• Genes and Genomics
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• 제40권11호
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• pp.1119-1125
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• 2018

Melanocortin 4 receptor: (MC4R) and Myostatin (MSTN) are two important growth trait-related genes in animals. In this study, we showed that two SNPs, MC4R-719A>G and MSTN-519C>T, found in the promoters of the MC4R and MSTN genes, respectively, are both associated with growth traits in Spinibarbus hollandi. Furthermore, we observed that there were significant associations between the expression levels of the MC4R and MSTN genes and these two growth trait-related SNPs. The expression level of MC4R gene in brain was lower in GG genotype fish with extremely high growth performance than that in AA genotype fish with extremely low growth performance. Expression level of the MSTN gene in muscle was lower in TT genotype fish with extremely high growth performance than that in CC and CT genotype fish with lower growth performance. The results indicated that these SNPs located in the promoters of MC4R and MSTN are associated with growth-related traits through modification of gene expression levels. The MSTN and MC4R SNPs may have useful application in effective marker-assisted selection aimed to increase output in S. hollandi.

• Asian Pacific Journal of Cancer Prevention
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• 제14권2호
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• pp.941-946
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• 2013

Objective: The nucleotide excision repair (NER) and base excision repair (BER) pathways, two DNA repair pathways, are related to platinum resistance in cancer treatment. In this paper, we studied the association between single nucleotide polymorphisms (SNPs) of involved genes and response to platinum-based chemotherapy in epithelial ovarian cancer. Method: Eight SNPs in XRCC1 (BER), XPC and XPD (NER) were assessed in 213 patients with epithelial ovarian cancer using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and primer-introduced restriction analysis-polymerase chain reaction (PIRA-PCR) techniques. Results: The median progression-free survival (PFS) of patients carrying the Lys/Lys and Lys/Gln+Gln/Gln genotype of the XPC Lys/Gln polymorphism were 25 and 12 months, respectively (P=0.039); and the mean overall survival (OS) of patients was 31.1 and 27.8 months, respectively (P=0.048). Cox's multivariate analysis suggested that patients with epithelial ovarian cancer with the Gln allele had an increased risk of death (HR=1.75; 95% CI=1.06-2.91) compared to those with the Lys/Lys genotype. There are no associations between the XPC PAT+/-, XRCC1 Arg194Trp, Arg280His, Arg399Gln, and XPD Asp312Asn, Lys751Gln polymorphisms and the survival of patients with epithelial ovarian cancer when treated with platinum-based chemotherapy. Conclusion: Our results indicated that the XPC Lys939Gln polymorphism may correlate with clinical outcome of patients with epithelial ovarian cancer when treated with platinum-based chemotherapy in Northern China.

• Asian-Australasian Journal of Animal Sciences
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• 제23권4호
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• pp.417-424
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• 2010

The purpose of this study was to detect significant SNPs for carcass quality traits using DNA chips of high SNP density in Hanwoo populations. Carcass data of two hundred and eighty nine steers sired by 30 Korean proven sires were collected from two regions; the Hanwoo Improvement Center of National Agricultural Cooperative Federation in Seosan, Chungnam province and the commercial farms in Gyeongbuk province. The steers in Seosan were born between spring and fall of 2006 and those in Gyeonbuk between falls of 2004 and 2005. The former steers were slaughtered at approximately 24 months, while the latter steers were fed six months longer before slaughter. Among the 55,074 SNPs in the Illumina bovine 50K chip, a total of 32,756 available SNPs were selected for whole genome association study. After adjusting for the effects of sire, region and slaughter age, phenotypes were regressed on each SNP using a simple linear regression model. For the significance threshold, 0.1% point-wise p value from F distribution was used for each SNP test. Among the significant SNPs for a trait, the best set of SNP markers were selected using a stepwise regression procedure, and inclusion and exclusion of each SNP out of the model was determined at the p<0.001 level. A total of 118 SNPs were detected; 15, 20, 22, 28, 20, and 13 SNPs for final weight before slaughter, carcass weight, backfat thickness, weight index, longissimus dorsi muscle area, and marbling score, respectively. Among the significant SNPs, the best set of 44 SNPs was determined by stepwise regression procedures with 7, 9, 6, 9, 7, and 6 SNPs for the respective traits. Each set of SNPs per trait explained 20-40% of phenotypic variance. The number of detected SNPs per trait was not great in whole genome association tests, suggesting additional phenotype and genotype data are required to get more power to detect the trait-related SNPs with high accuracy for estimation of the SNP effect. These SNP markers could be applied to commercial Hanwoo populations via marker-assisted selection to verify the SNP effects and to improve genetic potentials in successive generations of the Hanwoo populations.

