• Mycobiology
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• 제49권1호
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• pp.61-68
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• 2021

Agaricus bisporus, commonly known as the button mushroom, is widely cultivated throughout the world. To breed new strains with more desirable traits and improved adaptability, diverse germplasm, including wild accessions, is a valuable genetic resource. To better understand the genetic diversity available in A. bisporus and identify previously unknown diversity within accessions, a phylogenetic analysis of 360 Agaricus spp. accessions using single-nucleotide polymorphism genotyping was performed. Genetic relationships were compared using principal coordinate analysis (PCoA) among accessions with known origins and accessions with limited collection data. The accessions clustered into four groups based on the PCoA with regard to genetic relationships. A subset of 67 strains, which comprised a core collection where repetitive and uninformative accessions were not included, clustered into 7 groups following analysis. Two of the 170 accessions with limited collection data were identified as wild germplasm. The core collection allowed for the accurate analysis of A. bisporus genetic relationships, and accessions with an unknown pedigree were effectively grouped, allowing for origin identification, by PCoA analysis in this study.

• Asian-Australasian Journal of Animal Sciences
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• 제28권11호
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• pp.1551-1557
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• 2015

The missing heritability has been a major problem in the analysis of best linear unbiased prediction (BLUP). We introduced the traditional genome-wide association study (GWAS) into the BLUP to improve the heritability estimation. We analyzed eight pork quality traits of the Berkshire breeds using GWAS and BLUP. GWAS detects the putative quantitative trait loci regions given traits. The single nucleotide polymorphisms (SNPs) were obtained using GWAS results with p value <0.01. BLUP analyzed with significant SNPs was much more accurate than that with total genotyped SNPs in terms of narrow-sense heritability. It implies that genomic estimated breeding values (GEBVs) of pork quality traits can be calculated by BLUP via GWAS. The GWAS model was the linear regression using PLINK and BLUP model was the G-BLUP and SNP-GBLUP. The SNP-GBLUP uses SNP-SNP relationship matrix. The BLUP analysis using preprocessing of GWAS can be one of the possible alternatives of solving the missing heritability problem and it can provide alternative BLUP method which can find more accurate GEBVs.

• Journal of Plant Biotechnology
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• 제48권1호
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• pp.26-33
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• 2021

당귀는 일반적으로 이용되는 대표적인 다년생의 약용식물이다. 최근 국제적 추세에 따라 자국의 유전자원의 발굴, 보존 등이 강화됨에 따라 인접국가와 국내 자생 당귀 계통을 판별할 수 있는 기준설정에 관한 연구의 필요성이 대두되고 있지만, 분자생물학적 판별 기술의 개발은 아직 미흡한 실정이다. 본 연구에서는 국내 토종 당귀인 참당귀와 세발당귀, 그리고 해외 유래 당귀 종의 기원을 판별하기 위해 핵의 리보솜에 존재하는 ITS 유전자단편에서 SNP를 이용한 판별 프라이머를 확보하였으며, 이를 보완하여 보다 신속하게 판별하기 위하여 ARMS-PCR 기술을 이용한 판별 마커와 그 조건을 확립하였다. 그러므로, 본 연구에서 개발된 SNP 마커는 다양한 지역 또는 국가에서 서식하는 당귀 종들의 신속한 확인을 위해 매우 유용하게 이용될 것으로 생각된다.

• Animal Bioscience
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• 제36권1호
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• pp.19-28
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• 2023

Objective: The objective of this study was to perform genome (genome wide association studies [GWAS]) and chromosome (CWAS) wide association analyses to identify single nucleotide polymorphisms (SNPs) associated with growth traits in registered Simmental and Simbrah cattle. Methods: The phenotypes were deregressed BLUP EBVs for birth weight, weaning weight direct, weaning weight maternal, and yearling weight. The genotyping was performed with the GGP Bovine 150k chip. After the quality control analysis, 105,129 autosomal SNP from 967 animals (473 Simmental and 494 Simbrah) were used to carry out genotype association tests. The two association analyses were performed per breed and using combined information of the two breeds. The SNP associated with growth traits were mapped to their corresponding genes at 100 kb on either side. Results: A difference in magnitude of posterior probabilities was found across breeds between genome and chromosome wide association analyses. A total of 110, 143, and 302 SNP were associated with GWAS and CWAS for growth traits in the Simmental-, Simbrah- and joint -data analyses, respectively. It stands out from the enrichment analysis of the pathways for RNA polymerase (POLR2G, POLR3E) and GABAergic synapse (GABRR1, GABRR3) for Simmental cattle and p53 signaling pathway (BID, SERPINB5) for Simbrah cattle. Conclusion: Only 6,265% of the markers associated with growth traits were found using CWAS and GWAS. The associated markers using the CWAS analysis, which were not associated using the GWAS, represents information that due to the model and priors was not associated with the traits.

