• Journal of Animal Science and Technology
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• 제55권1호
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• pp.13-18
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• 2013

본 연구는 농협 한우개량사업소 후대검정우 552두의 도체중, 배최장근단면적, 등지방두께 및 근내지방도를 측정한 후 고밀도 SNP 패널(777K)을 사용하여 유전체 혈연 행렬(Genetic Relationship Matrix, GRM)을 추정하고 GBLUP (Genomic Best Linear Unbiased Prediction) 방법으로 GEBV (Genomic Estimated Breeding Value)를 구하여 교차 검증(Cross-validation) 방법으로 그 정확도를 추정함으로써 유전체 선발 기법을 한우 유전평가 체계에 적용하기 위한 기초자료로 이용하고자 수행하였다. 교차 검증 방법으로 각 형질별로 추정된 유전체 육종가의 정확도는 0.915~0.957로 상당히 높게 추정되었다. 대립유전자의 빈도로 계산된 유전체 혈연 행렬을 이용하여 GBLUP 방법으로 추정된 육종가 정확도의 최대 차이는 후대검정우 534두에 대하여 도체중, 배최장근단면적, 등지방 두께 및 근내지방도 순으로 각각 9.56%, 5.78%, 5.78% 및 4.18% 정도의 수준으로 상승했고, 혈통 기록상의 모든 개체 3,674두에 대해서는 형질 별로 최대 13.54%, 6.50%, 6.50% 및 4.31% 정도의 수준으로 증가한 결과가 추정되었다. 이는 한우 보증씨수소의 선발 시스템에서 아직 표현형 자료를 생산할 수 없는 당대검정 후보축 대한 집단을 조성할 때 유전체 정보를 이용한 사전 선발을 활용하면 기존의 상대적으로 낮았던 육종가의 정확도의 상승 효과와 세대 간격의 단축으로 인하여 유전적 개량량을 증대시킬 수 있을 것으로 기대된다. 본 연구에서 genomic breeding value 추정을 위하여 조성된 집단의 경우는 후대 검정우 집단으로서 개체들 간의 혈연관계가 높으며, 이미 전통적인 BLUP 방법으로도 상당히 높은 정확도를 가진 집단을 이용하였다. 그러나, 현재 한우 집단에 대한 유전체 자료 구축 시 이용할 수 있는 정확한 자료는 후대검정우 집단 외에는 참조 집단을 조성할 수 있는 대안이 없으므로, 지속적인 유전체 검정을 위해서는 다양한 유전적 조성이 구축된 참조 집단을 구축해야 할 것으로 사료된다. 또한 유전체 검정을 통한 정확도 상승효과를 기대하기 위해서 지속적으로 참조 집단의 크기를 늘릴 필요성이 있다.

• The Korean Journal of Physiology and Pharmacology
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• 제12권2호
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• pp.83-87
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• 2008

The fyn-related kinase (FRK) belongs to the tyrosine kinase family of protein kinases. Recent studies have shown that Frk affects pancreatic beta cell number during embryogenesis and promotes beta cell cytotoxic signals in response to streptozotocin. To investigate the genetic association between FRK polymorphisms and the risk of obesity in Korean population, single nucleotide polymorphisms (SNPs) in the FRK gene region were selected and analyzed. The body mass index (BMI) was calculated, and biochemical data (systolic blood pressure, diastolic blood pressure, hemoglobin A1C, triglyceride, total cholesterol, high density lipoprotein, and low density lipoprotein) of blood sample from each subject were also measured. One hundred fifty five healthy control and 204 overweight/obesity subjects were recruited. Genotype frequencies of six SNPs [rs6568920 (+8391G>A), rs3756772 (+56780A>G), rs3798234 (+75687C>T), rs9384970 (+68506G>A), rs1933739 (+72978G>A), and rs9400883 (+75809A>G)] in the FRK gene were determined by Affymetrix Targeted Genotyping Chip data. According to the classification of Korean Society for the Study of Obesity, control (BMI 18 to < 23) and overweight/obesity (BMI$\geq$23) subjects were recruited. For the analysis of genetic data, EM algorithm, SNPStats, Haploview, HapAnalyzer, SNPAnalyzer, and Helixtree programs were used. Multiple logistic regression analysis (codominant, dominant, and recessive models) was performed. Age and gender as covariates were adjusted. For biochemical data, Student's t test was used. The mean value of BMI in the control and overweigh/obesity groups was 21.1${\pm}$1.2 (mean${\pm}$SD) and 25.6${\pm}$2.0, respectively. All biochemical data of the overweight/obesity group were statistically significance, compared with the control group. Among six SNPs, two linkage disequilibrium (LD) blocks were discovered. One block consisted of rs1933739 and rs9400883, and the other comprised rs3756772 and rs3798234. One SNP (rs9384970, +68506G>A) showed an association with overweight/obesity in the codominant model (p=0.03). Interestingly, the AA genotype distribution in the overweight/obesity group (n=7, 3.5%) was higher than those in the control group (n=1, 0.6%), which is not found in either Japanese or Chinese subjects. Therefore, the AA genotype of rs9384970 may be a risk factor for development of obesity in Korean population. The results suggest that FRK may be associated with overweight/obesity in Korean population.

