• Journal of Life Science
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• v.28 no.7
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• pp.795-801
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• 2018

This study was conducted to investigate the association of single nucleotide polymorphism (SNP) markers on equine chromosomes (ECA) 3 and 9 with body weight in Jeju horses. We used DNA samples and body weight data of 320 horses provided by the Livestock Promotion Agency, Jeju Special Self-Governing Province, and the Korean Racing Association, respectively. We genotyped all the experimental animals using nine SNP markers located on ECA 3 (BIEC2-808466, BIEC2-808543, BIEC2-808967, and BIEC2-809370) and ECA 9 (BIEC2-1105370, BIEC2-1105372, BIEC2-1105377, BIEC21105505, and BIEC2-1105840). These markers were selected due to their effects on body conformation traits in horses. The joint effect of the genotypes of the two SNP markers (BIEC2-808467 and BIEC2-1105377) regarding body weight were also evaluated. The estimated breeding value (EBV) of body weight was obtained as the dependent variable for association analyses using a linear mixed model. Significant associations were detected between SNP markers (BIEC2-808543, BIEC2-808967, BIEC2-809370, BIEC2-1105370, BIEC2-1105372, and BIEC2-1105377) and the body weight EBV. In addition, the joint genotype effect of the BIEC2-808467 and BIEC2-1105377 on the body weight EBV was significant. These results indicate that the SNP markers, which showed their significant effects on body conformation, can be used as genetic markers to improve the efficiency of the selective breeding program for the body weight traits in Jeju horses.

• Journal of Animal Science and Technology
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• v.53 no.1
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• pp.1-6
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• 2011

This simulation study was performed to investigate the accuracy of the estimated breeding value by using genomic information (GEBV) by way of Bayesian framework. Genomic information by way of single nucleotide polymorphism (SNP) from a chromosome with length of 100cM were simulated with different marker distance (0.1cM, 0.5cM), heritabilities (0.1, 0.5) and half sibs families (20 heads, 4 heads). For generating the simulated population in which animals were inferred to genomic polymorphism, we assumed that the number of quantitative trait loci (QTL) were equal with the number of no effect markers. The positions of markers and QTLs were located with even and scatter distances, respectively. The accuracies of estimated breeding values by way of indicating correlations between true and estimated breeding values were compared on several cases of marker distances, heritabilities and family sizes. The accuracies of breeding values on animals only having genomic information were 0.87 and 0.81 in marker distances of 0.1cM and 0.5cM, respectively. These accuracies were shown to be influenced by heritabilities (0.87 at $h^2$ =0.10, 0.94 at $h^2$ =0.50). According to half sibs' family size, these accuracies were 0.87 and 0.84 in family size of 20 and 4, respectively. As half sibs family size is high, accuracy of breeding appeared high. Based on the results of this study it is concluded that the amount of marker information, heritability and family size would influence the accuracy of the estimated breeding values in genomic selection methodology for animal breeding.

• Genomics & Informatics
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• v.16 no.2
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• pp.36-41
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• 2018

Kawasaki disease (KD) is an acute febrile vasculitis predominately affecting infants and children. The dominant incidence age of KD is from 6 months to 5 years of age, and the incidence is unusual in those younger than 6 months and older than 5 years of age. We tried to identify genetic variants specifically associated with KD in patients younger than 6 months or older than 5 years of age. We performed an age-stratified genome-wide association study using the Illumina HumanOmni1-Quad BeadChip data (296 cases vs. 1,000 controls) and a replication study (1,360 cases vs. 3,553 controls) in the Korean population. Among 26 candidate single nucleotide polymorphisms (SNPs) tested in replication study, only a rare nonsynonymous SNP (rs4365796: c.1106C>T, p.Thr369Met) in the lymphoid enhancer binding factor 1 (LEF1) gene was very significantly associated with KD in patients younger than 6 months of age (odds ratio [OR], 3.07; $p_{combined}=1.10{\times}10^{-5}$), whereas no association of the same SNP was observed in any other age group of KD patients. The same SNP (rs4365796) in the LEF1 gene showed the same direction of risk effect in Japanese KD patients younger than 6 months of age, although the effect was not statistically significant (OR, 1.42; p = 0.397). This result indicates that the LEF1 gene may play an important role as a susceptibility gene specifically affecting KD patients younger than 6 months of age.

