• Asian-Australasian Journal of Animal Sciences
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• v.18 no.8
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• pp.1061-1065
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• 2005

Growth rate is one of the economically important quantitative traits that affect carcass quantity in beef cattle. Two genes, bovine insulin-like growth factor I (IGF-I) and myogenic factor 5 (MYF5), were chosen as candidate genes for growth traits due to their important role in growth and development of mammals. The objectives of this study were to determine gene-specific single nucleotide polymorphism (SNP) markers of the IGF-I and MYF5 positional candidate genes and to investigate their associations with growth traits in Korean cattle. Genotyping of the SNP markers in these candidate genes was carried out using the single strand conformation polymorphism (SSCP) analysis. The frequencies of A and B alleles were 0.72 and 0.28 for IGF-I gene and 0.39 and 0.61 for MYF5 gene, respectively, in Korean cattle population examined. The gene-specific SNP marker association analysis indicated that the SNP genotype in IGF-I gene showed a significant association (p<0.05) with weight at 3 months (W3), and cows with AB genotype had higher W3 than BB genotype cows. The SNP genotype of MYF5 gene was found to have a significant effect (p<0.05) on the weight at 12 months (W12) and average daily gain (ADG), and cows with BB and AB genotypes had higher W12 and ADG compared with cows with AA genotype, respectively. However, no significant association between the SNP genotypes and any other growth traits was detected. The gene-specific SNP markers in the IGF-I and MYF5 candidate genes may be useful for selection on growth traits in Korean cattle.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.143-143
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• 2022

Plant defense systems against pathogens have been studied extensively and are currently a hot topic in plant science. Using a reverse genetics technique, this study looked into the involvement of the NO-downregulated NAD(P)-binding Rossmann-fold superfamily gene in plant growth and defense in Arabidopsis thaliana. For this purpose, the knockout and overexpressing plant of the candidate gene along with the relevant controls were exposed to control, oxidative and nitro-oxidative stresses. The results showed that candidate gene negatively regulates plants' root and shoot lengths. To investigate the role of the candidate gene in plant basal defense, R-gene-mediated resistance and systemic acquired resistance (SAR) plants were challenged with virulent or avirulent strains of Pseudomonas syringae pathovar tomato (Psf) DC3000. The results showed that the candidate gene negatively regulates plants' basal defense, R-gene-mediated resistance and SAR. Further characterization via GO analysis associated the candidate gene with metabolic and cellular processes and response to light stimulus, nucleotide binding and cellular location in the cytosol and nucleus. Protein structure analysis indicated the presence of a canonical Oxidoreductase family NAD (P)-binding Rossmann fold domain of 120 amino acids with a total of 121 plant homologs across 35 different plant species in the clad streptophyta. Arabidopsis eFP browser showed its expression in almost all the above-ground parts. Protein analysis indicated C225 and C359 as potential targets for S-Nitrosylation by NO. SMART analysis indicated possible interactions with mevalonate/galactokinase, galacturonic acid kinase, arabinose kinase, putative xylulose kinase, GroES-like zinc-binding alcohol dehydrogenase and various glyceraldehyde-3-phosphate dehydrogenases.

• Animal cells and systems
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• v.5 no.4
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• pp.341-346
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• 2001

Hypertension is a complex disease with strong genetic influences. Essential hypertension has been shown to be associated with insulin resistance. To clarify the genetic basis of insulin resistance in Hypertension, case-control association studies were performed to examine candidate genes for insulin resistance in hypertension. Polymorphisms investigated were the BstO I polymorphism of the $\beta$3-adrenergic receptor (ADRB3) gene, the Xba I Polymorphism of the glycogen synthase (GSY) gene, the Dde I polymorphism of the protein phosphatase 1 G subuit (PP1G) gene, the BstE II polymorphism of the glucagon receptor (GCG-R) gene, the Pst 1 polymorphism of the insulin (INS) gene and the Acc I polymorphism of the glucokinase (GCK) gene. No significant differences were observed in the distribution of alleles and genotypes of the ADRB3, GSY PP1G, GCG-R, INS, and GCK genes between hypertensive and normotensive groups. Although the frequencies in each of these polymorphisms were not significantly different between essential hypertensive and normotensive individuals, our results may provide additional information for linkage analysis and associative studies of disorders in carbohydrate metabolism or in cardiovascular disease.

• Reproductive and Developmental Biology
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• v.37 no.4
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• pp.185-192
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• 2013

Many countries have implemented genetic evaluation for fertility traits in recent years. In particular, reproductive trait is a complex trait and need to require a system-level approach for identifying candidate genes related to the trait. To find the candidate gene associated with reproductive trait, we applied a weighted gene co-expression network analysis from expression value of bovine genes. We identified three co-expressed modules associated with reproductive trait from bovine microarray data. Hub genes (ZP4, FHL2 and EGR4) were determined in each module; they were topologically centered with statistically significant value in the gene co-expression network. We were able to find the highly co-expressed gene pairs with a correlation coefficient. Finally, the crucial functions of co-expressed modules were reported from functional enrichment analysis. We suggest that the network-based approach in livestock may an important method for analyzing the complex effects of candidate genes associated with economic traits like reproduction.

