• 한국산학기술학회논문지
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• 제21권1호
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• pp.240-246
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• 2020

본 연구는 백우 품종 육성을 위해 분자생물학적 방법을 이용하여 유전적 특성을 파악하고 백우 품종을 식별하기 위한 백우 품종 특이적인 Single Nucleotide Polymorphism (SNP) 마커를 개발하기 위해 수행되었다. 한우 48두와 백우 22두의 혈액에서 추출된 DNA를 이용하여 Illumina Bovine HD 777K SNP chip으로 SNP genotyping을 실시하였다. 각 SNP의 Minor Allele Frequency (MAF) difference (한우와 백우의 차이 절대값)을 계산하고, Fisher's Exact test (Genotype)을 통해 MAF difference의 통계적 유의성(P-value)을 계산하였다. 품종 별 차이를 나타낼 수 있는 마커를 선발기준으로 MAF difference가 100%의 차이를 나타내는 SNP를 식별하였다. 이러한 유전적 차이를 보이는 9개의 단일염기다형성 마커(rs42125585, rs42125591, rs42125833, rs109461720, rs134735704, rs109447299, rs42164846, rs42160000 및 rs137353829)가 선발되었다. 선발된 마커들은 한우와 백우 특이적인 대립유전자를 가지고 서로 다른 대립유전자를 나타내고 있다. 이들 9개의 SNP 마커들을 이용하여 한우와 백우의 품종을 식별할 수 있음을 확인하였고, 이러한 결과들을 바탕으로 백우 품종 식별 마커 특허를 등록하였다. 백우는 원종인 한우에서 분리되어 한국재래종의 특성을 잘 나타내 주는 계통으로, 이러한 백우가 가지고 있는 유전적 특성 연구는 백우를 식별하고 품종으로서 육종하는데 사용되어 종축으로서의 가치 증진을 위한 기반 연구가 될 것으로 생각된다.

• 한국패류학회지
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• 제29권4호
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• pp.335-341
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• 2013

본 연구는 우리나라의 주요양식 품종인 북방전복을 대상으로 지금까지 전복류에서는 사용되지 않았던 mtDNA의 protein coding 영역 ND2, ND5, ND4, ND4L, ND6, ND1의 6개영역과 protein noncoding 영역인 12SrRNA(ribosomal RNA) 을 포함해 총 7개 영역을 이용하여 각 영역의 유전적 변이성 및 개체간 유전적 유연관계 등을 분석하여 각 영역별 특성을 파악하고 이러한 특성을 고려하여 유전학적 분석에 적합한 분자유전마커를 개발하였다. 유전적 변이성은 ND4 영역 (Haplotype diversity = 1.000, Nucleotide diversity = 0.010823) 이 가장 높게 나타났으며, 개체간의 유전적 차이는 ND2 및 ND1 영역이 각각 90% 및 87%로 유의적으로 명확히 구분할 수 있었다. 따라서 유전적 변이성이 가장 높은 ND4 영역과 영역내의 클러스터 간의 유전적 차이가 명확한 ND2 및 ND1 영역을 복합적으로 활용할 경우 북방 전복의 집단유전학 및 계통분류학 분석에 유용한 분자유전마커로 사용할 수 있을 것이라 생각된다.

• 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.

• 한국가금학회지
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• 제41권1호
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• pp.29-37
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• 2014

닭을 구분하는데 있어 가장 눈에 띠는 것이 모색이며, 모색 관련 유전자인 MC1R, MITF, TYRP1의 SNP에 따른 유전자형을 확인하고, 각 품종별로 구별이 가능한 SNP 마커를 개발하고자 하는데, 본 연구의 목적이 있다. 마커들을 조합으로 haplotype을 보았을 때, MC1R 유전자의 SNP 조합에서 CGG type일 경우, 재래닭 만을 특별히 구별할 수 있었으며, TAG, TGG, TAA type일 경우에는 아라카나 만을 구별할 수 있었고, CAA type의 경우, 레그혼 만을 특이적으로 구별할 수 있었다. TYRP1 유전자의 SNP 조합에서는 TTTCA, CCTCA type의 경우, 레그혼 만을 구별할 수 있으며, CTTTA type의 경우, 오골계 만을 특이적으로 구별할 수 있었다. MC1R 유전자의 SNP 조합으로 재래닭, 레그혼, 아라카나를 구별할 수 있었고, TYRP1 유전자의 각각의 SNP 및 조합으로 4가지 품종 모두 구별할 수 있었다. 이렇게 품종 간의 유전적 다형성에 대한 연구가 더 많이 진행된다면, 단순 모색만으로 품종을 구별하기보다는 분자생물학적으로 품종 간의 차이를 이해할 수 있게 될 것이라고 생각된다.