• IMMUNE NETWORK
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• 제5권4호
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• pp.205-214
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• 2005

Background: We examined global gene expression profiles of peripheral blood mononuclear cells (PBMCs) in patients with ulcerative colitis (DC), and tested whether the identified genes with the altered expression might be associated with susceptibility to UC. Methods: PBMCs from 8 UC and 8 normal healthy (NH) volunteers were collected, and total RNAs were subjected to the human 8.0K cDNA chip for the micro array analysis. Real time-PCR (RT-PCR) was performed to verify the results of micro array. One hundred forty UC patients and 300 NH controls were recruited for single nucleotide polymorphism (SNP) analysis. Results: Twenty-five immune function-related genes with over 2-fold expression were identified. Of these genes, two chemokines, namely, CXCL1 and CCL20, were selected because of their potential importance in the evocation of host innate and adaptive immunity. Four SNPs were identified in the promoter and coding regions of CXCL1, while there was no significant difference between all patients with UC and controls in their polymorphisms, except minor association at g.57A>G (rs2071425, p=0.02). On the other hand, among three novel and one known SNPs identified in the promoter region of CCL20, g. -1,706 G>A (p=0.000000055), g. -1,458 G>A (p=0.0048), and g. -962C>A (p=0.0006) were found to be significantly associated with the susceptibility of Uc. Conclusion: Altered gene expression in mononuclear cells may contribute to IBD pathogenesis. Although the findings need to be confirmed in other populations with larger numbers of patients, the current results demonstrated that polymorphisms in the promoter region of CCL20 are positively associated with the development of Uc.

• Nutrition Research and Practice
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• 제2권4호
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• pp.289-294
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• 2008

Pre-B-cell leukemia transcription factor 1 (PBX1), which is located on chromosome 1q23, was recently reported to be associated with type 2 diabetes mellitus. We examined whether single nucleotide polymorphisms (SNPs) of the PBX1 gene are associated with overweight/obesity in a Korean population. We genotyped 66 SNPs in the PBX1 gene and investigated their association with clinical phenotypes found in 214 overweight/obese subjects and 160 control subjects using the Affymetrix Targeted Genotyping chip array. Seven SNPs (g.+75l86C>T, g.+78350C>A, g.+80646C>T, g.+138004C>T, g.+185219G>A, g.+191272A>C, and g.+265317T>A) were associated with the risk of obesity in three models (codominant, dominant, and recessive) (P=0.007-0.05). Haplotype 1 (CAC) and 3 (TAC) of block 3 and haplotype 2 (GGAAT) of block 10 were also strongly associated with the risk of obesity. In the control group, subjects that had homozygote for the major allele for both g.+185219G>A and g.+191272A>C showed lower high density lipoprotein-cholesterol (HDL-C) level compared to those possessing the minor allele, suggesting that the association between the homozygote for the major allele for both g.+185219G>A and g.+191272A>C and HDL-C is attributable to the increased risk of obesity. This study suggests that the PBX1 gene is a possible risk factor in overweight/obese patients.

