• Asian-Australasian Journal of Animal Sciences
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• v.27 no.3
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• pp.303-309
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• 2014

The increasing importance of meat quality has implications for animal breeding programs. Research has revealed much about the genetic background of pigs, and many studies have revealed the importance of various genetic factors. Since meat quality is a complex trait which is affected by many factors, consideration of the overall phenotype is very useful to study meat quality. For integrating the phenotypes, we used principle component analysis (PCA). The significant SNPs refer to results of the GRAMMAR method against PC1, PC2 and PC3 of 14 meat quality traits of 181 Duroc pigs. The Genome-wide association study (GWAS) found 26 potential SNPs affecting various meat quality traits. The loci identified are located in or near 23 genes. The SNPs associated with meat quality are in or near five genes (ANK1, BMP6, SHH, PIP4K2A, and FOXN2) and have been reported previously. Twenty-five of the significant SNPs also located in meat quality-related QTL regions, these result supported the QTL effect indirectly. Each single gene typically affects multiple traits. Therefore, it is a useful approach to use integrated traits for the various traits at the same time. This innovative approach using integrated traits could be applied on other GWAS of complex-traits including meat-quality, and the results will contribute to improving meat-quality of pork.

• Genomics & Informatics
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• v.12 no.4
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• pp.231-235
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• 2014

Elevated serum uric acid levels are associated with a variety of adverse health outcomes, including gout, hypertension, diabetes mellitus, metabolic syndrome, and cardiovascular diseases. Several genome-wide association studies on uric acid levels have implicated the ATP-binding cassette, subfamily G, member 2 (ABCG2) gene as being possibly causal. We investigated an association between the single-nucleotide polymorphism (SNP) rs2725220 in the ABCG2 gene and uric acid levels in the Korean population. A total of 991 subjects in Seoul City were used for a replication study with ABCG2 SNP rs2725220. The rs2725220 SNP in the ABCG2 gene was associated with mean uric acid levels (effect per allele 0.25 mg/dL, p < 0.0001). Subjects with the GC/CC genotype had a 1.78-fold (range, 1.22- to 2.62-fold) higher risk of having abnormal uric acid levels (${\geq}7.0mg/dL$) than subjects with the GG genotype. When analyzed by gender, the association with ABCG2 was stronger in men than in women. The association with ABCG2 was much stronger in male subjects with body mass index (BMI) ${\geq}26.4$ (odds ratio, 5.09; 95% confidence interval, 2.41 to 10.8) than in male subjects with BMI < 26.4. This study clearly demonstrates that genetic variations in ABCG2 influence uric acid levels in Korean adults.

• Genomics & Informatics
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• v.7 no.4
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• pp.195-202
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• 2009

BIRC5 (Survivin) belongs to the inhibitor of apoptosis gene family. The BIRC5 protein inhibits caspases and consequently blocks apoptosis. Thus, BIRC5 contributes to the progression of cancer allowing for continued cell proliferation and survival. In this study, we identified eight sequence variants of BIRC5 through direct DNA sequencing. Among the eight single nucleotide polymorphisms (SNPs), six common variants with frequencies higher than 0.05 were selected for larger-scale genotyping (n=1,066). Results of the study did not show any association between the promoter region polymorphisms and the clearance of hepatitis B virus (HBV) infection and hepatocellular carcinoma (HCC) occurrence. This is in line with a previous study in which polymorphisms in the promoter region does not influence the function of BIRC5. Initially, we were able to detect a signal with the ＋9194A>G, which disappeared after multiple corrections but led to a change in amino acid. Similarly, we were also able to detect an association signal between two haplotypes (haplotype-2 and haplotype-5) on the onset age of HCC and/or HCC occurrence, but the signals also disappeared after multiple corrections. As a result, we concluded that there was no association between BIRC5 polymorphisms and the clearance HBV infection and/or HCC occurrence. However, our results might useful to future studies.

