• Journal of Animal Science and Technology
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• 제55권4호
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• pp.231-235
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• 2013

Carcass weight (CW) is one of the most important economic traits in pigs, directly affecting the income of farmers. In this study, a genome wide association study was performed to detect significant single nucleotide polymorphisms (SNPs) affecting CW in pigs derived from a $F_2$ intercross between Landrace and Korean native pig (KNP). Using high-density porcine SNP chips, highly significant SNPs were identified on SSC12. Two candidate genes, LOC100523510 and LOC100621652, were subsequently selected within this region and further investigated. Within these candidate genes, five SNPs were identified and genotyped using the VeraCode GoldenGate assay. The results revealed that one SNP in the LOC100621652 gene and four SNPs in the LOC100523510 gene are highly associated with CW. These SNP markers can thus have significant applications for improving CW in KNP. However, the functions of these candidate genes are not fully understood and require further study.

• 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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• 제5권4호
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• pp.188-193
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• 2007

The Functional Element SNPs Database (FESD) categorizes functional elements in human genic regions and provides a set of single nucleotide polymorphisms (SNPs) located within each area. Users may select a set of SNPs in specific functional elements with haplotype information and obtain flanking sequences for genotyping. Our previous version of FESD has been improved in several ways. We regenerated all the data in FESD II from recently updated source data such as HapMap, UCSC GoldenPath, dbSNP, OMIM, and $TRANSFAC^{(R)}$. Users can obtain information about tagSNPs and simulate LD blocks for each gene from four ethnicities in the HapMap project on the fly. FESD II employs a Java/JSP web interface for better platform portability and higher speed than PHP in the previous version. As a result, FESD II provides its users with more powerful information about functional element SNPs of human ethnicities.

• Journal of Plant Biotechnology
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• 제47권2호
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• pp.124-130
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• 2020

The sweet potato (Ipomoea batatas [L.] Lam.) is the sixth-most important crop in the world following rice, wheat, potato, maize, and cassava. Four varieties ('Beniharuka', 'Annobeni', 'Pungwonmi', 'Hogammi') and their Japanese cultivars are broadly distributed in South Korea. In the Korean marketplace, sweet potatoes are classified by color and shape, not by variety, making it necessary to differentiate varieties for uniform production and consumption. In this study, molecular markers were developed to distinguish the four varieties of sweet potato using SNPs and genotyping-by-sequencing (GBS) analysis via a tetra-primer amplification refractory mutation system (ARMS)-PCR. The results revealed that three variety-specific fragments (164 bp and 241 bp of SNP 04-27457768 and 292 bp of SNP 03-16195623) were amplified in the 'Beniharuka', 'Pungwonmi', and 'Annobeni' sweet potato varieties. There were instances where some varieties produced three bands within the gel electrophoresis, indicating heterozygosity at the given SNPs loci. DNA sequencing analysis also confirmed the results of electrophoresis at the SNPs loci. Overall, these molecular markers would provide a useful, rapid, and, simple evaluation method for the Korean sweet potato marketplace, where the mixing of varieties is a serious issue.

• Archives of Pharmacal Research
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• 제29권12호
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• pp.1132-1139
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• 2006

Single nucleotide polymorph isms (SNPs) in the MDR1 gene that are responsible for drug efflux can cause toxicity. Therefore, this study determined the SNPs of the Korean MDR1 gene, and analyzed the haplotypes and a linkage disequilibrium (LD) of the SNPs determined. The frequency of 9 SNPs from the MDR1 gene was determined by PCR-RFLP analyses of 100 to 500 healthy individuals. The frequcies of the SNPs were C3435T (47.7%), G2677T (37.6%), G2677A (4.4%), T1236C (21.7%), T129C (8%), A2956G (2.5%), T307C (1.5%), A41aG (9.2%), C145G (0%), and G4030C (0%). Analyses of the haplotype structure and an estimation of the LD of the combined polymorph isms demonstrated that the frequency of the 1236T-2677G-3435T haplotype is much higher in Koreans (14.1%) than in Chinese and western black Africans and the C3435T SNP in Koreans appears to have LD with T129C in Koreans for the first time. These results provide insight into the genetic variation of MDR1 in Koreans, and demonstrated the possibility of a new LD in this gene.

• 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.

