• Clinical and Experimental Pediatrics
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• 제55권10호
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• pp.388-392
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• 2012

Purpose: Single-nucleotide polymorphism (SNP) markers within LIN28B have been reported to be related to the timing of pubertal growth. However, no study has investigated the frequency of genetic markers in girls with precocious puberty (PP) or early puberty (EP). This study aimed to determine the frequency of putative genetic markers in girls with PP or EP. Methods: Genomic DNAs were obtained from 77 and 109 girls that fulfilled the criteria for PP and EP, respectively. The controls in this study were 144 healthy volunteers between 20 and 30 years of age. The haplotypes were reconstructed using 11 SNPs of LIN28B, and haplotype association analysis was performed. The haplotype frequencies were compared. Differences in the clinical and laboratory parameters were analyzed according to the haplotype dosage. Results: Eleven SNPs in LIN28B were all located in a block that was in linkage disequilibrium. The haplotype could be reconstructed using 2 representative SNPs, rs4946651 and rs369065. The AC haplotype was less frequently observed in the PP group than in the controls (0.069 vs. 0.144, P=0.010). The trend that girls with non-AC haplotypes tended to have earlier puberty onset (P=0.037) was illustrated even in the EP+PP patient group by Kaplan-Meier analysis. Conclusion: The results of the present study showed that non-AC haplotypes of LIN28B had a significant association with PP in girls.

• Journal of the Korean Data and Information Science Society
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• 제26권6호
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• pp.1249-1258
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• 2015

젖소의 유생산 형질에 가장 큰 영향을 미치는 유전자들 중 하나로 알려진 DGAT1 유전자의 효과를 국내 젖소 종축의 고밀도 유전체 정보를 이용하여 검증하기 위하여 본 연구를 수행하였다. 국내 젖소 씨수소로 구성된 353두의 고밀도 유전체 정보, 혈통, 추정 육종가 및 신뢰도 정보를 수집하였으며, 단일염기다형성 효과를 추정하기 위한 종속변량으로 가장 정확한 유전체 육종가를 예측할 수 있는 DeRegressed EBV를 산출하여 분석에 이용하였다. BovineSNP50 v2 패널을 이용하여 구명한 고밀도 유전자형 정보 중 유효성검증 과정을 통하여 41,051개 SNP을 선정하였으며, 각 단일 염기다형성의 실제적 유전체 육종가 기여도를 확인하기 위하여 유전체 선발방법 중 하나인 베이즈B (pi=0.99) 방법을 이용하여 SNP 효과를 추정하였다. 1메가 베이스페어의 구간으로 구성된 유전체 전장의 2,516개 윈도우 별 유전분산 설명력을 계산한 결과 상위 1, 3 윈도우가 DGAT1유전자 주변에서 발견되었으며, 이 두 윈도우의 유전분산 설명력은 각각 0.51% 및 0.48%인 것으로 나타났다. DGAT1유전자는 유전체 선발에 상업적으로 이용되는 50k SNP chip에 포함되어있지 않기 때문에 직접적인 유전자의 효과가 명확하게 드러나지는 않지만 DGAT1 유전자에 인접한 단일염기다형성들간의 연관불평형에 의하여 주변 윈도우에서 가장 높은 유전분산 설명력을 보이는 것으로 사료된다.

• Genomics & Informatics
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• 제6권3호
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• pp.99-109
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• 2008