• Journal of Animal Science and Technology
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• v.65 no.6
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• pp.1194-1204
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• 2023

Meat quality comprises a set of key traits such as pH, meat color, water-holding capacity, tenderness and marbling. These traits are complex because they are affected by multiple genetic and environmental factors. The aim of this study was to investigate the molecular genetic basis underlying nine meat quality-related traits in a Yorkshire pig population using a genome-wide association study (GWAS) and subsequent biological pathway analysis. In total, 45,926 single nucleotide polymorphism (SNP) markers from 543 pigs were selected for the GWAS after quality control. Data were analyzed using a genome-wide efficient mixed model association (GEMMA) method. This linear mixed model-based approach identified two quantitative trait loci (QTLs) for meat color (b^*) on chromosome 2 (SSC2) and one QTL for shear force on chromosome 8 (SSC8). These QTLs acted additively on the two phenotypes and explained 3.92%-4.57% of the phenotypic variance of the traits of interest. The genes encoding HAUS8 on SSC2 and an lncRNA on SSC8 were identified as positional candidate genes for these QTLs. The results of the biological pathway analysis revealed that positional candidate genes for meat color (b^*) were enriched in pathways related to muscle development, muscle growth, intramuscular adipocyte differentiation, and lipid accumulation in muscle, whereas positional candidate genes for shear force were overrepresented in pathways related to cell growth, cell differentiation, and fatty acids synthesis. Further verification of these identified SNPs and genes in other independent populations could provide valuable information for understanding the variations in pork quality-related traits.

• Toxicological Research
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• v.22 no.2
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• pp.69-74
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• 2006

Hypertension leads to major health problems in many industrialized countries, and multiple etiologic factors are involved in the pathogenesis of this disorder. The genetic components of the natriuretic peptide system might be involved in the pathogenesis of hypertension. In this regard, the atrial natriuretic peptide (ANP) gene has been proposed as a candidate hypertension gene. Therefore, we investigated the G1837A and C-664G polymorphisms of the ANP gene in 143 Korean normotensives and 118 hypertensives. There were no significant differences in the genotype and allele frequencies between the two groups. Although the frequencies in each of these polymorph isms were not significantly different between normotensives and hypertensives, our results provide additional ethnic information for linkage analysis and associated studies of this disorder with cardiovascular disease.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.10
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• pp.1478-1484
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• 2007

To determine the origin and genetic diversity of Red Chittagong (RC) cattle in Bangladesh, we analyzed mitochondrial DNA displacement loop (D-loop) sequences of 48 samples along with 22 previously published sequences from Bos indicus and Bos taurus breeds. Twenty five haplotypes were identified in RC cattle that were defined by 44 polymorphic sites and nucleotide diversity was $0.0055{\pm}0.0026$. The estimated sequence divergence times between RC and other zebu cattle breeds studied ranged between 22,700-26,900 years before present (YBP) which, it is suggested, predate domestication of RC cattle. Furthermore, it is assumed that introgressions have occurred in this breed mainly from Indian zebu breeds in the recent millennia. The phylogenetic studies showed RC cattle clustered with Bos indicus lineage with two distinct haplogroups representing high genetic variability of this breed. These findings can be used for designing proper breeding and conservation strategies for RC cattle in Bangladesh.

• Journal of Electrodiagnosis and Neuromuscular Diseases
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• v.20 no.2
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• pp.148-152
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• 2018

Myotonic dystrophy type 1 (DM1) is an autosomal dominant multisystem disorder and one of the most common muscular dystrophies affecting adults. Charcot-Marie-Tooth (CMT) disease, a common hereditary neuropathy, is characterized by atrophy of the distal limbs and peripheral nerve abnormalities. The authors report a rare case involving a 24-year-old female who was diagnosed simultaneously with both DM1 and CMT1A based on the results of a nerve conduction study (NCS). The patient, who had previously been diagnosed with DM1, was admitted for lower extremity pain. Her electrodiagnostic examination continued to reveal severe sensorimotor demyelinating polyneuropathy, and a genetic study was performed to confirm whether she had other hereditary neuropathies, except DM1, that suggested CMT1A, the most common phenotype of CMT. Severe abnormalities in an NCS in a DM1 patient may suggest the incidental coexistence of hereditary neuropathies, and further evaluations, such as genetic studies, should be performed for proper diagnosis.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.8
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• pp.3705-3713
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• 2014

