• Asian-Australasian Journal of Animal Sciences
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• v.27 no.9
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• pp.1254-1262
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• 2014

Lymphoid enhancer binding factor 1 (LEF-1) is a member of the T-cell specific factor (TCF) family, which plays a key role in the development of breast endothelial cells. Moreover, LEF-1 gene has been identified as a candidate gene for teat number trait. In the present study, we detected two novel mutations (NC_010450.3:g. 99514A>G, 119846C>T) by DNA sequencing and polymerase chain reaction-restriction fragment length polymorphism in exon 4 and intron 9 of LEF-1 in Guanzhong Black, Hanjiang Black, Bamei and Large White pigs. Furthermore, we analyzed the association between the genetic variations with teat number trait in these breeds. The 99514A>G mutation showed an extremely significant statistical relevance between different genotypes and teat number trait in Guanzhong (p<0.001) and Large White (p = 0.002), and significant relevance in Hanjiang (p = 0.017); the 119846C>T mutation suggested significant association in Guanzhong Black pigs (p = 0.042) and Large White pigs (p = 0.003). The individuals with "AG" or "GG" genotype displayed more teat numbers than those with "AA"; the individuals with "TC" or "CC" genotype showed more teat numbers than those with "TT". Our findings suggested that the 99514A>G and 119846C>T mutations of LEF-1 affected porcine teat number trait and could be used in breeding strategies to accelerate porcine teat number trait improvement of indigenous pigs breeds through molecular marker assisted selection.

• Journal of the Korean Academy of Child and Adolescent Psychiatry
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• v.21 no.1
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• pp.17-22
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• 2010

Objectives ： Autism spectrum disorder (ASD) is a neurodevelopmental disorder that is characterized by abnormalities of social functioning, communication and behavior. The association of the 7q21-34 region with ASD has been reported. The DLX6 gene, which is located at the 7q22 region, is one of the positional and functional candidate genes for ASD. We found that there is no association between DLX6 polymorphisms and ASD in the Korean male population. Methods ： We selected three single nucleotide polymorphisms (SNPs) that might be implicated in the change of the DLX6 gene expression. The genomic DNA was collected from the venous blood of 147 male controls and 179 male patients with ASD. The genotypes of the selected SNPs were determined using the Illumina GoldenGate assay, and the statistical analyses were performed using HapAnalyzer software and SAS Enterprise. Results ： We found no association of the three SNPs in the DLX6 gene with ASD in the Korean male population. Conclusion ： Our study suggests that the three SNPs in the DLX6 gene are not associated with ASD, and we need to analyze the previously reported regions for their associations with ASD.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.4
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• pp.489-493
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• 2008

In 2004, Jorgensen and coworkers proposed the MUC4 gene as a candidate gene of enterotoxigenic Escherichia coli (ETEC) F4ab/ac receptor in piglets and a mutation of $G{\rightarrow}C$ in intron 7 of MUC4 was identified to be associated with the ETEC F4ab/ac adhesion phenotypes. In this study, we used 310 piglets of three breeds (Landrace, Large White and Chinese Songliao Black) to analyze the relationship between this mutation and the F4ab/ac adhesion phenotype. The results show that the genotypes at this site and the ETEC F4ab/ac adhesion phenotypes were not completely consistent, although they are very strongly associated. Among the individuals with genotype CC, which was identified as a resistant genotype to F4ab/ac adhesion, only 72.1% (124/172) were non-adhesive to ETEC F4ab and 77.9% (134/172) were non-adhesive to ETEC F4ac infections. This suggests that this mutation may not be the causative mutation for ETEC F4ab/ac adhesion, rather, the actual causative mutation may be in another gene closely linked to MUC4, or at aother site within the MUC4 gene. Our results also suggest that the receptors of F4ab and F4ac may be determined by two different but closely linked loci. In order to screen other genes related to F4ab/ac adhesion in piglets, the mRNA profiles from six full sib piglets, of which three were adhesive to ETEC F4ab/ac and three non-adhesive, were analyzed by suppression subtractive hybridization (SSH). One up-regulated gene, Ep-CAM, was selected for further analysis based on its role in the intestinal epithelial cells adhesion. Using real-time RT-PCR, we found that the Ep-CAM gene was significantly up-regulated in the piglets adhesive to F4ab/ac. It was mapped to SSC3q11-q14 by radiation hybrid mapping.

