• Asian-Australasian Journal of Animal Sciences
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• 제28권10호
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• pp.1394-1406
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• 2015

The AT motif-binding factor (ATBF1) not only interacts with protein inhibitor of activated signal transducer and activator of transcription 3 (STAT3) (PIAS3) to suppress STAT3 signaling regulating embryo early development and cell differentiation, but is required for early activation of the pituitary specific transcription factor 1 (Pit1) gene (also known as POU1F1) critically affecting mammalian growth and development. The goal of this study was to detect novel nucleotide variations and haplotypes structure of the ATBF1 gene, as well as to test their associations with growth-related traits in goats. Herein, a total of seven novel single nucleotide polymorphisms (SNPs) (SNP 1-7) within this gene were found in two well-known Chinese native goat breeds. Haplotypes structure analysis demonstrated that there were four haplotypes in Hainan black goat while seventeen haplotypes in Xinong Saanen dairy goat, and both breeds only shared one haplotype (hap1). Association testing revealed that the SNP2, SNP5, SNP6, and SNP7 loci were also found to significantly associate with growth-related traits in goats, respectively. Moreover, one diplotype in Xinong Saanen dairy goats significantly linked to growth related traits. These preliminary findings not only would extend the spectrum of genetic variations of the goat ATBF1 gene, but also would contribute to implementing marker-assisted selection in genetics and breeding in goats.

• Journal of Animal Science and Technology
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• 제52권5호
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• pp.357-366
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• 2010

한우의 유전체 전장의 정보를 Illumina BeadArray$^{TM}$ Bovine SNP50 assay를 이용하여 단일염기다형 현상을 조사한 결과, 유전적 다양성을 보이는 좌위가 약 32,567 좌위 이상에서 다양성을 보이고 있었으며 약 5,554 좌위에서 다양성이 조사되지 않았다. 이는 조사된 자료의 가계집단의 수가 크게 제한되었기 때문에 기인될 수 있으며 또 다른 원인으로는 한우 종축집단의 크기가 작을 수 있다는 현상을 반증한다고 사료된다. 유전분석의 기초가 되는 혈통기록에 의한 개체간 혈연관계를 유전체 정보에 의한 혈연관계와 비교하여 본 결과, 유전체 정보에 의한 혈연관계의 크기가 혈통기록에 의한 혈연관계보다 좀 더 정확하게 추정될 수 있다는 장점이 있으며 혈통기록상의 오류로 그릇된 혈연관계의 크기를 유전체 정보를 통하여 보완할 수 있다는 장점이 있다. 이러한 장점을 활용하면 유전체정보를 이용한 유전능력 평가의 정확성을 크게 향상시킬 수 있을 것으로 사료되었다.

• 대한임상검사과학회지
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• 제52권1호
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• pp.45-52
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• 2020

고혈압은 종종 심혈관 질환 및 신장 질환으로 이어지며 전 세계적으로 중요한 문제이다. 유전적으로 많은 단일 염기 다형성이 고혈압과 관련이 있다. 많은 GWAS 연구에서 ATP2B1 유전자가 혈압과 연관성이 높다는 것을 발견했다. 본 연구에서는 한국인 994명을 대상으로 수축기 혈압, 이완기 혈압과 ATP2B1 유전자의 SNP와 연관성을 분석하였다. 또한, BMI수치에 따라 하위그룹으로 계층화하여 차이가 있는지 확인하고자 하였다. 다중선형회귀분석에서 수축기 혈압 및 이완기 혈압과 가장 높은 통계적 유의성을 보인 SNP를 선정하였다. 수축기 혈압과 이완기 혈압에서의 one-way analysis of variance를 시행하였고, 고혈압 발생 위험에 대한 다중로지스틱회귀분석을 시행하였다. 다중로지스틱회귀분석은 연령 기준으로 구분하여 시행하였으며, 연령, BMI, 공복 시 혈당을 통제한 방법에서 비교하였다. 수축기 혈압에서는 4개의 SNP (rs10506974, rs7136259, rs17249754, rs17836882)가, 이완기 혈압에서는 6개의 SNP(rs10506974, rs10777237, rs7136259, rs17249754, rs1371075, rs10506983)가 유의하게 관련성을 보였다. 추가적으로, 유전자형(genotype)에 따른 분석에서는 남성에게서 고혈압 위험에 대한 유의한 odd ratio 값을 보였다. 본 연구는 ATP2B1 다형성이 수축기 혈압과 이완기 혈압에 영향을 미치는 것을 제안한다.