• Journal of the Korean Data and Information Science Society
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• 제20권4호
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• pp.639-647
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• 2009

컴퓨터공학의 발전으로 인해, 여러 개의 변수가 존재하는 비선형 문제와 같은 최적해 탐색과 최적화에 사용되는 유전자 알고리즘은 많은 분야에서 활발하게 응용되고 있다. 그 중, 데이터마이닝분야에서 유전자 알고리즘을 이용하여 정확도를 최대로 하는 입력변수 선택방법과 여러 예측모형을 통합하는 방법 등이 제시되었다. 한편, 우리나라 축산업을 대표하는 한우의 유전자원 보존과 능력향상을 위해서는 다음세대에 유전이 되는 단일염기다형성에서 특정 유전자형을 가진 한우가 경제형질이 우수한지를 찾아낼 필요가 있다. 이에 따라, 유전자 알고리즘을 이용하여 한우의 경제형질에 가장 많은 영향을 주는 단일염기다형성 조합마커의 유전자형을 선택하는 방법을 제시하였다. 그리고 실제 한우 유전 데이터에 적용하여 주요 단일염기다형성 조합마커에서 우수 유전자형들을 선별하였다.

• Asian Pacific Journal of Cancer Prevention
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• 제17권3호
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• pp.953-956
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• 2016

The risk of developing cervical cancer in women infected with human papillomavirus (HPV) may be influenced by an individual's genetic susceptibility. Published data linking single nucleotide polymorphisms (SNPs) in the tumor necrosis factor-alpha (TNF-${\alpha}$) promoter region at positions -308G>A (rs1800629) and -238G>A (rs361525) to cervical cancer risk have been inconclusive. In this study, we examined 251 cervical specimens and classified them into two groups according to their cytological findings: 121 cancer cases and 130 controls (low-grade squamous intraepithelial lesion and normal cytology). All specimens were typed by PCR and sequencing for TNF-${\alpha}$ promoter -308G>A (rs1800629) and -238G>A (rs361525). The genotype distribution of SNPs in either rs1800629 or rs361525 did not significantly demonstrate higher frequency in the cancer group (p=0.621 and p=0.68, respectively). Based on these results, neither the TNF-${\alpha}$ promoter -308G>A (rs1800629) nor the -238G>A (rs361525) polymorphism presents a major risk factor for cervical cancer among Thai women. Larger studies are necessary to elucidate possible genetic mechanisms influencing cervical cancer development.

• Asian-Australasian Journal of Animal Sciences
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• 제31권8호
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• pp.1078-1087
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• 2018

Objective: The genetic diversity of the Landrace population, a representative maternal pig breed in Korea, is important for genetic improvement. Previously, the effective population size (Ne) has been used to infer the genetic diversity of a population of interest. In this study, we aimed to use single nucleotide polymorphism (SNP) data to characterize linkage disequilibrium (LD) and the Ne of the Korean Landrace population. Methods: We genotyped 1,128 Landrace individuals from three representative Korean major grand-grand-parent (GGP) farms using the Illumina PorcineSNP60 version2 BeadChip, which covers >61,565 SNPs located across all autosomes and mitochondrial and sex chromosomes. We estimated the expected LD and current Ne, as well as ancestral Ne. Results: In the Korean Landrace population, the mean LD ($r^2$) of 3.698 million SNP pairs was $0.135{\pm}0.204$. The mean $r^2$ decreased slowly with as the distance between SNPs increased, and remained constant beyond 3 Mb. According to the $r^2$ calculations, 8,085 of 3.698 million SNP pairs were in complete LD. The current Ne (${\pm}$standard deviation) of the Korean Landrace population is approximately 92.27 [79.46; 105.07] individuals. The ancestral Ne exhibited a slow and steady decline from 186.61 to 92.27 over the past 100 generations. Additionally, we observed more a rapid Ne decrease from the past 20 to 10 generations ago, compared with other intervals. Conclusion: We have presented an overview of LD and the current and ancestral Ne values in the Korean Landrace population. The mean LD and current Ne for the Korean Landrace population confirm the genetic diversity and reflect the history of this pig population in Korea.