• Korean Journal of Biological Psychiatry
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• v.19 no.3
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• pp.128-133
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• 2012

Objectives : Located on chromosome 10q22-q23, the human neuregulin 3 (NRG3) is suggested as a strong positional and functional candidate gene involved in the pathogenesis of schizophrenia. Several case-control studies examining the association between polymorphisms on NRG3 gene with schizophrenia and/or its traits (such as delusion) have been reported recently in cohorts of Han Chinese, Ashkenazi Jews, Australians, white Americans of Western European ancestry and Koreans. Thus, this study aimed to investigate the association of one SNP in exon 9 (rs2295933) of NRG3 gene with the risk of schizophrenia in a Korean population. Methods : Using TaqMan assay, rs2295933 in the exon 9 of NRG3 was genotyped in 435 patients with schizophrenia as cases and 393 unrelated healthy individuals as controls. Differences in frequency distributions were analyzed using logistic regression models following various modes of genetic inheritance and controlling for age and sex as covariates. Results : Subsequent analysis revealed that the frequency distribution of rs2295933 of NRG3 was not different between schizophrenia patients and healthy controls of Korean ethnicity. Conclusions : This study does not support the role of NRG3 in schizophrenia in a Korean population.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.9
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• pp.1319-1326
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• 2007

Fructose-1,6-bisphosphatase (FBP1) is a key regulatory enzyme of gluconeogenesis that catalyzes the hydrolysis of fructose-1,6-bisphosphate to generate fructose-6-phosphate and inorganic phosphate. Deficiency of fructose-1, 6-bisphosphatase is associated with fasting hypoglycemia and metabolic acidosis. The enzyme has been shown to occur in bacteria, fungi, plants and animals. The bovine FBP1 gene was cloned and characterized in this study. The full length (1,241 bp) FBP1 mRNA contained an open reading frame (ORF) encoding a protein of 338 amino acids, a 63 bp 5' untranslated region (UTR) and a 131 bp 3' UTR. The bovine FBP1 gene was 89%, 85%, 82%, 82% and 74% identical to the orthologs of pig, human, mouse, rat and zebra fish at mRNA level, and 97%, 96%, 94%, 93% and 91% identical at the protein level, respectively. This gene was broadly expressed in cattle with the highest level in testis, and the lowest level in heart. An intronic single nucleotide polymorphism (SNP) (A/G) was identified in the $5^{th}$ intron of the bovine FBP1 gene. Genotyping of 133 animals from four beef breeds revealed that the average frequency for allele A (A-base) was 0.7897 (0.7069-0.9107), while 0.2103 (0.0893-0.2931) for allele B (G-base). Our preliminary association study indicated that this SNP is significantly associated with traits of Average Daily Feed Intake (ADFI) and Carcass Length (CL) (p<0.01). In addition, the FBP1 gene was assigned on BTA8 by a hybrid radiation (RH) mapping method.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.6
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• pp.765-773
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• 2009

Sterol regulatory element binding factor 1 (SREBF1) and fatty acid synthase (FASN) genes play an important role in the biosynthesis of fatty acids and cholesterol, and in lipid metabolism. This study used polymorphisms in the intron 5 of bovine SREBF1 and in the thioesterase (TE) domain of FASN genes to evaluate their associations with beef fatty acid composition. A previously identified 84-bp indel (L: insertion/long type and S: deletion/short type) of the SREBF1 gene in Korean cattle had significant associations with the concentration of stearic (C18:0), linoleic (C18:2) and polyunsaturated fatty acids (PUFA). The stearic acid concentration was 6.30% lower in the SS than the LL genotype (p<0.05), but the linoleic and PUFA contents were 11.06% and 12.20% higher in SS compared to LL (p<0.05). Based on the sequence analysis, five single nucleotide polymorphisms (SNPs) g.17924G>A, g.18043C>T, g.18440G>A, g.18529G>A and g.18663C>T in the TE domain of the FASN gene were identified among the different cattle breeds studied. Among these, only g.17924 G>A and g.18663C>T SNPs were segregating in the Hanwoo population. The g.17924G>A SNP is a non-synonymous mutation (thr2264ala) and was significantly associated with the contents of palmitic (C16:0) and oleic acid (C18:1). The oleic acid concentration was 3.18% and 2.79% higher in Hanwoo with the GG genotype than the AA and AG genotypes, respectively (p<0.05), whereas the GG genotype had 3.8% and 4.01% lower palmitic acid than in those cattle with genotype AA and AG, respectively (p<0.05). Tissue expression data showed that SREBFI and FASN genes were expressed in a variety of tissues though they were expressed preferentially in different muscle tissues. In conclusion, the 84-bp indel of SREBF1 and g.17924G>A SNP of the FASN gene can be used as DNA markers to select Hanwoo breeding stock for fatty acid composition.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.5
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• pp.770-777
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• 2020