• The korean journal of orthodontics
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• v.38 no.2
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• pp.133-143
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• 2008

Objective: This study was performed to identify the characteristics of the MSX1 gene (locus chromosome 4p16) in Korean nonsyndromic cleft lip and palate (CL/P), which is assumed to be a major candidate gene acting as a causal factor in nonsyndromic CL/P and missing teeth. Methods: The 36 individuals (23 males and 13 females) who had visited the department of orthodontics at from 1998 to 2002 and who had nonsyndromic CL/P were included in the study. Using a PCR-based assay, the MSX1 gene was amplified, sequenced, and searched for inferred protein products (Reference: Homo sapiens MSX1, accession number AF426432 and NP_002439). The common single nucleotide polymorph isms were observed. Results: In exon 1, nucleotide "A" of the 253 basepair (bp) region was substituted for "G", and in the 255 bp region, nucleotide "G" was inserted. In exon 2, nucleotide "C" of the 11 bp region was substituted for "A", and "T" or "G" was inserted into the 351 bp region whereas "T" or "A" was inserted into the 352 bp region. In protein analysis, "Thr85Ala" missense mutation was found. The "Thr85Ala" missense mutation in this study is different from those of studies using subjects of other races. Conclusions: The results suggest that there is specific mutation of MSX1 in Korean and it plays an important role in Korean nonsyndromic CL/P. However, any distinct genetic polymorphisms between CL/P with missing teeth in the cleft region and CL/P without missing teeth could not be found.

• Korean Journal of Poultry Science
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• v.41 no.3
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• pp.191-196
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• 2014

The identification and utilization of potential candidate genes with significant effects on economically important traits have become increasingly important in poultry breeding programs. The ovocalyxin-32 (OCX-32) gene is located chromosome 9 in chicken, plays an important role in eggshell formation. This study was performed to assess the association between single nucleotide polymorphisms (SNPs) of OCX-32 gene and egg production traits in the Korean native chicken. Four Korean native chicken population (n = 181; including 46 females of Ogol, 46 females of white, 43 females of gray and 46 females of black) were used to analyze two SNPs (c.494A>C and c.267T>G) in the OCX-32 gene by PCR-RFLP (Polymerase Chain Reaction-Restricted Fragment Length Polymorphism). We measured egg production traits of age at first egg, first egg weight, egg production ratio and egg weight. The SNP c.494A>C was significantly associated with egg production ratio in Korean Ogol chickens (p<0.001) and egg weight in Korean white chickens (p<0.05). SNP c.267T>C was significantly associated with egg weight in Korean Ogol chickens (p<0.05). But there was no significant association in Korean gray and black chickens. Results suggest the possibility of using molecular markers in OCX-32 gene as a tool for performance and egg production traits in Korean native chicken breeding program.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.2
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• pp.187-196
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• 2020

Objective: Porcine respiratory disease is one of the most important health problems causing significant economic losses. To understand the genetic basis for susceptibility to swine enzootic pneumonia (EP) in pigs, we detected 102,809 single nucleotide polymorphisms in a total of 249 individuals based on genome-wide sequencing data. Methods: Genome comparison of susceptibility to swine EP in three pig breeds (Jinhua, Erhualian, and Meishan) with two western lines that are considered more resistant (Duroc and Landrace) using cross-population extended haplotype homozygosity and F-statistic (F_ST) statistical approaches identified 691 positively selected genes. Based on quantitative trait loci, gene ontology terms and literature search, we selected 14 candidate genes that have convincible biological functions associated with swine EP or human asthma. Results: Most of these genes were tested by several methods including transcription analysis and candidate genes association study. Among these genes: cytochrome P450 1A1 and catenin beta 1 (CTNNB1) are involved in fertility; transforming growth factor beta receptor 3 plays a role in meat quality traits; Wnt family member 2, CTNNB1 and transcription factor 7 take part in adipogenesis and fat deposition simultaneously; plasminogen activator, urokinase receptor (completely linked to AXL receptor tyrosine kinase, r² = 1) plays an essential role in the successful ovulation of matured oocytes in pigs; colipase like 2 (strongly linked to SAM pointed domain containing ETS transcription factor, r² = 0.848) is involved in male fertility. Conclusion: These adverse genes susceptible to swine EP may be selected while selecting for economic traits (especially reproduction traits) due to pleiotropic and hitchhiking effect of linked genes. Our study provided a completely new point of view to understand the genetic basis for susceptibility or resistance to swine EP in pigs thereby, provides insight for designing sustainable breed selection programs. Finally, the candidate genes are crucial due to their potential roles in respiratory diseases in a large number of species, including human.

• The Journal of Korean Medicine
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• v.26 no.1 s.61
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• pp.85-92
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• 2005