• Journal of Plant Biotechnology
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• 제44권4호
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• pp.372-378
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• 2017

과육색이 다르게 발현되는 사과(Malus domestica L.) 품종의 유전자 발현을 비교하기 위해 2개의 cDNA library를 제작하였다. 붉은 색 과육 품종인 'Redfield'와 백색 과육 품종인 'Granny Smith'의 유전자 발현 차이를 보기 위해 차세대 염기서열 분석(NGS) 기술을 사용하였고 두 품종으로부터 얻은 EST의 염기서열을 결정하고 기존에 보고된 유전자와의 상동성을 분석하였다. HRM 기술은 붉은 색 과육 품종 사과와 백색 과육 품종 사과의 짧은 PCR 증폭산물에서 한 개의 서로 다른 염기서열을 구분하여 분리해낼 수 있다. 'Redfield'와 'Granny Smith'의 EST database로부터 103쌍의 단일염기다형성(SNP) 분자표지를 선발하였고, 붉은 색 과육 품종 10개와 백색 과육 품종 11개를 구분할 수 있는 SNP 분자표지를 HRM 방법으로 분석하였다. 본 연구에서는 사과 EST database를 기반으로 HRM 분석 방법을 이용하여 사과 품종의 적육계와 백육계를 구분할 수 있는 효율적인 SNP 분자표지를 개발하였다. 이러한 SNP 분자표지는 사과육종에 유용하게 사용할 수 있으며 사과 품종의 다양한 색 변화에 관한 분자 기작 연구에 좋은 참고자료가 될 수 있을 것이다.

• Asian-Australasian Journal of Animal Sciences
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• 제28권11호
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• pp.1537-1544
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• 2015

Meat and carcass quality attributes are of crucial importance influencing consumer preference and profitability in the pork industry. A set of 400 Berkshire pigs were collected from Dasan breeding farm, Namwon, Chonbuk province, Korea that were born between 2012 and 2013. To perform genome wide association studies (GWAS), eleven meat and carcass quality traits were considered, including carcass weight, backfat thickness, pH value after 24 hours (pH24), Commission Internationale de l'Eclairage lightness in meat color (CIE L), redness in meat color (CIE a), yellowness in meat color (CIE b), filtering, drip loss, heat loss, shear force and marbling score. All of the 400 animals were genotyped with the Porcine 62K SNP BeadChips (Illumina Inc., USA). A SAS general linear model procedure (SAS version 9.2) was used to pre-adjust the animal phenotypes before GWAS with sire and sex effects as fixed effects and slaughter age as a covariate. After fitting the fixed and covariate factors in the model, the residuals of the phenotype regressed on additive effects of each single nucleotide polymorphism (SNP) under a linear regression model (PLINK version 1.07). The significant SNPs after permutation testing at a chromosome-wise level were subjected to stepwise regression analysis to determine the best set of SNP markers. A total of 55 significant (p<0.05) SNPs or quantitative trait loci (QTL) were detected on various chromosomes. The QTLs explained from 5.06% to 8.28% of the total phenotypic variation of the traits. Some QTLs with pleiotropic effect were also identified. A pair of significant QTL for pH24 was also found to affect both CIE L and drip loss percentage. The significant QTL after characterization of the functional candidate genes on the QTL or around the QTL region may be effectively and efficiently used in marker assisted selection to achieve enhanced genetic improvement of the trait considered.

• Asian-Australasian Journal of Animal Sciences
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• 제23권8호
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• pp.993-999
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• 2010

Serum lysozyme gene is one of the important genes influencing the immune system as its product can cause lysis of bacterial cell wall by cleaving the peptidoglycan layer. The present investigation on the serum lysozyme gene of Indian riverine buffalo was undertaken with the objectives to identify and characterize single nucleotide polymorphic patterns by PCR-SSCP method as well as to study the effect of different genotypes on serum lysozyme activity and somatic cell count. A total of 280 animals comprising four different famous bubaline breeds (Murrah, Mehsana, Surti and Bhadawari), spread over six different farms across the country were used for this study. A 276 bp (partial intron 2, complete exon 3 and partial intron 3) fragment of lysozyme gene was screened for polymorphism using the SSCP technique. Four genotypes namely AA, AB, BC and AC were observed, out of which BC genotype was found to be the most frequent. Among these three alleles, C allele (0.38) was most prevalent in these populations. Various SSCP allelic variants were cloned for sequencing and sequences were submitted to NCBI Genbank. From the alignment of the nucleotide sequences of various allelic variants, it was found that there were differences in 12 positions among the alleles, out of which maximum variation (at 8 places) was found in the intronic region. The allele A was closer to allele-C than allele-B. Allele B was phylogenetically equidistant from both of the other alleles. Mean lysozyme activity determined in serum samples of different animals of Murrah buffalo was $27.35{\pm}2.42\;{\mu}g$ per ml of serum, whereas the mean somatic cell count was $1.25{\pm}0.13{\times}10^5$ cells per ml of milk. The SSCP pattern-wise effects of various genotypes on lysozyme activity and SCC were analyzed. Although the mean values were apparently different in various genotypes, these differences were statistically non-significant. It can be concluded that the riverine buffaloes are sufficiently polymorphic with respect to serum lysozyme gene. The absence of AA genotype in Bhadawari breed of buffalo can be considered as a marker for breed characterization. The difference of four nucleotides in exon-3 indicates high selection pressure on the gene.

