• 농업과학연구
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• 제45권4호
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• pp.707-713
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• 2018

This study was done to search for positional candidate genes associated with the back fat thickness trait using a Genome-Wide Association Study (GWAS) in purebred Yorkshires (N = 1755). Genotype and phenotype analyses were done for 1,642 samples. As a result of the associations with back fat thickness using the Gemma program (ver. 0.93), when the genome-wide suggestive threshold was determined using the Bonferroni method ($p=1.61{\times}10^{-5}$), the single nucleotide polymorphism (SNP) markers with suggestive significance were identified in 1 SNP marker on chromosome 2 (MARC0053928; $p=3.65{\times}10^{-6}$), 2 SNP markers on chromosome 14 (ALGA0083078; $p=7.85{\times}10^{-6}$, INRA0048453; $p=1.27{\times}10^{-5}$), and 1 SNP marker on chromosome 18 (ALGA0120564; $p=1.44{\times}10^{-5}$). We could select positional candidate genes (KCNQ1, DOCK1, LOC106506151, and LOC110257583), located close to the SNP markers. Among these, we identified a potassium voltage-gated channel subfamily Q member gene (KCNQ1) and the dedicator of cytokinesis 1 (DOCK1) gene associated with obesity and Type-2 diabetes. The SNPs and haplotypes of the KCNQ1 and DOCK1 genes can contribute to understanding the genetic structure of back fat thickness. Additionally, it may provide basic data regarding marker assisted selection for a meat quality trait in pigs.

• Clinical and Experimental Reproductive Medicine
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• 제32권3호
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• pp.279-286
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• 2005

Objective: Although several genetic factors have been associated with defects in human spermatogenesis, the unambiguous causative genes have not been elucidated. The male infertility by haploinsufficiency of PRM1 or PRM2 has been reported in mouse model. The aim of this study was to identify the single nucleotide polymorphisms (SNPs) of PRM1 and PRM2, related to the genotype of Korean infertile men. Methods: Genomic DNAs were extracted from peripheral bloods of infertile men with oligozoospermia or azoospermia, and analyzed using polymerase chain reaction (PCR) and direct sequencing. We carried out the direct sequencing analysis of amplified fragments in PRM1 (557 nucleotides from -42 to 515) and PRM2 (599 nucleotides from 49 to 648) genes, respectively. Results: Three SNPs of coding region in the PRM1 gene was found in the analysis of 130 infertile men. However, the SNPs at a133g (aa 96.9%, ag 3.1% and gg 0.0%), c160a (cc 99.2%, ca 0.8% and aa 0.0%) and c321a (cc 56.9%, ca 35.4% and aa 7.7%) coded the same amino acids, in terms of silence phenotypes. On the other hand, as results of the PRM2 gene sequencing in 164 infertile men, only two SNPs, g398c (gg 62.2%, gc 31.1% and ga 6.7%) and a473c (aa 63.4%, ac 29.9% and cc 6.7%), were identified in the intron of the PRM2 gene. Conclusions: There was no mutation and significant SNPs on PRM1 and PRM2 gene in Korean infertile men. These results suggest that the PRM1 and PRM2 genes are highly conserved and essential for normal fertility of men.

• Asian-Australasian Journal of Animal Sciences
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• 제23권7호
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• pp.863-866
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• 2010

Myostatin, which is also known as growth and differentiation factor 8 (GDF8), has been reported to act as a negative regulator of skeletal muscle development. Variation in the myostatin gene (MSTN) has been associated with variation in muscularity in certain "meaty" sheep breeds. Polymerase Chain Reaction-Single Strand Conformational Polymorphism (PCR-SSCP) analysis was used to investigate allelic variation in the previously described g+6223G>A single-nucleotide polymorphism (SNP) in the 3' untranslated region (3' UTR) of MSTN. The sheep studied were 79 New Zealand (NZ) Romney lambs derived from a single sire heterozyous for g+6223G>A, which is in itself notable as this polymorphism has not been described previously in this breed. Allelic variation was observed to be associated with an abnormal gender ratio (p = 0.046) in the progeny. The presence of allele A was observed to have an effect (p<0.05) on birth weight, mean loin yield, proportion yield loin and total muscle yield. Allelic variation did not significantly affect mean shoulder yield, leg yield, proportion yield shoulder and proportion yield leg. This preliminary result suggests that while the A allele at MSTN g+6223 appears to improve some valuable traits in NZ Romney sheep, further research is required to understand if and how it may affect other traits.