Protein phosphorylation at tyrosine residues is a key regulatory event that modulates insulin signal transduction. We studied the PTPN1 gene with regard to susceptibility to Korean type 2 diabetes mellitus (T2DM) and its related quantitative traits. A total of seven SNPs [g.36171G>A (rs941798), g.58166G>A (rs3787343), g.58208A>G (rs2909270), g.64840C>T (rs754118), g.69560C>G (rs6020612), g.69866G>A (rs718050), and g.69934T>G (rs3787343)] were selected based on frequency (>0.05), linkage disequilibrium (LD) status, and haplotype tagging status. We studied the seven SNPs in 483 unrelated patients with type 2 diabetes (age: $64{\pm}2.8$ years, onset age: $56{\pm}8.1$ years; 206 men, 277 women) and 1138 nondiabetic control subjects (age: $64{\pm}2.9$; 516 men, 622 women). The SNP rs941798 had protective effects against T2DM with an odds ratio of 0.726 (C.I. $0.541{\sim}0.975$) and p-value=0.034, but none of the remaining six SNPs was associated with T2DM. Also, rs941798 was associated with blood pressure, HDL cholesterol, insulin sensitivity. rs941798 also has been associated with T2DM in previous reports of Caucasian-American and Hispanic-American populations. This is the first report that shows an association between PTPN1 and T2DM in the Korean as well as Asian population.

• Journal of Animal Science and Technology
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• 제47권1호
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• pp.1-10
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• 2005

Intramuscular fat content(lMF) is considered as one of major economic traits in the pig breeding and industry. In general, high IMF results in better meat quality. Several approaches to detect quantitative trait 10ci( QTL) for IMF indicated a strong possibility of the existence of a QTL related to IMF between the microsatellite marker SW71 and SW1881 on SSC6q. Porcine FABP3 has been considered as a candidate gene affecting IMF due to its physiological roles and position on the pig genome. Two novel mutations, g.-114T> C and g.-158T>G were detected by duplicate sequencing of the porcine FABP3 promoter region. These two mutations were identified as absolute linkage disequilibrium. The g.-158T> G mutation was used for investigating relationships with growth and fat deposition traits. The GG genotype of the g.-158T> G polymorphism showed highly negative effects(P< 0.01) on body weights at 3 and 12 weeks of age, and a positive effect(P< 0.05) on IMF. However, backfat thickness(BF) and carcass fat(CF) content were not significantly associated with the genotype. The result indicates that the novel mutations, identified in this study, could be utilized as possible genetic markers to improve IMF, independent with BF.

• Asian-Australasian Journal of Animal Sciences
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• 제32권12호
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• pp.1801-1808
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• 2019

Objective: As an iconic symbol of Qinghai-Tibetan Plateau and of high altitude, yak are subjected to hypoxic conditions that challenge aerobic metabolism. Matrix metalloproteinases-3 (MMP3) is assumed to be a key target gene of hypoxia-inducible factor-$1{\alpha}$ that function as a master regulator of the cellular response to hypoxia. Therefore, the aim of this investigation was to identify the DNA polymorphism of MMP3 gene in domestic yak and to explore its possible association with high-altitude adaptation. Methods: The single-nucleotide polymorphisms (SNPs) genotyping and mutations scanning at the MMP3 locus were conducted in total of 344 individuals from four domestic Chinese yak breeds resident at different altitudes on the Qinghai-Tibetan Plateau, using high-resolution melting analysis and DNA sequencing techniques. Results: The novel of SNPs rs2381 $A{\rightarrow}G$ and rs4331 $C{\rightarrow}G$ were identified in intron V and intron VII of MMP3, respectively. Frequencies of the GG genotype and the G allele of SNP rs2381 $A{\rightarrow}G$ observed in high-altitude Pali yak were significantly higher than that of the other yak breeds resident at middle or low altitude (p<0.01). No significant difference was mapped for SNP rs4331 $C{\rightarrow}G$ in the yak population (p>0.05). Haplotype GC was the dominant among the 4 yak breeds, and Pearson correlation analysis showed that the frequencies of GC was significantly lower in Ganan (GN), Datong (DT), and Tianzhu white yaks (TZ) compared with Pali (PL) yak. The two SNPs were in moderate linkage disequilibrium in high-altitude yaks (PL) but not in middle-altitude (GN, DT) and low-altitude (TZ) yaks. Conclusion: These results indicate that MMP3 may have been subjected to positive selection in yak, especially that the SNP rs2381 $A{\rightarrow}G$ mutation and GC haplotypes might contribute to adaptation for yak in high-altitude environments.