• Genomics & Informatics
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• 제11권2호
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• pp.93-96
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• 2013

The prediction of externally visible characteristics from DNA has been studied for forensic genetics over the last few years. Externally visible characteristics include hair, skin, and eye color, height, and facial morphology, which have high heritability. Recent studies using genome-wide association analysis have identified genes and variations that correlate with human visible phenotypes and developed phenotype prediction programs. However, most prediction models were constructed and validated based on genotype and phenotype information on Europeans. Therefore, we need to validate prediction models in diverse ethnic populations. In this study, we selected potentially useful variations for forensic science that are associated with hair and eye color, iris pattern, and facial morphology, based on previous studies, and analyzed their frequencies in 1,920 Koreans. Among 20 single nucleotide polymorphisms (SNPs), 10 SNPs were polymorphic, 6 SNPs were very rare (minor allele frequency < 0.005), and 4 SNPs were monomorphic in the Korean population. Even though the usability of these SNPs should be verified by an association study in Koreans, this study provides 10 potential SNP markers for forensic science for externally visible characteristics in the Korean population.

• Genomics & Informatics
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• 제14권3호
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• pp.85-89
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• 2016

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease that affects multiple organ systems. Although the etiology of SLE remains unclear, it is widely accepted that genetic factors could be involved in its pathogenesis. A number of genome-wide association studies (GWASs) have identified novel single-nucleotide polymorphisms (SNPs) associated with the risk of SLE in diverse populations. However, not all the SNP candidates identified from non-Asian populations have been validated in Koreans. In this study, we aimed to replicate the SNPs that were recently discovered in the GWAS; these SNPs have not been validated in Koreans or have only been replicated in Koreans with an insufficient sample size to conclude any association. For this, we selected five SNPs (rs1801274 in FCGR2A and rs2286672 in PLD2, rs887369 in CXorf21, rs9782955 in LYST, and rs3794060 in NADSYN1). Through the replication study with 656 cases and 622 controls, rs1801274 in FCGR2A was found to be significantly associated with SLE in Koreans (odds ratio, 1.26, 95% confidence interval, 1.06 to 1.50; p = 0.01 in allelic model). This association was also significant in two other models (dominant and recessive). The other four SNPs did not show a significant association. Our data support that FCGR polymorphisms play important roles in the susceptibility to SLE in diverse populations, including Koreans.

• Genes and Genomics
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• 제40권11호
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• pp.1119-1125
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• 2018

Melanocortin 4 receptor: (MC4R) and Myostatin (MSTN) are two important growth trait-related genes in animals. In this study, we showed that two SNPs, MC4R-719A>G and MSTN-519C>T, found in the promoters of the MC4R and MSTN genes, respectively, are both associated with growth traits in Spinibarbus hollandi. Furthermore, we observed that there were significant associations between the expression levels of the MC4R and MSTN genes and these two growth trait-related SNPs. The expression level of MC4R gene in brain was lower in GG genotype fish with extremely high growth performance than that in AA genotype fish with extremely low growth performance. Expression level of the MSTN gene in muscle was lower in TT genotype fish with extremely high growth performance than that in CC and CT genotype fish with lower growth performance. The results indicated that these SNPs located in the promoters of MC4R and MSTN are associated with growth-related traits through modification of gene expression levels. The MSTN and MC4R SNPs may have useful application in effective marker-assisted selection aimed to increase output in S. hollandi.

• Journal of Animal Science and Technology
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• 제63권1호
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• pp.25-35
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• 2021

The purpose of this study is to estimate the single nucleotide polymorphism (SNP) effect for pH values affecting Berkshire meat quality. A total of 39,603 SNPs from 1,978 heads after quality control and 882 pH values were used estimate SNP effect by single step genomic best linear unbiased prediction (ssGBLUP) method. The average physical distance between adjacent SNP pairs was 61.7kbp and the number and proportion of SNPs whose minor allele frequency was below 10% were 9,573 and 24.2%, respectively. The average of observed heterozygosity and polymorphic information content was 0.32 ± 0.16 and 0.26 ± 0.11, respectively and the estimate for average linkage disequilibrium was 0.40. The heritability of pH45m and pH24h were 0.10 and 0.15 respectively. SNPs with an absolute value more than 4 standard deviations from the mean were selected as threshold markers, among the selected SNPs, protein-coding genes of pH45m and pH24h were detected in 6 and 4 SNPs, respectively. The distribution of coding genes were detected at pH45m and were detected at pH24h.