• 생명과학회지
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• 제26권1호
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• pp.1-7
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• 2016

돼지에게 있어서 지방 형질은 가장 중요한 경제형질 중 하나다. 돼지의 렙틴수용체 유전자(LEPR)는 염색체 상의 위치와 그 생리 활성 측면에서 돼지 6번 염색체 상의 지방형질 관련 양적형질좌위(QTL)에 대한 주요 후보유전자로 알려져 있다. 본 연구에서는 LEPR 유전자의 구조 변이와 돼지 경제형질과의 연관성을 분석하였다. 이를 위하여 돼지 LEPR 유전자를 포함하고 있는 박테리아 인공 염색체(BAC) 클론에 대한 샷건 염기서열 해독을 수행하여 114 kb 크기의 유전체 서열을 확보하였다. 그리고 전사개시 코돈으로부터 1.2 kb 상위 영역에서 여러 전사인자 결합부위를 발견하였다. 또한 LEPR 유전자 엑손 영역의 6개 SNP와 5’ 조절영역의 18개 SNP에 대해 550두의 두록 개체를 대상으로 연관성 분석을 수행하였다. 이들 SNP 중, −790C/G만이 등지방두께와 정육율 형질과 유의적으로 연관되어 있었으며, 2개의 미스센스 다형성 SNP를 포함하여 다른 SNP에서는 어떤 형질과도 연관성을 보이지 않았다. 결론적으로 −790C/G SNP는 두록 돼지에서 지방과 정육형질을 유전적으로 개량하는데 유용한 마커로 활용될 수 있을 것이다.

• IMMUNE NETWORK
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• 제2권4호
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• pp.242-247
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• 2002

Background: Tumor necrosis factor-alpha (TNF-$\alpha$) is known to play an important role in various conditions such as inflammation, autoimmunity, apoptosis, insulin resistance and sleep induction. Five single nucleotide polymorphisms (SNPs) have been known to affect the transcriptional activities of TNF-$\alpha$: -1,031T/C, -863C/A, -857C/T, -308G/A and -238G/A. Methods: We have investigated 5 SNPs of the promoter region of TNF-$\alpha$ gene, the distribution of 5-locus TNF-$\alpha$ haplotypes, and their haplotypic associations with previously typed HLA-A, -B and -DRB1 loci in 107 healthy unrelated Koreans. TNF-$\alpha$ SNPs were typed using PCR-single-strand conformation polymorphism (SSCP) and PCR-restriction fragment length polymorphism (RFLP) methods. Results: The allele frequencies of -1,031C, -863A, -857T, -308A, and-238A, which are known as the high-producer-type, were 19.3%, 15.9%, 14.0%, 5.9%, and 2.9%, respectively. The frequency of -308A allele, known to be associated with autoimmune diseases, was 5.9% in Koreans which was lower than Caucasians (14~17%) and somewhat higher than Japanese (1.7%). Five most common TNF-$\alpha$ haplotypes (-1,031/-863/-857/-308/-238) comprised over 95% of total haplotypes: TCCGG (58.4%), CACGG (14.8%), TCTGG (13.7%), TCCAG (5.3%), and CCCGA (3.1%). Strong positive associations (P<0.001) were observed between TCCGG and B62; between CACGG and B51, $DRB1^*0901$; between TCTGG and B35, B54, B59, $DRB1^*1201$; and between TCCAG and A33, B58, $DRB1^*0301$, $DRB1^*1302$. Five most common extended haplotypes (>3%) comprised around 16% of total haplotypes: A33-B58-TCCAG-$DRB1^*1302$, A24-B52-TCCGG-$DRB1^*1502$, A33-B44-TCCGG-$DRB1^*1302$, A24-B7-TCCGG-$DRB1^*0101$, and A11-B62-TCCGG-$DRB1^*0406$. The distribution of extended HLA and TNF-$\alpha$ haplotypes showed that most of HLA haplotypes were almost exclusively associated with particular TNF-$\alpha$ haplotypes. Conclusion: The results obtained in this study would be useful as basic data for anthropologic studies and disease association studies in Koreans.