• Genes and Genomics
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• 제40권11호
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• pp.1249-1258
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• 2018

The Jeju horse is an indigenous Korean horse breed that is currently registered with the Food and Agriculture Organization of the United Nations. However, there is severe lack of genomic studies on Jeju horse. This study was conducted to investigate genetic characteristics of horses including Jeju horse, Thoroughbred and Jeju crossbred (Jeju${\times}$Thoroughbred) populations. We compared the genomes of three horse populations using the Equine SNP70 Beadchip array. Short-range Linkage disequilibrium was the highest in Thoroughbred, whereas $r^2$ values were lowest in Jeju horse. Expected heterozygosity was the highest in Jeju crossbred (0.351), followed by the Thoroughbred (0.337) and Jeju horse (0.311). The level of inbreeding was slightly higher in Thoroughbred (-0.009) than in Jeju crossbred (-0.035) and Jeju horse (-0.038). $F_{ST}$ value was the highest between Jeju horse and Thoroughbred (0.113), whereas Jeju crossbred and Thoroughbred showed the lowest value (0.031). The genetic relationship was further assessed by principal component analysis, suggesting that Jeju crossbred is more genetically similar to Thoroughbred than Jeju horse population. Additionally, we detected potential selection signatures, for example, in loci located on LCORL/NCAPG and PROP1 genes that are known to influence body. Genome-wide analyses of the three horse populations showed that all the breeds had somewhat a low level of inbreeding within each population. In the population structure analysis, we found that Jeju crossbred was genetically closer to Thoroughbred than Jeju horse. Furthermore, we identified several signatures of selection which might be associated with traits of interest. To our current knowledge, this study is the first genomic research, analyzing genetic relationships of Jeju horse, Thoroughbred and Jeju crossbred.

• Animal Bioscience
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• 제35권9호
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• pp.1340-1350
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• 2022

Objective: Luxi Black Head sheep (LBH) is the first crossbreed specialized for meat production and was developed by crossbreeding Black Head Dorper sheep (DP) and Small Tailed Han sheep (STH) in the farming areas of northern China. Research on the genomic variations and selection signatures of LBH caused by continuous artificial selection is of great significance for identifying the genetic mechanisms of important traits of sheep and for the continuous breeding of LBH. Methods: We explored the genetic relationships of LBH, DP, and several Mongolian sheep breeds by constructing phylogenetic tree, principal component analysis and linkage disequilibrium analysis. In addition, we analysed 29 whole genomes of sheep. The genome-wide selection signatures have been scanned with four methods: heterozygosity (H_P), fixation index (F_ST), cross-population extended haplotype homozygosity (XP-EHH) and the nucleotide diversity (𝜃_π) ratio. Results: The genetic relationships analysis showed that LBH appeared to be an independent cluster closer to DP. The candidate signatures of positive selection in sheep genome revealed candidate genes for developmental process (HoxA gene cluster, BCL2L11, TSHR), immunity (CXCL6, CXCL1, SKAP2, PTK6, MST1R), growth (PDGFD, FGF18, SRF, SOCS2), and reproduction (BCAS3, TRIM24, ASTL, FNDC3A). Moreover, two signalling pathways closely related to reproduction, the thyroid hormone signalling pathway and the oxytocin signalling pathway, were detected. Conclusion: The selective sweep analysis of LBH genome revealed candidate genes and signalling pathways associated with developmental process, immunity, growth, and reproduction. Our findings provide a valuable resource for sheep breeding and insight into the mechanisms of artificial selection.

• Tuberculosis and Respiratory Diseases
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• 제44권3호
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• pp.534-546
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• 1997