• Asian-Australasian Journal of Animal Sciences
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• 제28권8호
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• pp.1084-1089
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• 2015

Chemerin, highly expressed in adipose and liver tissues, regulates glucose and lipid metabolism and immunity in these tissues in ruminants and mice. Our previous reports showed that chemerin is involved in adipogenesis and lipid metabolism in adipose tissue as an adipokine. The aim of the present study was to identify single nucleotide polymorphisms (SNPs) in the coding region of the chemerin gene and to analyze their effects on carcass traits and intramuscular fatty acid compositions in Japanese Black cattle. The SNPs in the bovine chemerin gene were detected in 232 Japanese Black steers (n = 161) and heifers (n = 71) using DNA sequencing. The results revealed five novel silent mutations: NM_001046020: c.12A>G (4aa), c.165GT (92aa), c.321 A>G (107aa), and c.396C>T (132aa). There was no association between 4 of the SNPs (c.12A>G [4aa], c.165GG [107aa], and c.396C>T) and carcass traits or intramuscular fatty acid compositions. Regarding the remaining SNP, c.276C>T, we found that cattle with genotype CC had a higher beef marbling score than that of cattle with genotype CT, whereas cattle with genotype CT had a higher body condition score (p<0.10). Further, cattle with genotype CC had significantly higher C18:0 content in their intramuscular fat tissue than that of cattle with genotype CT (p<0.05). On the other hand, cattle with genotype CT had significantly higher C14:0 and C16:0 content in their intramuscular fat tissue (p<0.05). Moreover, the number of individuals carrying the minor allele of c.276C>T SNP is small. It is suggested that the c.276C>T SNP of the chemerin gene has potential in cattle breeding using modern methods, such as marker assisted selection. So, further functional and physiological research elucidating the impact of the chemerin gene on bovine lipid metabolism including fatty acid synthesis will help in understanding these results.

• 생명과학회지
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• 제25권11호
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• pp.1304-1310
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• 2015

주기성 시계 유전자 3(period circadian clock gene 3, PER3)는 포유류에서 생물학적 주기 타이밍 시스템의 역할을 수행 한다. 이 유전자는 규칙적인 운동 체계에 의해 근육에서 전사 개시 되는 것으로 알려져 있다. 인간과 마우스에서는 본 유전자에 대해 잘 알려져 있지만, 주기 및 연주기 동안 낮의 길이에 영향을 많이 받는 말에서 운동 연관 연구는 존재하지 않는다. 운동 시 근육의 기능에 중요한 역할을 하는 PER3 유전자에 대해 대표적인 경주마인 국내산 더러브렛 품종의 운동 전과 운동 후 유전자 발현을 분석하기 위해 본 연구를 수행하였다. 그 결과, 골격근에서 PER3 유전자의 발현은 운동 전에 비해 운동 후에 유의적으로 증가하는 것으로 나타났다. 또한, 인실리코상에서 4개의 비동의성 단일 염기 변이(non-synonymous single nucleotide polymorphism, nsSNP) 분석과 이러한 nsSNP의 단백질 구조 및 기능 분석 결과, 전체 자유 에너지와 RMSD 값은 돌연변이의 원인이 될 수 있음으로 나타났다. 이 중, nsSNP–s395916798 (G72R)은 구조적 기능적 측면에서 중요한 잔기의 안정화 효과와 연관된 것을 알 수 있었다. 본 연구는 운동에 따라 더러브렛 골격근 내 PER3 발현 차이는 운동이라는 표현형에 대표될 수 있음을 확인하였다. 또한, SNP의 조합을 활용하여 운동 후 경주마의 조기 회복의 평가 지표로써 유용한 바이오마커가 될 수 있음을 시사한다.

