$ and ante-hyper-$BayesC{\pi}$ were comparable with $BayesC{\pi}$, ante-BayesB, and ante-BayesA regarding the prediction accuracy and bias, except the situation in which ante-BayesB performed significantly worse when using a few SNPs and ${\pi}=0.95$. Conclusion: Hyper-$BayesC{\pi}$ is recommended because it avoids pre-estimated total genetic variance of a trait compared with $BayesC{\pi}$ and shortens computing time compared with ante-BayesB. Although the antedependence model in $BayesC{\pi}$ did not show the advantages in our study, larger real data with high density chip may be used to validate it again in the future.