연구배경 : p53 및 망막모세포 암종(Rb) 항암 유전자는 인체의 여러 임종의 발암 과정에 관련되는 것으로 잘 알려져 있다. 또한 최근에 p53 등의 유전자 다형성이 암 발생에 관여하는 것으로 보고되고 있다. 그러나 Rb 유전자 다형성이 폐암 발생에 영향을 주는지는 아직 보고된 바가 없어 이들 유전자의 다형성의 반도 및 흡연 관련 폐암과 이들 유전자의 다형성과의 관계를 알아보고자 했다. 방 법 : 한국인 폐암 환자 발생의 유전적 감수성을 결정하기 위하여 128명의 폐암 환자군과 145명의 대조군에 대한 p53 유전자(exon 4 및 intron 6 부위) 및 망막모세포 암종(retinoblastoma, Rb) 유전자(intron 17 부위)의 다형성을 분석하였다. p53 유전자의 16bp 반복 다형성을 제외한 유전자 분석은 중합효소연쇄반응-제한효소절편길이 다형현상(PCR-RFLPs)을 이용하였으며, 16bp 반복 다형성은 중합효소연쇄 반응 후 전기영동으로 직접 분석하였다. 결 과 : p53 유전자의 exon 4/AccII 다형성 : 대조군 및 환자군에 대한분석에서 다형적인 3가지 유전자형(Arg/Arg, Arg/Pro, Pro/Pro)이 관찰되었으며, Arg과 Pro 유전자 빈도는 각각 0.66, 0.34 였다. 폐암 환자군에서는 대조군에 비해 Arg/Pro 유전자형은 높고, Pro/Pro 유전자형은 낮게 관찰되었으나 통계적으로 유의하지는 않았다. 조직학적으로 소세포 폐암의 경우 유전자형의 분포가 대조군과 유의한 차이를 보였다. p53 유전자의 intron 3/16bp 중복 다형성 : 대조군과 환자군에서 156bp 동형 접합체와 156bp와 172bp의 이형 접합체만이 관찰되었으며, 172bp 동형 접합체는 관찰되지 않았다. 156bp와 172bp 대립인자 각각 0.98, 0.02로 172bp 대립인자의 빈도가 아주 낮았다. 전반적으로 폐암 환자군과 대조군간의 유전자형 분포에는 유의한 차이가 없었다. p53 유전자의 intron 6/MspI 다형성 : Intron 3의 16bp 중복 다형성과 완전 연관 관계에 있었으며, m1 동형접합체와 m1/m2 이형접합체만 관찰 되었다. 16bp 중복 다형성에서와 같이 m1, m2의 유전인자의 빈도는 각각 0.98, 0.02 으로 MspI 절단부위가 없는 m2 대립인자의 빈도가 아주 낮았다. 전반적으로 폐암환자군과 대조군간의 유전자형 분포에는 유의한 차이가 없었다. Rb 유전자의 intron 17/XbaI 다형성 세가지 다형적인 유전자형(r1/r1, r1/r2, r2/r2)이 관찰 되었으며, 대조군에서 r1, r2의 유전자 빈도는 각각 0.50, 0.50 이었다. 유전자형의 분포가 조직학적으로 흡연관련 폐암군(Kreyberg type I)과 대조군 또는 폐 선암종군 사이에는 통계적으로 유의한 차이를 보였다(p < 0.05). Kreyberg type I군에서는 폐 선암종군에 비해 동행접합체(r2/r2 또는 r1/r1) 빈도가 높고 이형접합체(r1/r2) 빈도는 유의하게 낮은 반면, 선암군에서는 이형접합체 빈도가 73.4%로 특징적으로 높았다. 또한 고흡연자군에서의 유전자형의 비흡연자를 포함한 저흡연자군의 유전자형 분포와 유의한 차이를 보였으며(p = 0.0258), 이형접합체의 빈도가 유의하게 낮게 검출되었다. 따라서 Rb 유전자의 유전자형이 이형접합체인 경우 흡연관련 폐암 발생 위험이 감소되며, 동형접합체일 경우는 상대적으로 발생 위험이 증가되는 것으로 판단된다. 결 론 : 이상의 결과를 종합해보면, p53 유전자의 다형성 보다는 Rb 유전자 다형성이 한국인의 흡연관련 폐암발생의 유전적 감수성 결정에 밀접한 관련이 있을 것으로 사료되며, 앞으로 보다 명확한 연관관계 규명을 위해서는 다른 인종 및 더 많은 수의 환자군에 대한 분석이 요망된다.