• Asian-Australasian Journal of Animal Sciences
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• 제20권12호
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• pp.1812-1819
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• 2007

Heart fatty acid-binding protein gene (H-FABP) is an important candidate gene for meat quality. One of the objectives of this study was to screen single nucleotide polymorphisms (SNP) of chicken H-FABP gene among 252 individuals that included 4 Chinese domestic chicken breeds (Fengkai Xinghua (T04), Huiyang Huxu (H), Qingyuan Ma (Q), Guangxi Xiayan (S1)), 2 breeds developed by the Institute of Animal Science, Guangdong Academy of Agricultural Sciences (Lingnan Huang (DC), dwarf chicken (E4)) and one introduced broiler (Abor Acre (AA)). Another objective of this study was to analyze the associations between polymorphisms of the H-FABP gene and fat deposition traits in chickens. PCR-SSCP was used to analyze SNPs in H-FABP and 4 SNPs (T260C, G675A, C783T and G2778A) were detected. Associations between polymorphic loci and intramuscular fat (IMF), abdominal fat weight (AFW) and abdominal fat percentage (AFP) were analyzed by ANCOVA method. The results showed that the T260C genotypes were significantly associated with IMF (p = 0.0233) and AFP (p = 0.0001); the G675A genotypes were significantly associated with AFW, AFP (p<0.01) and IMF (p<0.05); at the C783T locus, AFW and AFP differed highly between genotypes. However, the G2778A loci did not show any significant effect on fat deposition traits in this study. In addition, we found that there were some differences between AFP and definite haplotypes through a nonparametric statistical method, so the haplotypes based on the SNPs except G2778A loci were also significantly associated with IMF, AFW (g) (p<0.05) and AFP (%) (p<0.001). Significantly and suggestively dominant effects of H4H4 haplotype were observed for IMF and the H2H3 was dominant for AFW (g) and AFP (%). The results also revealed that H5H7 haplotype had a negative effect on IMF, while the H5H6 had a positive effect on AFW (g) and AFP (%).

• 대한의생명과학회지
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• 제26권4호
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• pp.344-350
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• 2020

Asthma is a chronic disease and occurs in airway in the lung. The cause of the disease has not been identified, it is assumed that both genetic and environmental risk factors play an important role in the development of asthma. Interleukin (IL)-12 is a cytokine regulating T-cell and NK cell. In this study, we analyzed the genetic polymorphisms of IL-12 receptor genes (IL-12Rβ1 and IL-12Rβ2) in asthma patients and normal individuals in a Korean population. We analyzed single nucleotide polymorphisms (SNPs) in IL-12Rβ1 and IL-12Rβ2 using the genotype data of 193 asthma cases and 3,228 healthy controls from the Korea Association REsource for their correlation with asthma case. IL-12Rβ1 and IL-12Rβ2 genes showed statistically significant polymorphism association with asthma case. As a results, 16 SNPs from IL-12Rβ1 and IL-12Rβ2 genes showed statistically significant association with asthma. Among them, rs375947 SNP in IL-12Rβ1 showed the greatest statistical correlation with asthma (P-value = 0.028, Odds Ratio = 1.27, 95% Confidence Interval = 1.03~1.57). The groups with minor allele of IL-12Rβ1 and IL-12Rβ2 showed increased risk of asthma. The genotype-based mRNA expression analysis showed that the group of minor allele of IL-12Rβ1 showed decreased mRNA expression. Decreased IL-12Rβ1 expression causes decreased IL-12 signaling, and this affects developing asthma. In conclusion, the SNPs in IL-12Rβ1 and IL-12Rβ2 may contribute to development of asthma in a Korean population.