• Asian-Australasian Journal of Animal Sciences
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• 제28권7호
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• pp.936-942
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• 2015

The purpose of this study was to characterize genetic architecture of behavior patterns in Sapsaree dogs. The breed population (n=8,256) has been constructed since 1990 over 12 generations and managed at the Sapsaree Breeding Research Institute, Gyeongsan, Korea. Seven behavioral traits were investigated for 882 individuals. The traits were classified as a quantitative or a categorical group, and heritabilities ($h^2$) and variance components were estimated under the Animal model using ASREML 2.0 software program. In general, the $h^2$ estimates of the traits ranged between 0.00 and 0.16. Strong genetic ($r_G$) and phenotypic ($r_P$) correlations were observed between nerve stability, affability and adaptability, i.e. 0.9 to 0.94 and 0.46 to 0.68, respectively. To detect significant single nucleotide polymorphism (SNP) for the behavioral traits, a total of 134 and 60 samples were genotyped using the Illumina 22K CanineSNP20 and 170K CanineHD bead chips, respectively. Two datasets comprising 60 (Sap60) and 183 (Sap183) samples were analyzed, respectively, of which the latter was based on the SNPs that were embedded on both the 22K and 170K chips. To perform genome-wide association analysis, each SNP was considered with the residuals of each phenotype that were adjusted for sex and year of birth as fixed effects. A least squares based single marker regression analysis was followed by a stepwise regression procedure for the significant SNPs (p<0.01), to determine a best set of SNPs for each trait. A total of 41 SNPs were detected with the Sap183 samples for the behavior traits. The significant SNPs need to be verified using other samples, so as to be utilized to improve behavior traits via marker-assisted selection in the Sapsaree population.

• 대한한방내과학회지
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• 제31권4호
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• pp.752-762
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• 2010

Objective : In the present study, we investigated genetic distribution of eight single nucleotide polymorphisms of PON1 between Dampness and Phlegm and non Dampness and Phlegm pattern identification(PI) among Korean stroke patients. Materials and Methods : One hundred forty stroke subject without Dampness and Phlegm and fifty eight stroke subjects with Dampness and Phlegm were participated in this study. After informed consents, eight single nucleotide polymorphisms(SNPs) in PON1 of each subjects were identified by DNA sequencing and primer extension method and statistical analysis was performed to determine the significant difference between Dampness and Phlegm and non Dampness and Phlegm groups. Results : Among anthropometric characteristics and blood parameters, waist circumference and total cholesterol were significantly higher in Dampness and Phlegm. Among 8 SNPs of PON1, frequency of M allele and subjects with M allele in L55M SNP were significantly higher in Dampness and Phlegm group (p=0.0032 and p=0.0053, respectively) but subjects with T allele in C-2033T SNP were lower in Dampness and Phlegm group(p=0.0302). Effect of L55M and C-2033T on Dampness and Phlegm were 3.07% and 1.75%, respectively. Conclusion : Our results suggest that L55M SNP in exon and C-2033T in promoter region of PON1 maybe affect to Dampness and Phlegm pattern identification. However, further study should be carried out to find out the detailed mechanism how L55M and C-2033T can affect Dampness and Phlegm stroke patients.