• Asian Pacific Journal of Cancer Prevention
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• 제15권3호
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• pp.1255-1262
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• 2014

Background: The aim of the study was to investigate any associations between benign prostate hyperplasia (BPH) and single nucleotide polymorphisms (SNPs) in the VDR gene (FokI, BsmI, ApaI and Taq${\alpha}$I loci) and the CYP17 gene (MspA1I locus), as well as TA repeat polymorphism in SRD5A2 gene among Lebanese men. Materials and Methods: DNA extracted from blood of 68 subjects with confirmed BPH and 79 age-matched controls was subjected to PCR/PCR-restriction fragment length polymorphism analysis. The odds ra=tio (OR) of having a genotype and the relative risk (RR) of developing BPH for having the genotype were calculated and the alleles were designated risk-bearing or protective. Results: Our data indicated that the A and B alleles of the VDR ApaI and BsmI SNPs were highly associated with increased risk of BPH (p=0.0168 and 0.0002, respectively). Moreover, 63% of the controls compared to 43% of the subjects with BPH were homozygous for none of the risk-bearing alleles (p=0.0123) whereas 60% of the controls and 28% of the subjects with BPH were homozygous for two or more protective alleles (p<0.0001). Conclusions: For the first time, our study demonstrated that ApaI and BsmI of the VDR gene are associated with risk of BPH among Lebanese men. Our study also indicated that overall polymorphism profile of all the genes involved in prostate physiology could be a better predictor of BPH risk.

• Asian Pacific Journal of Cancer Prevention
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• 제16권7호
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• pp.2713-2717
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• 2015

Background: Possible associations between the single nucleotide polymorphism (SNP) rs8034191 in the aminoglycosidephosphotransferase domain containing 1 (AGPHD1) gene and lung cancer risk have been studied by many researchers but the results have been contradictory. Materials and Methods: A computerized search for publications on rs8034191 and lung cancer risk was performed. Odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to assess the association between rs8034191 and lung cancer risk with 13 selected case-control studies. Sensitivity analysis, test of heterogeneity, cumulative meta-analysis, and assessment of bias were also performed. Results: A significant association between rs8034191 and lung cancer susceptibility was found using the dominant genetic model (OR=1.344, 95% CI: 1.285-1.406), the additive genetic model (OR=1.613, 95% CI: 1.503-1.730), and the recessive genetic model (OR=1.408, 95% CI: 1.319-1.503). Moreover, an increased lung cancer risk was found with all genetic models after stratification of ethnicity. Conclusions: The association between rs8034191 and lung cancer risk was significant using multiple genetic models, suggesting that rs8034191 is a risk factor for lung cancer. Further functional studies of this polymorphism and lung cancer risk are warranted.

• 생명과학회지
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• 제24권2호
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• pp.181-185
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• 2014

본 연구에서는 eNOS 유전자에 대한 한국인 특이적 SNP를 확인하고자 하였다. eNOS (endothelial nitric oxide synthase)는 내피세포에서 발현되는 산화질소(nitric oxide, NO)를 합성하는 유전자로 관동맥 연축 및 혈압에 영향을 미친다. 이 유전자는 발현이 항상 일정한 constitutivegene으로 7번 염색체에 위치한다. 최근 연구 보고에 따르면 exon 7에 해당하는 894번째 염기 변이[G894T (Glu298Asp)]의 다형성이 심근경색 및 관상동맥 경련의 발병원에 기여하는 유전적 요소일 가능성으로 제시되었다. SNP가 모든 환자에게서 직접적으로 질환의 원인은 아닐지라도 일부 환자에게서는 상당한 연관성이 있다고 보여지고, 인종 간에도 차이가 있기 때문에 인종별로 이를 정확히 분석하는 것이 유전자 진단에 핵심이 될 것으로 생각된다. eNOS 유전자에서 다형성 부분에 해당하는 sense primer와 antisense primer를 고안, 제작하였으며, ARMS 기법에 기초한 방법으로 allele 특이적인 산물이 생성될 수 있게 하였다. eNOS의 G894T는 wild type (W/W)이 95명, heterozygote type (W/S)이 9명 확인되었다. SNP homozygote type (S/S)은 나타나지 않았다. 환자에서는 W/W 19명, W/S 1명으로 역시 S/S은 나타나지 않았다. 본 연구를 통해 eNOS에 대한 한국인 특이적 다형성의 확인과 진단이 보다 신속 정확하게 이루어질 수 있는 기반이 마련될 것으로 기대된다.