Objective: A number of candidate genes have been in implicated in the pathogenesis of obesity in humans. Tumor necrosis factor-alpha $(TNF-{\alpha})$ is expressed primarily in adipocytes, and elevated levels of this cytokine have been linked to obesity and insulin resistance. Recently, the A allele of a polymorphism at position 308 in the promoter region of $TNF-{\alpha}$ (G-308A) has been shown to increase transcription of the gene in adipocytes. Therefore, we designed this study to test whether obese and non-obese subjects differ in $TNF-{\alpha}$ genotype distribution, and how the genotypes affect anthropometric parameters, including degrees of body mass index (BMI). Methods : The study included 153 obese but otherwise healthy women ($BMI{\geq}kg/m^2$, range 25-54.7, age range 15-40 years) and 82 non-obese healthy women ($BMI, age range 15-40 years). Total fat mass and percent body fat were determined by dual-energy X-ray absorptiometry. Genomic DNA was extracted and used for Ncol restriction fragment length polymorphism (RFLP) based genotyping of $TNF-{\alpha}$. Results: No differences were observed for allelic and genotype frequencies between the obese ($BMI{\geq}25$) and non-obese women. Also, no association of TNF-(l polymorphism was observed with body mass index (BMI) for genotype in obese women. In addition, age, pertent body fat, BMI, and cholesterol levels did not differ by $TNF-{\alpha}$ genotype. However, waist-to­hip ratio (WHR) was significantly lower in subjects with $TNF-{\alpha}$ GA or AA genotype (0.94 0.07 vs. 0.920.03, P<0.005). Conclusion: These results suggest that $TNF-{\alpha}$ promoter polymorphism at position-308 is not a significant factor for BMI, but affects the WHR in obese healthy women from Koreans.

• Korean Journal of Poultry Science
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• v.40 no.2
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• pp.157-162
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• 2013

Both ODC and PRDM16 genes were known to be associated with body weight traits in chicken. These two genes were located on GGA3 and GGA21, respectively, where the QTLs of body weights are located. Therefore, the objectives of this study were to identify the SNPs in these two genes and their associations with body weight traits in Korean native chicken. Fluidigm Dynamic Array integrated fluidic circuits (IFCs) assay was used to genotype 7 SNPs consisting g.-353C>T, g.2136A>G, g.2524T>C, g.3607C>T SNPs of the ODC gene, and g.182216C>T, g.182290A>T, g.182491A>T SNPs of the PRDM16 gene. Statistical analysis showed that g.2136A>G SNP of the ODC was associated with body weight at 20 weeks of age and slaughter weight, and g.3607C>T SNP of the ODC was associated with body weight at 2 weeks of age. Association between g.182216C>T SNP of the PRDM16 and body weight at 12 weeks of age has also been revealed. In addition, g.182491A>T SNP of PRDM16 has significant correlation with body weight (BW) at 8 weeks, BW at 10 weeks and BW at 14 weeks of age. These results suggested that both ODC and PRDM16 could be strong candidate genes for body weight traits in Korean native chicken.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.6
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• pp.782-787
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• 2015

The myogenic regulatory factors is a family of transcription factors that play a key role in the development of skeletal muscle fibers, which are the main factors to affect the meat taste and texture. In the present study, we performed candidate gene analysis to identify single-nucleotide polymorphisms in the MyoD, Myf5, MyoG, and Mrf4 genes using polymerase chain reaction-single strand conformation polymorphism in 360 Erlang Mountain Chickens from three different housing systems (cage, pen, and free-range). The general linear model procedure was used to estimate the statistical significance of association between combined genotypes and muscle fiber traits of chickens. Two polymorphisms (g.39928301T>G and g.11579368C>T) were detected in the Mrf4 and MyoD gene, respectively. The diameters of thigh and pectoralis muscle fibers were higher in birds with the combined genotypes of GG-TT and TTCT (p<0.05). Moreover, the interaction between housing system and combined genotypes has no significant effect on the traits of muscle fiber (p>0.05). Our findings suggest that the combined genotypes of TT-CT and GG-TT might be advantageous for muscle fiber traits, and could be the potential genetic markers for breeding program in Erlang Mountain Chickens.

• Korean journal of dermatology
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• v.56 no.10
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• pp.609-613
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• 2018

Background: Psoriasis is a chronic inflammatory skin disease with an incidence of 0.5~3% of the worldwide population. The pathogenesis of psoriasis is related to dysregulated keratinocyte function and immune reactions. Notably, genetic factors are considered important etiological contributors. Globally, several researchers have recently performed genome-wide association studies (GWAS) to identify the genes related with psoriasis. Objective: We aimed to investigate the expression pattern of 2 candidate genes that were identified by GWAS. These include interleukin 28 receptor alpha (IL28RA) and CUB and Sushi multiple domains 1 (CSMD1). Methods: We applied imiquimod cream to develop a psoriasis-like mouse model and obtained skin tissue. We performed immunohistochemistry to detect the expression of IL-28A and CSMD1. Results: IL28RA expression increased at an early time point such as 1 day after the topical application of 5% imiquimod cream. However, its expression returned to baseline levels 2 weeks after the topical application of imiquimod cream. CSMD1 expression also increased after the topical application of imiquimod, with increased expression particularly observed in the upper epidermal layer. Notably, CSMD1 expression decreased 7 days after imiquimod cream application. Conclusion: These results suggest that IL28RA and CSMD1 may play key roles in the pathogenesis of psoriasis.