E-Cadherin (CDH1) genetic variations may be involved in invasion and metastasis of various cancers by altering gene transcriptional activity of epithelial cells. However, published studies on the association of CDH1 gene polymorphisms and cancer risk remain contradictory, owing to differences in living habits and genetic backgrounds. To derive a more better and comprehensive conclusion, the present meta-analysis was performed including 57 eligible studies of the association between polymorphisms of CDH1 gene promoter -160 C>A, -347 G>GA and 3'-UTR +54 C>T and cancer risk. Results showed that these three polymorphisms of CDH1 were significantly associated with cancer risk. For -160 C>A polymorphism, -160A allele carriers (CA and CA+AA) had an increased risk of cancer compared with the homozygotes (CC), and the similar result was discovered for the -160A allele in the overall analyses. In the subgroup analyses, obvious elevated risk was found with -160A allele carriers (AA, CA, CA+AA and A allele) for prostate cancer, while a decreased colorectal cancer risk was shown with the AA genotype. For the -347 G>GA polymorphism, the GAGA genotype was associated with increased cancer risk in the overall analysis with homozygous and recessive models. In addition, results of subgroup analysis indicated that the elevated risks were observed in colorectal cancer and Asian descendants. For +54 C>T polymorphism, a decreased risk of cancer was found in heterozygous, dominant and allele models. Moreover, +54T allele carriers (CT, CT+TT genotype and T allele) showed a potential protective factor in gastric cancer and Asian descendants.

• Genomics & Informatics
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• v.12 no.4
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• pp.165-170
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• 2014

Genome-wide association (GWA) studies have found many important genetic variants that affect various traits. Since these studies are useful to investigate untyped but causal variants using linkage disequilibrium (LD), it would be useful to explore the haplotypes of single-nucleotide polymorphisms (SNPs) within the same LD block of significant associations based on high-density variants from population references. Here, we tried to make a haplotype catalog affecting body mass index (BMI) through an integrative analysis of previously published whole-genome next-generation sequencing (NGS) data of 7 representative Korean individuals and previously known Korean GWA signals. We selected 435 SNPs that were significantly associated with BMI from the GWA analysis and searched 53 LD ranges nearby those SNPs. With the NGS data, the haplotypes were phased within the LDs. A total of 44 possible haplotype blocks for Korean BMI were cataloged. Although the current result constitutes little data, this study provides new insights that may help to identify important haplotypes for traits and low variants nearby significant SNPs. Furthermore, we can build a more comprehensive catalog as a larger dataset becomes available.

• Journal of Preventive Medicine and Public Health
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• v.42 no.6
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• pp.356-359
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• 2009

In the more than 100 genome wide association studies (GWAS) conducted in the past 5 years, more than 250 genetic loci contributing to more than 40 common diseases and traits have been identified. Whilst many genes have been linked to a trait, both their individual and combined effects are small and unable to explain earlier estimates of heritability. Given the rapid changes in disease incidence that cannot be accounted for by changes in diagnostic practises, there is need to have well characterized exposure information in addition to genomic data for the study of gene-environment interactions. The case-control and cohort study designs are most suited for studying associations between risk factors and occurrence of an outcome. However, the case control study design is subject to several biases and hence the preferred choice of the prospective cohort study design in investigating geneenvironment interactions. A major limitation of utilising the prospective cohort study design is the long duration of follow-up of participants to accumulate adequate outcome data. The GWAS paradigm is a timely reminder for traditional epidemiologists who often perform one- or few-at-a-time hypothesis-testing studies with the main hallmarks of GWAS being the agnostic approach and the massive dataset derived through large-scale international collaborations.