• Korean Journal of Plant Resources
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• v.27 no.6
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• pp.680-686
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• 2014

Acanthopanacis Cortex has been used for oriental medicinal purposes in Asian countries especially in Korea and China. In the Korean Pharmacopeia, the cortexes of the dried roots, stems and branches of all species in Eleutherococcus and Eleutherococcus sessiliflorus are known as 'Ogapi'. Mostly the cortexes of E. gracilistylus roots and E.senticosus roots were used as 'Ogapi' in China and Japan, respectively. Therefore, the purpose of this study was to determine and compare the molecular authentication of Korean 'Ogapi' by using the ribosomal internal transcribed spacer (ITS) region. The ITS region has the highest possibility of effective and successful identification for the widest variety of molecular authentication. The ITS region was targeted for molecular analysis with Single nucleotide polymorphisms (SNPs) specific for morphologically similar to E. gracilistylus, E. senticosus, E. sessiliflorus from their adulterant, moreover, E. sieboldianus were detected within sequence data. Thus, based on these SNP sites, specific primers were designed and multiplex PCR analysis were conducted for molecular authentication of four plants (E. gracilistylus, E. senticosus, E. sessiliflorus, and E. sieboldianus). The findings of results indicated that ITS region might be established multiplex-PCR analysis systems and hence were proved to be an effective tools for molecular evaluation and comparison of 'Ogapi' with other plants.

• Genomics & Informatics
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• v.8 no.3
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• pp.103-107
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• 2010

The imputation of untyped SNPs enables researchers to validate association findings across SNP arrays and also enables them to test a large number of SNPs to reveal the fine structure of the association peak, facilitating interpretation of the results and the location of causal polymorphisms. In this study, we applied the imputation method to a genomewide association study and recapitulated the previously associated gene loci of blood pressure traits in Korean cohorts. A total of 1,827,004 SNPs were imputed by the IMPUTE program, and we conducted a genomewide association study for systolic and diastolic blood pressure. While no SNPs passed the Bonferroni correction p-value (p=$2.74{\times}10^{-8}$ for 1,827,004 SNPs), 12 novel loci for systolic blood pressure and 16 novel loci for diastolic blood pressure were detected by imputed SNPs, with $10^{-5}$ < p-value < $10^{-4}$. Moreover, 7 regions (ATP2B1, 10p15.1, ARHGEF12, ALX4, LIPC, 7q31.1, and TCF7L2) out of 14 genetic loci that were previously reported revealed that the imputed SNPs had lower p-values than those of genotyped SNPs. Moreover, a nonsynonymous SNP in the CSMD1 gene, one of the 14 genes, was found to be associated with systolic blood pressure (p<0.05). These results suggest that the imputation method can facilitate the discovery of novel SNPs as well as enhance the fine structure of the association peak in the loci.

• 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.