• Genomics & Informatics
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• v.6 no.3
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• pp.153-156
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• 2008

Complex diseases such as stroke and cancer have two or more genetic loci and are affected by environmental factors that contribute to the diseases. Due to the complex characteristics of these diseases, identifying candidate genes requires a system-level analysis of the following: gene ontology, pathway, and interactions. A database and user interface, termed StrokeBase, was developed; StrokeBase provides queries that search for pathways, candidate genes, candidate SNPs, and gene networks. The database was developed by using in silico data mining of HGNC, ENSEMBL, STRING, RefSeq, UCSC, GO, HPRD, KEGG, GAD, and OMIM. Forty candidate genes that are associated with cerebrovascular disease were selected by human experts and public databases. The networked cerebrovascular disease gene maps also were developed; these maps describe genegene interactions and biological pathways. We identified 1127 genes, related indirectly to cerebrovascular disease but directly to the etiology of cerebrovascular disease. We found that a protein-protein interaction (PPI) network that was associated with cerebrovascular disease follows the power-law degree distribution that is evident in other biological networks. Not only was in silico data mining utilized, but also 250K Affymetrix SNP chips were utilized in the 320 control/disease association study to generate associated markers that were pertinent to the cerebrovascular disease as a genome-wide search. The associated genes and the genes that were retrieved from the in silico data mining system were compared and analyzed. We developed a well-curated cerebrovascular disease-associated gene network and provided bioinformatic resources to cerebrovascular disease researchers. This cerebrovascular disease network can be used as a frame of systematic genomic research, applicable to other complex diseases. Therefore, the ongoing database efficiently supports medical and genetic research in order to overcome cerebrovascular disease.

• Korean Journal of Poultry Science
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• v.38 no.2
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• pp.145-154
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• 2011

By a series of positional cloning, we successfully narrowed down the AM candidate region to approximately 1.2 Mbp on GGA2q including 7 functional genes. Subsequently, we identified WWP1 gene as the most likely AM candidate by sequence comparison. The amino acid sequence around the candidate mutation was highly conserved among tetrapods, suggesting that WWP1 is the causative gene of chicken muscular dystrophy. Transfection of mutated WWP1 gene into $C_2C_{12}$ myoblasts disrupted muscle differentiation process. The abnormal muscle differentiation is a characteristic of chicken muscular dystrophy, so we could demonstrate a part of phenotype of the disease. Furthermore, western blotting revealed that accumulation of caveolin-3 protein is limited in damaged muscle of muscular dystrophic chicken, suggesting caveolin-3 may be associated with the pathological change of the disease. We could conclude that WWP1 gene is the responsible one for chicken muscular dystrophy from these results, but the mechanism leading the onset should be clarified in the future. The information will contribute to the study of chicken muscular dystrophy and the corresponding human dystrophies.

• Environmental Mutagens and Carcinogens
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• v.22 no.1
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• pp.39-46
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• 2002

Obesity is a complex metabolic disorder with a strong genetic component. There are many candidate genes for obesity and its related phenotypes. We studied genetic variations between Korean obese and lean groups. Polymorphisms investigated were the Msp I polymorphism of the $\alpha$$_{2A}$-adrenergic receptor ($\alpha$$_{2A}$-AR) gene, the Mnl I polymorphism of the $\alpha$$_2$-adrenergic receptor ($\alpha$$_2$-AR) gene, the BstO I polymorphism of the $\beta$$_3$-adrenergic receptor ($\beta$$_3$-AR) gene, the Pml I polymorphism of the lamin A/C (LMNA) gene, the Hga I polymorphism of the clearance receptor (NPRC) gene, the Msp I polymorphism of the leptin gene, BclI polymorphism of the uncoupling protein 1 (UCPI) gene and the Hha I polymorphism of the fatty acid binding protein 2 (FABP2) gene. Among these genetic markers, Pml I polymorphism at the LMNA gene and Bcl I polymorphism at the UCP1 gene were significantly associated with obesity. However, further studies are required whether thease findings are reproduced in large population, although two polymorphisms might be useful as genetic markers in the ethiology of obesity in Korean population.ion.

• Asian-Australasian Journal of Animal Sciences
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• v.14 no.4
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• pp.587-596
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• 2001

In the last decade, rapid developments in molecular biotechnology and of genomic tools have enabled the creation of dense linkage maps across whole genomes of human, plant and animals. Successful development and implementation of interval mapping methodologies have allowed detection of the quantitative trait loci (QTL) responsible for economically important traits in experimental and commercial livestock populations. The candidate gene approach can be used in any general population with the availability of a large resource of candidate genes from the human or rodent genomes using comparative maps, and the validated candidate genes can be directly applied to commercial breeds. For the QTL detected from primary genome scans, two incipient fine mapping approaches are applied by generating new recombinants over several generations or utilizing historical recombinants with identity-by-descent (IBD) and linkage disequilibrium (LD) mapping. The high resolution definition of QTL position from fine mapping will allow the more efficient implementation of breeding programs such as marker-assisted selection (MAS) or marker-assisted introgression (MAI), and will provide a route toward cloning the QTL.

• Journal of Animal Science and Technology
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• v.55 no.4
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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.

• Bioinformatics and Biosystems
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• v.2 no.1
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• pp.24-27
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• 2007

Human cell regulatory mechanism is one of suspicious problems among biologists. Here we tried to uncover the human breast cancer cell regulatory mechanism from gene expression data (Marc J. Van de vijver, et. al., 2002) using a module network algorithm which is suggested by Segal, et. al.(2003) Finally, we derived a module network which consists of 50 modules and 10 tree depths. Moreover, to validate this candidate network, we applied a GO enrichment test and known transcription factor-target relationships from Transfac(R) (V. Matys, et. al, 2006) and HPRD database (Peri, S. et al., 2003).