• 대한임상검사과학회지
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• 제53권3호
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• pp.249-256
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• 2021

천식은 만성 염증성 기도 폐쇄 질환이다. 질병 발생 요인은 다양하며 특히, 유전적 요인과 환경적 요인이 천식 발병에 영향을 미치는 것으로 추정된다. MAPK (mitogen-activated protein kinase)경로는 Th1/Th2의 균형을 조절하며, 천식 발생에 중요한 역할을 하는 것으로 알려져 있다. 본 연구에서는 MAPK 경로를 조절하는 NDFIP2 유전자와 천식 발병과의 상관관계를 분석하였다. 193건의 천식 환자와 3,228건의 정상 대조군의 유전형 데이터를 사용하였다. 그 결과 NDFIP2 안에 있는 4개의 SNP이 천식과 유의한 상관관계와 높은 상대적 위험도를 보였다. 특히 NDFIP2의 rs2783122는 천식과 통계적으로 가장 유의한 연관성을 나타냈다(P-value=9.76×10^-6, OR=1.67, 95% CI=1.33~2.10). NDFIP2 유전자에 대한 SNP imputation 결과 16개의 SNP가 추가 발견되었으며, 모두 유의한 상관 관계와 높은 상대적 위험도를 나타냈다. 유전자형 기반 mRNA 발현 분석을 통해 rs1408049가 minor allele을 가질 경우 유전자 발현이 증가됨을 알 수 있었다. 증가된 NDFIP2 발현은 MAPK 경로를 활성화시켜 천식 발병에 영향을 미칠 수 있다. 결론적으로 NDFIP2의 다형성은 천식 발병과 관련이 있으며, 이는 한국 인구의 천식 관리에 대한 새로운 지침을 제공할 수 있다.

• Journal of the Korean Data and Information Science Society
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• 제28권3호
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• pp.597-604
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• 2017

본 연구는 홀스타인 젖소, 923두에 대한 단일염기다형성 (SNP) 42,201개를 이용하여 국내 젖소집단의 유전적 특성 및 유효집단크기를 조사하고자 실시하였다. 염색체별 인접 단일염기다형성간의 평균 연관불평형 ($r^2$)은 0.22로 추정되었으며, 14번 염색체 (0.26)에서 가장 높은 반면, 27번 염색체 (0.17)에서 가장 낮게 나타났다. SNP간의 물리적 거리가 25Kb 미만인 경우에서 $r^2$은 $0.31{\pm}0.33$으로 추정되었으며, SNP간 물리적 거리가 증가할수록 $r^2$은 현저히 감소하였다. SNP간 물리적 거리가 2.5Mb 이상에서의 $r^2$은 0.04로 25Kb 미만인 경우와 비교할 때 0.27 (87.1%) 감소하였다. 국내 홀스타인 젖소의 유효집단크기는 세대수와 비례하여 감소하는 경향을 나타내었으며, 1~5세대에서 110두로 추정되었다.

• ETRI Journal
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• 제37권2호
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• pp.212-221
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• 2015

As the amount of re-sequencing genome data grows, minimizing the execution time of an analysis is required. For this purpose, recent computing systems have been adopting both high-performance coprocessors and host processors. However, there are few applications that efficiently utilize these heterogeneous computing resources. This problem equally refers to the work of single nucleotide polymorphism (SNP) detection, which is one of the bottlenecks in genome data processing. In this paper, we propose a method for speeding up an SNP detection by enhancing the utilization of heterogeneous computing resources often used in recent high-performance computing systems. Through the measurement of workload in the detection procedure, we divide the SNP detection into several task groups suitable for each computing resource. These task groups are scheduled using a window overlapping method. As a result, we improved upon the speedup achieved by previous open source applications by a magnitude of 10.