• Asian-Australasian Journal of Animal Sciences
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• 제22권8호
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• pp.1078-1084
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• 2009

The Jindo dog is a Korean natural monument and is recognized by the Fédération Cynologique Internationale. A prominent feature is the diverse coat color within the breed. To analyze the genetic basis of variation in the Jindo coat color, we sequenced the protein-coding regions of the melanocortin 1 receptor gene (MC1R). The MC1R coding sequence was determined from 154 dogs in five breeds (Jindo, Labrador Retriever, English Springer Spaniel, Belgian Malinois, and German Shepherd). To confirm the genetic structure of sampled populations, we tested for Hardy-Weinberg equilibrium (HWE) and computed $F_{st}$ The sample populations did not significantly deviate from HWE. $F_{st}$ was 0.02 between white and fawn Jindo dogs; this was lower than $F_{st}$ between breeds. Six single nucleotide polymorphisms (SNPs) were detected in the MC1R coding region. Among the six SNPs, five were non-synonymous (S90G, T105A, Q159P, M264V, and R306ter) and one was synonymous SNP (Y298Y). From the SNPs, we predicted four haplotypes (H1, H2, H3, and H4) for Jindo MC1R. Jindo dogs had different haplotypes corresponding to different coat colors. H1 was frequently observed in white Jindo dogs with an odds ratio of 5.03 (95% CI: 2.27-11.18, p<0.0001), whereas H2 and H4 were observed only in fawn Jindo dogs. Our findings indicate that SNP haplotype can influence coat color. Knowledge of MC1R haplotypes can help discriminate white and fawn coats in Jindo dogs. We hope this report will trigger more research into the genetics of this traditional Korean dog and will be a reference for dogs of Asian origin. Also, our results will provide a useful genetic marker for Jindo dog breeders who have selected for specific colors.

• 응용통계연구
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• 제22권6호
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• pp.1239-1247
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• 2009

인간의 질병 또는 가축의 경제적인 특성에 관한 유전자의 규명은 매우 중요한 관심사이며, 우리나라 축산업을 대표하는 한우의 유전자원 보존과 능력향상은 매우 중요한 과제이다. 이를 연구하기 위해 기존 EST_based SNP 연관지도를 사용하여 발굴한 유전자로 연구되어왔으나 이는 통계학적 모델에 기반한 연관지도 작성법으로 실제 위치와는 차이가 있을 수 있다. 따라서 Lee (2009)에 의해 EST_based SNP 연관지도와 염기서열 분석으로 작성되어지는 Gene on sequence를 함께 고려하여 한우의 경제형질 연관 후보 DNA marker들이 발견되었다. 한편, 통계모형의 상호작용 효과를 고려할 때, 유전자와 같은 범주형 data에서 범주가 많을 경우 상호작용의 조합이 많아지므로 종종 모수들의 상호작용에 대한 해석과 모형을 결정하는 것이 어려울 수 있다. 그래서 비모수적인 방법으로 다중인자 차원축소방법 (MDR)을 사용해왔으며, 사례_대조 데이터에만 적용가능 MDR방법을 연속형 데이터에도 적용하기 위해 CART알고리즘을 적용한 확장된 다중인자 차원축소방법(E-MDR)이 제안되었다. 본 연구에서는 새롭게 발견된 단일염기다형성 (SNP)으로부터 E-MDR방법을 적용하여 한우의 경제형질(일당중체량, 근내지방도)에 영향을 주는 우수 유전자 단일염기다형성을 규명하였다.

• Asian-Australasian Journal of Animal Sciences
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• 제33권10호
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• pp.1558-1565
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• 2020

Objective: The objective of this study was to characterize the number of loci affecting growth traits and the distribution of single nucleotide polymorphism (SNP) effects on growth traits, and to understand the genetic architecture for growth traits in Hanwoo (Korean cattle) using genome-wide association study (GWAS), genomic partitioning, and hierarchical Bayesian mixture models. Methods: GWAS: A single-marker regression-based mixed model was used to test the association between SNPs and causal variants. A genotype relationship matrix was fitted as a random effect in this linear mixed model to correct the genetic structure of a sire family. Genomic restricted maximum likelihood and BayesR: A priori information included setting the fixed additive genetic variance to a pre-specified value; the first mixture component was set to zero, the second to 0.0001×σ²_g, the third 0.001×σ²_g, and the fourth to 0.01×σ²_g. BayesR fixed a priori information was not more than 1% of the genetic variance for each of the SNPs affecting the mixed distribution. Results: The GWAS revealed common genomic regions of 2 Mb on bovine chromosome 14 (BTA14) and 3 had a moderate effect that may contain causal variants for body weight at 6, 12, 18, and 24 months. This genomic region explained approximately 10% of the variance against total additive genetic variance and body weight heritability at 12, 18, and 24 months. BayesR identified the exact genomic region containing causal SNPs on BTA14, 3, and 22. However, the genetic variance explained by each chromosome or SNP was estimated to be very small compared to the total additive genetic variance. Causal SNPs for growth trait on BTA14 explained only 0.04% to 0.5% of the genetic variance Conclusion: Segregating mutations have a moderate effect on BTA14, 3, and 19; many other loci with small effects on growth traits at different ages were also identified.