• Journal of Animal Science and Technology
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• 제58권4호
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• pp.14.1-14.9
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• 2016

Background: Peroxisome proliferator-activated receptor gamma (PPARG), CCAAT/enhancer binding protein alpha (CEBPA) and retinoid X receptor alpha (RXRA) are nuclear transcription factors that play important roles in regulation of adipogenesis and fat deposition. The objectives of this study were to characterise the variability of these three candidate genes in a mixed sample panel composed of several cattle breeds with different meat quality, validate single nucleotide polymorphisms (SNPs) in a local crossbred population (Angus - Hereford - Limousin) and evaluate their effects on meat quality traits (backfat thickness, intramuscular fat content and fatty acid composition), supporting the association tests with bioinformatic predictive studies. Results: Globally, nine SNPs were detected in the PPARG and CEBPA genes within our mixed panel, including a novel SNP in the latter. Three of these nine, along with seven other SNPs selected from the Single Nucleotide Polymorphism database (SNPdb), including SNPs in the RXRA gene, were validated in the crossbred population (N = 260). After validation, five of these SNPs were evaluated for genotype effects on fatty acid content and composition. Significant effects were observed on backfat thickness and different fatty acid contents (P < 0.05). Some of these SNPs caused slight differences in mRNA structure stability and/or putative binding sites for proteins. Conclusions: PPARG and CEBPA showed low to moderate variability in our sample panel. Variations in these genes, along with RXRA, may explain part of the genetic variation in fat content and composition. Our results may contribute to knowledge about genetic variation in meat quality traits in cattle and should be evaluated in larger independent populations.

• BMB Reports
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• 제38권5호
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• pp.555-562
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• 2005

Single nucleotide polymorphisms (SNPs) are becoming the most common type of markers used in genetic analysis. In the present report a SNP has been chosen to test the applicability of Real Time PCR to discriminate and quantify SNPs alleles on DNA pools. Amplification Refractory Mutation System (ARMS) and Mismatch Amplification Mutation Assay (MAMA) has been applied. Each assay has been pre-validated testing specificity and performances (linearity, PCR efficiency, interference limit, limit of detection, limit of quantification, precision and accuracy). Both the approaches achieve a precise and accurate estimation of the allele frequencies on pooled DNA samples in the range from 5% to 95% and don't require standard curves or calibrators. The lowest measurement that could be significantly distinguished from the background noise has been determined around the 1% for both the approaches, allowing to extend the range of quantifications from 1% to 99%. Furthermore applicability of Real Time PCR assays for general diagnostic purposes is discussed.

• Communications for Statistical Applications and Methods
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• 제16권4호
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• pp.579-586
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• 2009

통계모형의 상호작용 효과를 분석하기위해 비모수적인 방법인 다중인자 차원 축소(MDR)방법을 사용해 왔다. MDR 방법은 사례-대조 데이터에만 적용 할 수 있다. 본 논문에서는 Regression tree 알고리즘과 더미 변수를 활용한 회귀분석 알고리즘을 사용하여 다중 범주를 High 범주와 Low범주로 분류함으로써, MDR방법에서 연속형 데이터에 적용 할 수 없는 문제를 해결하는 방법으로 제시된 Expanded MDR방법과 Dummy MDR방법을 한우의 주요 경제형질(longissimus muscle dorsi area: LMA, carcass cold weight: CWT, average daily gain: ADG)데이터에 적용하여 한우의 경제형질에 영향을 주는 주요 SNPs 마커를 규명하고, Permutation test를 통해 그 결과를 비교한다.

• Journal of Animal Science and Technology
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• 제62권3호
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• pp.306-312
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• 2020

Korean army dogs are raised for special purposes and have contributed much to society. However, several diseases occur in dogs. Canine hip dysplasia (CHD) is a musculoskeletal disorder that occurs frequently in Korean army dogs and interferes with their activities. If we could control CHD, this would have a positive effect on their performance. This study performed a genome-wide association study (GWAS) in 69 Korean army dogs to find significant loci for CHD using 170K single nucleotide polymorphisms (SNPs). CHD was classified according to the Norberg angle criterion. The control group comprised 62 dogs classified as relatively normal, and 7 dogs with severe CHD formed the case group. From the GWAS analysis, we concluded that SNPs present on chromosome 4 might have a significant impact on the overall expression of canine hip dysplasia.

• 한국정보처리학회:학술대회논문집
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• 한국정보처리학회 2007년도 춘계학술발표대회
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• pp.605-608
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• 2007

천식(Asthma)과 같은 복합질환(Complex Disease)의 원인과 작용 모델을 찾기 위해서 여러가지 통계적인 방법들과 기계 학습(Machine Learning)의 방법 등이 사용되고 있다. 본 연구에서는 유전 알고리즘을 이용하여 천식 환자와 대조군들을 분류할 수 있는 단일염기 다형성(SNP, Single Nucleotide Polymorphism)의 조합에 대하여 조사한다.

