• 한국가금학회지
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• 제38권3호
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• pp.231-237
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• 2011

There is limited information of the genetic effect for fatty acid composition in chicken meat. This study assessed the association of FABP3 and FABP4 genes affecting fatty acid composition in broilers. Two single nucleotide polymorphisms (SNPs) were detected in FABP3 gene and five SNPs were identified in FABP4 gene. The SNPs located in intron 1 and exon 1 of FABP3 and FABP4, respectively, were used for genotyping using PCR-RFLP method. The SNPg.285C >T in FABP4 showed suggestive association with high arachidonic acid (C20 : 4) in CT genotypes (P = 0.068). However, the SNP g.508C > T in FABP3 showed no significant associations with fatty acid composition. These results are the first report to investigate the SNPs in FABP3 and FABP4 genes and their associations with fatty acid composition, although we only found the possible association of FABP4 SNP with fatty acid composition. These results should provide valuable information for further investigation of the genes affecting fatty acid composition in chicken.

• Genomics & Informatics
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• 제12권4호
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• pp.236-239
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• 2014

The genetic regulation of glucose and insulin levels might be modified by adiposity. With regard to the genetic factors that are altered by adiposity, a large meta-analysis on the interactions between genetic variants and body mass index with regard to fasting glucose and insulin levels was reported by the Meta-Analyses of Glucose- and Insulin-related trait Consortium (MAGIC), based on European ancestry. Because no replication study has been performed in other ethnic groups, we first examined the link between reported single-nucleotide polymorphisms (SNPs) and fasting glucose and insulin levels in a large Korean cohort (Korean Genome and Epidemiology Study cohort [KoGES], n = 5,814). The MAGIC study reported 7 novel SNPs for fasting glucose levels and 6 novel SNPs for fasting insulin levels. In this study, we attempted to replicate the association of 5 SNPs with fasting glucose levels and 5 SNPs with fasting insulin levels. One SNP (rs2293941) in PDX1 was identified as a significant obesity-modifiable factor in Koreans. Our results indicate that the novel loci that were identified by MAGIC are poorly replicated in other ethnic groups, although we do not know why.

• 대한의생명과학회지
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• 제27권3호
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• pp.187-194
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• 2021

Platelets are derived from fragments formed in the cytoplasm of bone marrow megakaryocytes. Platelet count (PLT) can be altered by factors such as platelet production, destruction, and inflammation. In a previous study, the significant single nucleotide polymorphisms (SNP) were reported by the genome-wide association study (GWAS) for PLT in Koreans. In this study, it was confirmed whether significant SNPs were replicated in the HEXA (The Health Examinees) cohort. As a result, the SNPs of the THPO (rs6141), BAK1 (rs210314, rs9296095), GGNBP1 (rs75080135), ACAD10 (rs6490294), and ABCC4 (rs4148441) were significantly correlated with PLT (P < 10^-8). At the same time, it was confirmed that the direction of influence was the same according to the genotype. In conclusion, it can be seen that common SNPs are associated with the platelet count regardless of the cohort for Koreans.

• Genomics & Informatics
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• 제21권3호
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• pp.28.1-28.13
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• 2023

Mild cognitive impairment (MCI) is a clinical syndrome characterized by the onset and evolution of cognitive impairments, often considered a transitional stage to Alzheimer's disease (AD). The genetic traits of MCI patients who experience a rapid progression to AD can enhance early diagnosis capabilities and facilitate drug discovery for AD. While a genome-wide association study (GWAS) is a standard tool for identifying single nucleotide polymorphisms (SNPs) related to a disease, it fails to detect SNPs with small effect sizes due to stringent control for multiple testing. Additionally, the method does not consider the group structures of SNPs, such as genes or linkage disequilibrium blocks, which can provide valuable insights into the genetic architecture. To address the limitations, we propose a Bayesian bi-level variable selection method that detects SNPs associated with time of conversion from MCI to AD. Our approach integrates group inclusion indicators into an accelerated failure time model to identify important SNP groups. Additionally, we employ data augmentation techniques to impute censored time values using a predictive posterior. We adapt Dirichlet-Laplace shrinkage priors to incorporate the group structure for SNP-level variable selection. In the simulation study, our method outperformed other competing methods regarding variable selection. The analysis of Alzheimer's Disease Neuroimaging Initiative (ADNI) data revealed several genes directly or indirectly related to AD, whereas a classical GWAS did not identify any significant SNPs.

• Asian-Australasian Journal of Animal Sciences
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• 제29권9호
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• pp.1256-1264
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• 2016

Adrenergic, alpha-1B-, receptor (ADRA1B) and peroxisome proliferator-activated receptor gamma, coactivator 1 beta (PPARGC1B) genes are involved in regulation of hen ovarian development. In this study, these two genes were investigated as possible molecular markers associated with hen-housed egg production, egg weight (EW) and body weight in Chinese Dagu hens. Samples were analyzed using the polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) technique, followed by sequencing analysis. Two novel single nucleotide polymorphisms (SNPs) were identified within the candidate genes. Among them, an A/G transition at base position 1915 in exon 2 of ADRA1B gene and a T/C mutation at base position 6146 in the 3'- untranslated region (UTR) of PPARGC1B gene were found to be polymorphic and named SNP A1915G and T6146C, respectively. The SNP A1915G (ADRA1B) leads to a non-synonymous substitution (aspartic acid 489-to-glycine). The 360 birds from the Dagu population were divided into genotypes AA and AG, allele A was found to be present at a higher frequency. Furthermore, the AG genotype correlated with significantly higher hen-housed egg production (HHEP) at 30, 43, 57, and 66 wks of age and with a higher EW at 30 and 43 wks (p<0.05). For the SNP T6146C (PPARGC1B), the hens were typed into TT and TC genotypes, with the T allele shown to be dominant. The TC genotype was also markedly correlated with higher HHEP at 57 and 66 wks of age and EW at 30 and 43 wks (p<0.05). Moreover, four haplotypes were reconstructed based on these two SNPs, with the AGTC haplotype found to be associated with the highest HHEP at 30 to 66 wks of age and with higher EW at 30 and 43 wks (p<0.05). Collectively, the two SNPs identified in this study might be used as potential genetic molecular markers favorable in the improvement of egg productivity in chicken breeding.