• 대한임상검사과학회지
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• 제56권1호
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• pp.66-72
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• 2024

지질 대사장애는 임상에서 흔히 볼 수 있는 질환이다. 이상지질혈증(dyslipidemia)과 그 유병률은 전세계적으로 심혈관질환의 이환율 및 사망률과 밀접한 관련이 있다. 한국인 대상 40~64세 성인 중년층을 대상으로 ABO 유전자의 다형성과 이상지질혈증과의 연관성을 확인하기 위해 유전자 분석을 실시하였다. 본 연구는 한국인 유전체분석자료(Korean Association REsource, KARE)에서 총 6,750명의 피험자를 선정하였다. KARE 자료의 이상지질혈증 환자 4,403명과 정상 대조군 2,347명의 유전자형 데이터를 사용하여 ABO 유전자의 단일염기다형성(single nucleotide polymorphisms, SNPs)과 유전적 상관관계를 분석하였다. 그 결과 ABO 유전자 중 11개 SNPs 가 이상지질혈증과 통계적으로 유의미한 연관성을 나타내었다. 이 중 ABO 유전자의 rs8176707이 통계적으로 이상지질혈증과 가장 유의한 상관관계를 보였다(P-value=0.002, odds ratio=0.82, 95% confidence interval 0.78~0.86). ABO minor allele T는 이상지질혈증 위험을 감소시키는 것으로 나타났다. 본 연구는 ABO 유전자의 유전적 다형성과 이상지질혈증 사이의 유의미한 연관성을 밝힌 연구이다. 이러한 결과는 ABO의 SNPs가 이상지질혈증의 원인과 유전적 상관관계가 있음을 시사한다고 하겠다.

• Asian Pacific Journal of Cancer Prevention
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• 제16권18호
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• pp.8405-8410
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• 2016

Hepatitis B virus (HBV) infection is the leading cause of hepatocellular carcinoma (HCC) development. Recent studies demonstrated that single nucleotide polymorphisms (SNPs) rs2293152 in signal transducer and activator of transcription 3 (STAT3) and rs7574865 in signal transducer and activator of transcription 4 (STAT4) are associated with chronic hepatitis B (CHB)-related HCC in the Chinese population. We hypothesized that these polymorphisms might be related to HCC susceptibility in Thai population as well. Study subjects were divided into 3 groups consisting of CHB-related HCC (n=192), CHB without HCC (n=200) and healthy controls (n=190). The studied SNPs were genotyped using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The results showed that the distribution of different genotypes for both polymorphisms were in Hardy-Weinberg equilibrium (P>0.05). Our data demonstrated positive association of rs7574865 with HCC risk when compared to healthy controls under an additive model (GG versus TT: odds ratio (OR)=2.07, 95% confidence interval (CI)=1.06-4.03, P=0.033). This correlation remained significant under allelic and recessive models (OR=1.46, 95% CI=1.09-1.96, P=0.012 and OR=1.71, 95% CI=1.13-2.59, P=0.011, respectively). However, no significant association between rs2293152 and HCC development was observed. These data suggest that SNP rs7574865 in STAT4 might contribute to progression to HCC in the Thai population.

• 한국축산식품학회지
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• 제33권6호
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• pp.715-722
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• 2013

Heugu (Korea Black Cattle) is one of the indigenous cattle breeds in Korea; however there has been severe lack of genomic studies on the breed. In this study, we report the first whole genome resequencing of Heugu at higher sequence coverage using Illumina HiSeq 2000 platform. More than 153.6 Giga base pairs sequence was obtained, of which 97% of the reads were mapped to the bovine reference sequence assembly (UMD 3.1). The number of non-redundantly mapped sequence reads corresponds to approximately 28.9-fold coverage across the genome. From these data, we identified a total of over six million single nucleotide polymorphisms (SNPs), of which 29.4% were found to be novel using the single nucleotide polymorphism database build 137. Extensive annotation was performed on all the detected SNPs, showing that most of SNPs were located in intergenic regions (70.7%), which is well corresponded with previous studies. Of the total SNPs, we identified substantial numbers of non-synonymous SNPs (13,979) in 5,999 genes, which could potentially affect meat quality traits in cattle. These results provide genome-wide SNPs that can serve as useful genetic tools and as candidates in searches for phenotype-altering DNA difference implicated with meat quality traits in cattle. The importance of this study can be further pronounced with the first whole genome sequencing of the valuable local genetic resource to be used in further genomic comparison studies with diverse cattle breeds.