• Asian-Australasian Journal of Animal Sciences
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• 제32권12호
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• pp.1836-1843
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• 2019

Objective: Social genetic effects (SGE) are an important genetic component for growth, group productivity, and welfare in pigs. The present study was conducted to evaluate i) the feasibility of the single-step genomic best linear unbiased prediction (ssGBLUP) approach with the inclusion of SGE in the model in pigs, and ii) the changes in the contribution of heritable SGE to the phenotypic variance with different scaling ${\omega}$ constants for genomic relationships. Methods: The dataset included performance tested growth rate records (average daily gain) from 13,166 and 21,762 pigs Landrace (LR) and Yorkshire (YS), respectively. A total of 1,041 (LR) and 964 (YS) pigs were genotyped using the Illumina PorcineSNP60 v2 BeadChip panel. With the BLUPF90 software package, genetic parameters were estimated using a modified animal model for competitive traits. Giving a fixed weight to pedigree relationships (${\tau}:1$), several weights (${\omega}_{xx}$, 0.1 to 1.0; with a 0.1 interval) were scaled with the genomic relationship for best model fit with Akaike information criterion (AIC). Results: The genetic variances and total heritability estimates ($T^2$) were mostly higher with ssGBLUP than in the pedigree-based analysis. The model AIC value increased with any level of ${\omega}$ other than 0.6 and 0.5 in LR and YS, respectively, indicating the worse fit of those models. The theoretical accuracies of direct and social breeding value were increased by decreasing ${\omega}$ in both breeds, indicating the better accuracy of ${\omega}_{0.1}$ models. Therefore, the optimal values of ${\omega}$ to minimize AIC and to increase theoretical accuracy were 0.6 in LR and 0.5 in YS. Conclusion: In conclusion, single-step ssGBLUP model fitting SGE showed significant improvement in accuracy compared with the pedigree-based analysis method; therefore, it could be implemented in a pig population for genomic selection based on SGE, especially in South Korean populations, with appropriate further adjustment of tuning parameters for relationship matrices.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.269-269
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• 2022

Pre-harvest sprouting (PHS) on rice panicles is getting problematic in recent several years in Korea due to climate changes such as high temperature and more frequent typhoons during harvesting season. PHS negatively affects grain quality severely and also yield. Genetic improvement of Korean varieties (Oryza sativa ssp. japonica) through a marker assisted-backcross breeding (MAB) with the known PHS resistant genes must be one of ideal solutions. However, the final breeding products of MAB occasionally exhibit unwanted traits, especially the cross between genetically distant parents. This might be caused by linkage drag and/or presence of the gene-unlinked donor introgressions, resulting that the final products could not be released to the farmers. The major PHS resistance gene, Sdr4 (Seed dormancy 4) originated from an indica cultivar, Kasalath was selected as a donor gene. In order to avoid unexpected phenotypes in the breeding products, we performed a precision marker-based breeding (PMBB) consisting of foreground, recombinant, and background selections (FS, RS, and BS) which aim to develop 'single small introgression lines' (~100 kb introgression). Korean varieties (Ilpum and Gopum) were crossed with Kasalath. We developed Sdr4-allele specific markers for FS and a set of polymorphic flanking markers near the Sdr4 (-350kb and +420kb) for RS. To minimize linkage drag, the small introgression (< 125kb) containing Sdr4 was selected in Ilpum background (BC₂F₄) through 1^st RS with ~1,200 F₂ or BC₁F₂ plants (one side trimmed) and then 2^nd RS with ~1,000 progenies from the 1^st RS selected plants (another side trimmed). After RS, the selected lines were genotyped by using Infinium 7K SNP chip to detect other donor introgressions and the lines were backcrossed. Currently BS is on-going from the backcross-derived progenies with BS markers to remove residual introgressions. During the PMBB process, genetic effect of Sdr-4-Kasalath allele was confirmed in Ilpum and Gopum backgrounds by PHS phenotyping using the segregating BC₂F₃ or BC₁F₄ materials. The Sdr4 PMBB lines in Ilpum background (< 125kb introgression) will be valuable genetic resources to improve PHS resistance in modem popular temperate japonica varieties.