• Asian-Australasian Journal of Animal Sciences
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• 제32권4호
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• pp.485-493
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• 2019

Objective: This study was undertaken to investigate the genetic characteristics of Berkshire (BS), Landrace (LR), and Yorkshire (YS) pig breeds raised in the Great Grandparents pig farms using the single nucleotide polymorphisms (SNP) information. Methods: A total of 25,921 common SNP genotype markers in three pig breeds were used to estimate the expected heterozygosity ($H_E$), polymorphism information content, F-statistics ($F_{ST}$), linkage disequilibrium (LD) and effective population size ($N_e$). Results: The chromosome-wise distribution of $F_{ST}$ in BS, LR, and YS populations were within the range of 0-0.36, and the average $F_{ST}$ value was estimated to be $0.07{\pm}0.06$. This result indicated some level of genetic segregation. An average LD ($r^2$) for the BS, LR, and YS breeds was estimated to be approximately 0.41. This study also found an average $N_e$ of 19.9 (BS), 31.4 (LR), and 34.1 (YS) over the last 5th generations. The effective population size for the BS, LR, and YS breeds decreased at a consistent rate from 50th to 10th generations ago. With a relatively faster $N_e$ decline rate in the past 10th generations, there exists possible evidence for intensive selection practices in pigs in the recent past. Conclusion: To develop customized chips for the genomic selection of various breeds, it is important to select and utilize SNP based on the genetic characteristics of each breed. Since the improvement efficiency of breed pigs increases sharply by the population size, it is important to increase test units for the improvement and it is desirable to establish the pig improvement network system to expand the unit of breed pig improvement through the genetic connection among breed pig farms.

• Asian Pacific Journal of Cancer Prevention
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• 제16권12호
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• pp.5025-5030
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• 2015

Immunoregulatory cytokines have an influence on hepatitis C virus (HCV) infection outcome. This study aimed to determine whether single nucleotide polymorphisms (SNP) in IFN- ${\gamma}$ and IL-10 genes are associated with susceptibility and/or are markers of prognosis regarding chronic hepatitis C outcomes. IFN ${\gamma}$ (+874T/A) and IL-10 (-1082G/A) genotypes were determined in 75 HCV genotype 4 patients with different disease severities (chronic hepatitis, n=25, liver cirrhosis and hepatocellular carcinoma (HCC) on top of liver cirrhosis, n=50) and 25 healthy participants using allele-specific polymerase chain reaction. No statistical differences in allele or genotype distributions of IFN ${\gamma}$ and IL-10 genes were detected between patients and controls or between patientgroups. No significant difference in the frequency of IL-10 SNP at position -1082 or IFN-${\gamma}$ at position +874T/A was found between chronic HCV genotype 4 and with progression of disease severity in liver cirrhosis or HCC. In conclusion; interferon-${\gamma}$ and interleukin-10 gene polymorphisms are not predictors of disease progression in patients with chronic hepatitis C (Genotype-4).

• Journal of Animal Science and Technology
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• 제53권6호
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• pp.511-516
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• 2011

Fas gene known to associate with intramuscular fat content in Korean cattle was selected for DNA marker development. Fas (APO-1, CD95), a member of the tumor necrosis factor (TNF) receptor superfamily, is a cell membrane protein that mediates apoptosis (programmed cell death). We discovered single nucleotide polymorphisms (SNPs) within Fas gene in order to develop novel DNA markers at genomic level. Of this gene to search for SNP, sequences of whole exon and 1kb range of both front and back of the gene using 24 cattle were determined by direct-sequencing methods. As a result, 16 SNPs in exon, 37 SNPs in intron and 2 SNPs in promoter region, a total of 55 SNPs were discovered. In these SNPs, thirty-one common polymorphic sites were selected considering their allele frequencies, haplotype-tagging status and Linkage Disequilibrium (LD) for genotyping in larger-scale subjects. Selected SNPs were confirmed genotype through SNaPshot method (n=274) and were examined for possible genetic association of Fas polymorphisms with carcass weight (CWT), eye muscle area (EMA), and backfat thickness (BF). So, the SNP have been identified significant g.-12T>G, g.1112T>G and g.32548T>C. These results suggest that polymorphism of Fas gene was associated with meat quality traits in Hanwoo.