Objective: This study was conducted to determine early hereditary endowment to establish a short-term feeding program. Methods: Hanwoo steers (n = 140) were equally distributed into four groups (35/group) based on genetic meat yield index (MYI) viz. the greatest, great, low, and the lowest at Jukam Hanwoo farm, Goheung. All animals were fed in group pens (5 animals/pen) with similar feed depending on the growth stage. Rice straw was provided ad libitum, whereas concentrate was fed at 5.71 kg during the growing period (6 to 13 mo) and 9.4 kg during the fattening period (13 to 28 mo). Body weight (BW) was measured at two-month intervals, whereas carcass weight was determined at slaughtering at about 31 months of age. The Affymetrix Bovine Axiom Array 640K single nucleotide polymorphism (SNP) chip was used to determine the meat quantity-related gene in the blood. Results: After 6 months, the highest (p<0.05) BW was observed in the greatest MYI group (190.77 kg) and the lowest (p<0.05) in the lowest MYI group (173.51 kg). The great MYI group also showed significantly (p<0.05) higher BW than the lowest MYI group. After 16 and 24 months, the greatest MYI group had the highest BW gain (p<0.05) and were therefore slaughtered the earliest. Carcass weight was significantly (p<0.05) higher in the greatest and the great MYI groups followed by the low and the lowest MYI groups. Back-fat thickness in the greatest MYI group was highly correlated to carcass weight and marbling score. The SNP array analysis identified the carcass-weight related gene BTB-01280026 with an additive effect. The steers with the allele increasing carcass weight had heavier slaughter weight of about 12 kg. Conclusion: Genetic MYI is a potential tool for calf selection, which will reduce the slaughter age while simultaneously increasing carcass weight, back-fat thickness, and marbling score.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.8
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• pp.4107-4111
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• 2016

Background: Oral cancers account for approximately 2% of all cancers diagnosed each year; however, the vast majority (80%) of the affected individuals are smokers whose risk of developing a lesion is five to nine times greater than that of non-smokers. Tobacco smoke contains numerous carcinogens that cause DNA damage, including oxidative lesions that are removed effectively by the base-excision repair (BER) pathway, in which poly (ADP-ribose) polymerase 1 (PARP-1), plays key roles. Genetic variations in the genes encoding DNA repair enzymes may alter their functions. Several studies reported mixed effects on the association between PARP-1 variants and the risk of cancer development. Till now no reported studies have investigated the association between PARP-1 variants and oral squamous cell carcinoma (OSCC) risk in an Indian population. Materials and Methods: In the present case control study 100 OSCC patients and 100 matched controls were genotyped using PARP1 single nucleotide peptides (SNP's) rs1136410 and rs3219090 using TaqMan assays. Results: The results indicated significantly higher risk with PARP1 rs1136410 minor allele "C" (OR=1.909; p=0.02942; CI, 1.060-3.439). SNP rs1136410 also showed significantly increased risk in patients with smoking habit at C/C genotype and at minor allele C. Conclusions: The PAPR-1 Ala762Val polymorphism may play a role in progression of OSCC. Larger studies with a greater number of samples are needed to verify these findings.

• BMB Reports
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• v.43 no.6
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• pp.445-449
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• 2010

Aspirin-intolerant asthma (AIA) is characterized by severe asthmatic attack after ingestion of aspirin and/or non-steroidal anti-inflammatory drugs. In this study, we investigated the relationship between Prostaglandin E2 receptor (PTGER) gene family polymorphisms and AIA in 243 AIA patients and 919 aspirin-tolerant asthma (ATA) controls of Korean ethnicity in two separate study cohorts. After genotyping 120 SNPs of the PTGER gene family for the $1^{st}$ cohort study, four SNPs in PTGER1, ten in PTGER3, six in PTGER3, and a haplotype of PTGER2 showed association signals with decreased or increased risk of AIA. Among the positively associated SNPs, one in PTGER1 and four in PTGER3 were analyzed in the $2^{nd}$ cohort study. The results show that rs7543182 and rs959 in PTGER3 retained their effect, although no statistical significance was retained in the $2^{nd}$ cohort study. Our findings provide further evidence that polymorphisms in PTGER3 might play a significant role in aspirin hypersensitivity among Korean asthmatics.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.4
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• pp.2093-2097
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• 2016

Background: HCV is a major global health problem. IL-27 is a member of the IL-6/IL-12 cytokine family with a broad range of anti-inflammatory properties. Recent studies highlighted the effect of a SNP in the IL-27 promoter region on modulating the progression of infectious diseases and individual responses to therapy. Aim of the work: The present study investigated the potential role of (-964 A/G) SNP in the promoter region of IL-27p28 gene (alleles rs153109) on the outcome of HCV infection among genotype 4a infected patients. Materials and Methods: HCV genotyping confirmed that all of the HCV-infected patients had genotype 4a infection. Genomic DNA was extracted from 111 patients with chronic HCV infection, 42 spontaneous resolvers (SR) and 16 healthy controls. IL- 27p28.rs153109 genotyping was assessed using PCR-RFLP then confirmed by DNA sequencing. Results: The frequency of IL-27-p28.rs153109AA, AG, and GG genotypes among chronically infected subjects were 74.8 %, 25.2%, and 0% while among the SR, they were 57.1%, 35.7%, and 7.14%, respectively. Our data show the unique presence of G/G genotype in the SR group (3 patients; 7.14%). Moreover, the "G" allele frequencies among chronic and resolved subjects were 12.6% and 25.0%, respectively (p=0.0136). Importantly, subjects with the GG genotype were more likely to clear their HCV infection than those with the AA genotype (p=0.0118). Conclusions: HCV genotype 4a subjects with the IL-27-p28.rs153109 A/G and G/G genotype were more likely to clear their HCV infection. Therefore, we propose IL- 27p28.rs153109SNPas a genetic biomarker for predicting HCV infection outcome.