• Genomics & Informatics
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• 제7권2호
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• pp.57-64
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• 2009

Fibrinogen alpha chain (FGA), a subunit of fibrinogen, might be a potential player for type 2 diabetes mellitus (T2DM), since the plasma levels of fibrinogen is known to be related to the incidence of T2DM. To elucidate the potential role of FGA in T2DM, we investigated whether FGA genetic variations are relevant in T2DM in the Korean population. Seven FGA single nucleotide polymorphisms (SNPs) were genotyped in Ansung and Ansan cohorts (474 T2DM subjects and 470 normal controls) in Korea. The association between SNPs and T2DM was determined by logistic regression analysis. Genetic relevance of SNPs to T2DM-related phenotypes was investigated by multiple linear regression analysis. Statistical analysis revealed that among seven FGA SNPs, significant associations with T2DM were observed in FGA rs2070011 (p=0.013-0.034, OR=0.72${\sim}$0.79), rs6050 (p=0.026${\sim}$0.048, OR=1.24${\sim}$1.37), and rs2070022 (p=0.016${\sim}$0.039, OR=0.70${\sim}$0.72). Two SNPs, rs2070011 and rs6050, also showed significant association with T2DM-related phenotypes such as triglyceride (p=0.005${\sim}$0.011 for rs2070011 and p=0.003${\sim}$0.008 for rs6050), total cholesterol (p=0.01 for rs2070011 and p=0.024 for rs6050) and fasting glucose (p=0.035${\sim}$0.036 for rs2070011 and p=0.048 for rs6050) in 470 normal controls. Our association study implies that FGA might be an important genetic factor in T2DM pathogenesis in the Korean population by affecting plasma lipid and glucose levels.

• International Journal of Industrial Entomology and Biomaterials
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• 제45권1호
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• pp.29-34
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• 2022

Silkworms have recently attracted attention as healthy functional foods. Different varieties of silkworms have functional differences; thus, there is an emerging need for variety identification. In this study, we sequenced complete mitochondrial genomes (mitogenomes) of ten government-recommended silkworm varieties (BaekHwang, BaekOk, DaeBaek, DaeBak, DaeHwang, GoldenSilk, HanSaeng, JooHwang, KumKang, and KumOk). Comparison of these sequences allowed us to select the single nucleotide polymorphisms (SNPs) in 34 sites that are specific to six silkworm varieties: 13 in DaeBak, 8 in GoldenSilk, 9 in KumKang, 2 in BaekHwang, 1 in BaekOk, and 1 in DaeHwang. Among these each one SNP per variety was amplified by preparing variety-specific primers and then using tetra-primer amplification refractory mutation system PCR (T-ARMS-PCR). As a result, it was possible to identify these six varieties among the ten silkworm varieties, evidencing that SNPs developed from mitogenomes are useful marker for the discrimination of genetically closer silkworm varieties.

• Biomolecules & Therapeutics
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• 제16권2호
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• pp.77-81
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• 2008

The major aim of the Korean Pharmacogenomic Database (KPD) is to offer to users a "bridging" function, making the search for useful information easier. This database has also been established to collect unique Korean genotype data from other databases and to directly link these data to other major databases that offer more informative data. In this way, searches for information about new drug developments and easier and faster evaluation of the more complex and larger databases are possible. The KPD is located at the National Institute of Toxicological Research homepage (http://www.nitr.go.kr/nitr/contents/m134700/view.do), and offers Korean single-nucleotide polymorphism (SNP) information for 154 genes and haplotype information. It also compares the Korean SNP and haplotype frequencies with those of the other ethnic groups registered in the International HapMap. Through the Pharmacogenomic Information and Education facility, we also provide evaluators and the public with information about the concept of pharmacogenomic information, research trends, and the drug regulations of other countries. Because the drug responses of Koreans are not necessarily the same as those of Chinese or Japanese people, it is expected that the systematic operation of the KPD will allow the definition of racial differences and various genomic biomarkers (haplotypes or SNPs) for use in bridging studies and in the approval of new drugs.

• Asian-Australasian Journal of Animal Sciences
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• 제30권6호
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• pp.765-772
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• 2017

Objective: This study examines the genetic factors influencing the phenotypes (four economic traits:oleic acid [C18:1], monounsaturated fatty acids, carcass weight, and marbling score) of Hanwoo. Methods: To enhance the accuracy of the genetic analysis, the study proposes a new statistical model that excludes environmental factors. A statistically adjusted, analysis of covariance model of environmental and genetic factors was developed, and estimated environmental effects (covariate effects of age and effects of calving farms) were excluded from the model. Results: The accuracy was compared before and after adjustment. The accuracy of the best single nucleotide polymorphism (SNP) in C18:1 increased from 60.16% to 74.26%, and that of the two-factor interaction increased from 58.69% to 87.19%. Also, superior SNPs and SNP interactions were identified using the multifactor dimensionality reduction method in Table 1 to 4. Finally, high- and low-risk genotypes were compared based on their mean scores for each trait. Conclusion: The proposed method significantly improved the analysis accuracy and identified superior gene-gene interactions and genotypes for each of the four economic traits of Hanwoo.