• 대한의생명과학회지
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• 제24권4호
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• pp.334-340
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• 2018

The cytoplasmic elicitor, nucleotide-binding domain and leucine-rich repeat containing domain receptors (NLRs) is well established molecules in its role in inflammatory response. Among 22 NLR receptors, NOD2 is one of the intensively studied genes of elucidating for the inflammatory bowel disease and Crohn's disease as well. Recent research have accumulated that common genetic mutations in Parkinson's disease (PD) are increasingly related to the susceptibility to Crohn's disease. In this study, with the Korean Genome and Epidemiology Study, we aimed to perform the association between NOD2 polymorphisms and blood cell counts [WBC (white blood cell) count, RBC (red blood cell) count, platelet count], which linked supposedly to cytoplasmic inflammatory responses with clinical specialty. Linear regression analyses were performed, controlling for residential area, sex, and age as covariates. As a results, 12 SNPs from NOD2 gene were significantly associated with WBC counts (Bonferroni correction P-value criteria < 0.05/23=0.00218). In this study, we could ensure an association with NOD2 gene and WBC counts. This is the first report to have relationship between SNPs of NOD2 gene and WBC counts.

• 한국균학회지
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• 제43권4호
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• pp.231-238
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• 2015

팽이버섯(Flammulina velutipes) 25품종의 유전체 재분석 데이터를 표준유전체(KACC42781)와 비교하여 genomewide single nucleotide polymorphism (SNP)를 선발하였다. 균주에 따른 mapping율의 차이는 균주간 변이를 반영하였으며, genome-wide SNP분포는 homozygous SNP, heterozygous SNP로 구분되었으며 모두 균주에 따른 변이가 크게 나타났다. 수집균주들 사이의 유연관계를 살펴보기 위해, 계통수를 그려본 결과, Group I은 F. velutipes var. 계통인 ASI 4062, 4148, 4195이 묶여지고, Group II는 ASI 4188 F. elastica, ASI 4190 F. fennae, ASI 4194 F. rossica의 다른 종이 별도의 그룹을 형성하였다. 그 외 F. velutipes 19개 계통은 같은 그룹으로 나타났으며 그 유전적 자리를 잘 반영하였다. 한편 백색 group과 갈색 group을 유연관계로 분석하고자 시도하였으나 색깔에 따른 group은 이루어지지 않았다. 한국 백색 품종인 ASI 4210, 4166, 4178과 일본 백색 품종인 ASI 4209, 4167을 분석한 결과 phylogenetic tree상에서 한국 백색 품종과 일본 백색 품종간의 유전적 상동성이 매우 높음을 확인할 수 있었다.

• Asian-Australasian Journal of Animal Sciences
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• 제29권9호
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• pp.1229-1238
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• 2016

This study was conducted to determine the relationships of five intragenic single nucleotide polymorphism (SNP) markers (protein kinase adenosine monophosphate-activated ${\gamma}3$ subunit [PRKAG3], fatty acid synthase [FASN], calpastatin [CAST], high mobility group AT-hook 1 [HMGA1], and melanocortin-4 receptor [MC4R]) and meat quality traits of Duroc breeding stocks in Korea. A total of 200 purebred Duroc gilts from 8 sires and 40 dams at 4 pig breeding farms from 2010 to 2011 reaching market weight (110 kg) were slaughtered and their carcasses were chilled overnight. Longissimus dorsi muscles were removed from the carcass after 24 h of slaughter and used to determine pork properties including carcass weight, backfat thickness, moisture, intramuscular fat, $pH_{24h}$, shear force, redness, texture, and fatty acid composition. The PRKAG3, FASN, CAST, and MC4R gene SNPs were significantly associated with the meat quality traits (p<0.003). The meats of PRKAG3 (A 0.024/G 0.976) AA genotype had higher pH, redness and texture than those from PRKAG3 GG genotype. Meats of FASN (C 0.301/A 0.699) AA genotype had higher backfat thickness, texture, stearic acid, oleic acid and polyunsaturated fatty acid than FASN CC genotype. While the carcasses of CAST (A 0.373/G 0.627) AA genotype had thicker backfat, and lower shear force, palmitoleic acid and oleic acid content, they had higher stearic acid content than those from the CAST GG genotype. The MC4R (G 0.208/A 0.792) AA genotype were involved in increasing backfat thickness, carcass weight, moisture and saturated fatty acid content, and decreasing unsaturated fatty acid content in Duroc meat. These results indicated that the five SNP markers tested can be a help to select Duroc breed to improve carcass and meat quality properties in crossbred pigs.