• Asian-Australasian Journal of Animal Sciences
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• 제27권9호
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• pp.1236-1243
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• 2014

Genetics is important for breeding and selection of horses but there is a lack of well-established horse-related browsers or databases. In order to better understand horses, more variants and other integrated information are needed. Thus, we construct a horse genomic variants database including expression and other information. Horse Single Nucleotide Polymorphism and Expression Database (HSDB) (http://snugenome2.snu.ac.kr/HSDB) provides the number of unexplored genomic variants still remaining to be identified in the horse genome including rare variants by using population genome sequences of eighteen horses and RNA-seq of four horses. The identified single nucleotide polymorphisms (SNPs) were confirmed by comparing them with SNP chip data and variants of RNA-seq, which showed a concordance level of 99.02% and 96.6%, respectively. Moreover, the database provides the genomic variants with their corresponding transcriptional profiles from the same individuals to help understand the functional aspects of these variants. The database will contribute to genetic improvement and breeding strategies of Thoroughbreds.

• Asian-Australasian Journal of Animal Sciences
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• 제27권10호
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• pp.1381-1386
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• 2014

In spite of variation in coat color, size, and production traits among indigenous Bangladeshi cattle populations, genetic differences among most of the populations have not been investigated or exploited. In this study, we used a high-density bovine single nucleotide polymorphism (SNP) 80K Bead Chip derived from Bos indicus breeds to assess genetic diversity and population structure of 2 Bangladeshi zebu cattle populations (red Chittagong, n = 28 and non-descript deshi, n = 28) and a semi-domesticated population (gayal, n = 17). Overall, 95% and 58% of the total SNPs (69,804) showed polymorphisms in the zebu and gayal populations, respectively. Similarly, the average minor allele frequency value was as high 0.29 in zebu and as low as 0.09 in gayal. The mean expected heterozygosity varied from $0.42{\pm}0.14$ in zebu to $0.148{\pm}0.14$ in gayal with significant heterozygosity deficiency of 0.06 ($F_{IS}$) in the latter. Coancestry estimations revealed that the two zebu populations are weakly differentiated, with over 99% of the total genetic variation retained within populations and less than 1% accounted for between populations. Conversely, strong genetic differentiation ($F_{ST}=0.33$) was observed between zebu and gayal populations. Results of population structure and principal component analyses suggest that gayal is distinct from Bos indicus and that the two zebu populations were weakly structured. This study provides basic information about the genetic diversity and structure of Bangladeshi cattle and the semi-domesticated gayal population that can be used for future appraisal of breed utilization and management strategies.

• Asian-Australasian Journal of Animal Sciences
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• 제31권1호
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• pp.13-18
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• 2018

Objective: Meat quality including muscle color in chickens is an important trait and continuous selective pressures for fast growth and high yield have negatively impacted this trait. This study was conducted to investigate genetic variations responsible for regulating muscle color. Methods: Whole genome re-sequencing analysis using Illumina HiSeq paired end read method was performed with pooled DNA samples isolated from two broiler chicken lines divergently selected for muscle color (high muscle color [HMC] and low muscle color [LMC]) along with their random bred control line (RAN). Sequencing read data was aligned to the chicken reference genome sequence for Red Jungle Fowl (Galgal4) using reference based genome alignment with NGen program of the Lasergene software package. The potential causal single nucleotide polymorphisms (SNPs) showing non-synonymous changes in coding DNA sequence regions were chosen in each line. Bioinformatic analyses to interpret functions of genes retaining SNPs were performed using the ingenuity pathways analysis (IPA). Results: Millions of SNPs were identified and totally 2,884 SNPs (1,307 for HMC and 1,577 for LMC) showing >75% SNP rates could induce non-synonymous mutations in amino acid sequences. Of those, SNPs showing over 10 read depths yielded 15 more reliable SNPs including 1 for HMC and 14 for LMC. The IPA analyses suggested that meat color in chickens appeared to be associated with chromosomal DNA stability, the functions of ubiquitylation (UBC) and quality and quantity of various subtypes of collagens. Conclusion: In this study, various potential genetic markers showing amino acid changes were identified in differential meat color lines, that can be used for further animal selection strategy.

• Journal of Preventive Medicine and Public Health
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• 제36권3호
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• pp.213-222
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• 2003

Genomic epidemiology is defined as 'an evoking field of inquiring that uses the systematic application of epidemiologic methods are approaches in population-based studies of the impact of human genetic variation on health and disease (Khoury, 1998)'. Most human diseases are caused by the intricate interaction among environmental exposures and genetic susceptibility factors. Susceptibility genes involved in disease pathogenesis are categorized into two groups: high penetrance genes (i.e., BRAC1, RB, etc.) and lour penetranoe genes (i.e., GSTs, Cyps, XRCC1, ets.), and low penetrance susceptibility genes has the higher priority for epidemiological research due to high population attributable risk. In this paper, the summarized results of the association study between single nucleotide polymorphisms (SNPs) and breast cancer in Korea were introduced and the international trends of genomic epidemiology research were reviewed with an emphasis on internee-based case-control and cohort consortium.