• Asian-Australasian Journal of Animal Sciences
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• 제32권4호
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• pp.508-518
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• 2019

Objective: This research aimed to determine biological pathways and protein-protein interaction (PPI) networks for 305-d milk yield (MY), 305-d fat yield (FY), and age at first calving (AFC) in the Thai multibreed dairy population. Methods: Genotypic information contained 75,776 imputed and actual single nucleotide polymorphisms (SNP) from 2,661 animals. Single-step genomic best linear unbiased predictions were utilized to estimate SNP genetic variances for MY, FY, and AFC. Fixed effects included herd-year-season, breed regression and heterosis regression effects. Random effects were animal additive genetic and residual. Individual SNP explaining at least 0.001% of the genetic variance for each trait were used to identify nearby genes in the National Center for Biotechnology Information database. Pathway enrichment analysis was performed. The PPI of genes were identified and visualized of the PPI network. Results: Identified genes were involved in 16 enriched pathways related to MY, FY, and AFC. Most genes had two or more connections with other genes in the PPI network. Genes associated with MY, FY, and AFC based on the biological pathways and PPI were primarily involved in cellular processes. The percent of the genetic variance explained by genes in enriched pathways (303) was 2.63% for MY, 2.59% for FY, and 2.49% for AFC. Genes in the PPI network (265) explained 2.28% of the genetic variance for MY, 2.26% for FY, and 2.12% for AFC. Conclusion: These sets of SNP associated with genes in the set enriched pathways and the PPI network could be used as genomic selection targets in the Thai multibreed dairy population. This study should be continued both in this and other populations subject to a variety of environmental conditions because predicted SNP values will likely differ across populations subject to different environmental conditions and changes over time.

• Tuberculosis and Respiratory Diseases
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• 제62권5호
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• pp.406-416
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• 2007

연구배경: 단일염기다형성(Single nucleotide polymorphism, SNP)은 인간의 유전자 서열 1000염기에 1개 빈도로 발견되어 인간은 대략 300만개의 유전자 다형성을 가지고 있다. 이 유전자 다형성의 조합결과로 인간의 개체 간 특성들이 결정되는 것으로 이해되고 있다. 이러한 다형성들의 조합양상에 따라 특이 질환에 대한 유전자 감수성 또한 달라지게 되므로 최근에는 많은 질환들과 유전자 다형성들과의 상관관계를 보는 연구들도 활발하게 진행되고 있다. 이러한 SNP분석은 큰 집단을 대상으로 진행되어 지므로 적은 비용으로 정확하게 그리고 대용량으로 분석할 수 있는 방법이 필요하다. 방 법: 대상 환자 89명의 genomic DNA를 가지고서 promotor상에 위치한 -37과 -524 염기부위에서 유전자 다형성을 보이는 것으로 보고되어져 있는 RRM1(ribonucleotide reductase M1) 유전자를 대상으로 PCR-RFLP(polymerase chain reaction-restriction fragment length polymorphism)와 real-time PCR(RTPCR, TaqMan probe assay)을 동시에 시행한 후 각각의 결과를 비교 분석하였다. 결 과: 대상 DNA 89예 중 -37에서는 2예(2.17%), -524에서는 15예(16.26%)가 서로 다른 양상을 보였다. 결과 차이를 보인 샘플 17예를 대상으로 직접 염기서열 분석을 시행하여 본 결과, 17예 모두 RT-PCR에서 확인되었던 결과와 일치함을 확인할 수 있었다. 추가 샘플 138예를 대상으로 RT-PCR을 2회 연속 실행하여 genotyping을 해 본 결과 98%이상의 높은 일치율을 보였으며, 그중 10예를 무작위로 골라 직접 염기서열 분석을 시행하여 본 결과, 역시 100%일치, 높은 정확도를 보였고 이는 in-tube assay 방식으로 샘플의 오염을 최소화 할 수 있었으며 72 well based system(Corbett Research)을 이용함으로 1회 유전자 증폭반응을 통해 많은 검체를 한 번에 확인할 수 있어 매우 빠른 검사방법 이었다. 결 론: 큰 집단을 대상으로 다량의 SNP를 분석하기 위한 실험 방법으로는 RT-PCR이 신속하면서도 정확한 결과를 얻을 수 있는 방법으로 사료된다.