• Journal of the Korean Institute of Intelligent Systems
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• v.21 no.5
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• pp.575-580
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• 2011

With the increasing expectation on personalized medicine, it is getting importance to analyze medical information in molecular biology perspective. Gene expression data are one of representative ones to show the microscopic phenomena of biological activities. In gene expression data analysis, one of major concerns is to identify markers which can be used to predict disease occurrence, progression or recurrence in the molecular level. Existing markers candidate identification methods mainly depend on statistical hypothesis test methods. This paper proposes a search method based decision tree induction to identify candidate markers which consist of multiple genes. The propose method discretizes numeric expression level into three categorical values and allows candidate markers' genes to be expressed by their negation as well as categorical values. It is desirable to have some number of genes to be included in markers. Hence the method is devised to try to find candidate markers with restricted number of genes.

• 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.

• Journal of Animal Science and Technology
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• v.48 no.2
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• pp.169-190
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• 2006

Researches in livestock are currently actively progressing to improve economically important traits using DNA markers. In cattle, the candidate genes have been selected based on their known functions in the target QTL (quantitative trait locus) region in order to identify QTN (quantitative trait nucleotide) for improving productivities. In this review, molecular genetic studies for the meat related traits, one of the major determinant of market prices, have been fully described. Also recent emerging microarray technique for identifying candidate genes in cattle has been discussed. In case of microarray, cDNA microarrays have been replaced to oligoarrays in order to minimize the experimental errors in cattle. Since the first draft of bovine genome sequences was appeared in the public domain, more markers in relation to the quantitative traits will be discovered in a short period of time and genes affecting difficult-to-measure traits, such as disease resistance, can also be selected for marker assisted selection in near future.

• Journal of Animal Science and Technology
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• v.56 no.7
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• pp.23.1-23.7
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• 2014

Background: Scanning of the genome for selection signatures between breeds may play important role in understanding the underlie causes for observable phenotypic variations. The discovery of high density single nucleotide polymorphisms (SNPs) provide a useful starting point to perform genome-wide scan in pig populations in order to identify loci/candidate genes underlie phenotypic variation in pig breeds and facilitate genetic improvement programs. However, prior to this study genomic region under selection in commercially selected Berkshire and Korean native pig breeds has never been detected using high density SNP markers. To this end, we have genotyped 45 animals using Porcine SNP60 chip to detect selection signatures in the genome of the two breeds by using the $F_{ST}$ approach. Results: In the comparison of Berkshire and KNP breeds using the FDIST approach, a total of 1108 outlier loci (3.48%) were significantly different from zero at 99% confidence level with 870 of the outlier SNPs displaying high level of genetic differentiation ($F_{ST}{\geq}0.490$). The identified candidate genes were involved in a wide array of biological processes and molecular functions. Results revealed that 19 candidate genes were enriched in phosphate metabolism (GO: 0006796; ADCK1, ACYP1, CAMK2D, CDK13, CDK13, ERN1, GALK2, INPP1; MAK, MAP2K5, MAP3K1, MAPK14, P14KB, PIK3C3, PRKC1, PTPRK, RNASEL, THBS1, BRAF, VRK1). We have identified a set of candidate genes under selection and have known to be involved in growth, size and pork quality (CART, AGL, CF7L2, MAP2K5, DLK1, GLI3, CA3 and MC3R), ear morphology and size (HMGA2 and SOX5) stress response (ATF2, MSRB3, TMTC3 and SCAF8) and immune response (HCST and RYR1). Conclusions: Some of the genes may be used to facilitate genetic improvement programs. Our results also provide insights for better understanding of the process and influence of breed development on the pattern of genetic variations.

• 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.

• 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.

• Journal of Animal Science and Technology
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• v.60 no.6
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• pp.11.1-11.7
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• 2018

After pubertal, cohort of small antral follicles enters to gonadotrophin-sensitive development, called recruited follicles. This study was aimed to identify candidate genes in follicular cyclic recruitment via analysis of protein-protein interaction (PPI) network. Differentially expressed genes (DEGs) in ovine granulosa cells of small antral follicles between follicular and luteal phases were accumulated among gene/protein symbols of the Ensembl annotation. Following directed graphs, PTPN6 and FYN have the highest indegree and outdegree, respectively. Since, these hubs being up-regulated in ovine granulosa cells of small antral follicles during the follicular phase, it represents an accumulation of blood immune cells in follicular phase in comparison with luteal phase. By contrast, the up-regulated hubs in the luteal phase including CDK1, INSRR and TOP2A which stimulated DNA replication and proliferation of granulosa cells, they known as candidate genes of the cyclic recruitment.

• Proceedings of the National Institute of Ecology of the Republic of Korea
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• v.1 no.1
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• pp.68-73
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• 2020

Korean fir (Abies koreana) is an evergreen coniferous tree species that is unique to South Korea. A. koreana is found in a limited sub-alpine habitat and is considered particularly vulnerable to climate change. Identification of populations vulnerable to climate change is an important component of conservation programs. In this study, a heat stress-induced transcriptome RNA-seq dataset was used to identify a subset of six genes for assessment as candidate marker genes for ecologically vulnerable populations. Samples of A. koreana were isolated from ecologically stable and vulnerable regions of the Halla and Jiri mountains, and the expression levels of the six candidate markers were assessed using quantitative real-time polymerase chain reaction. All six of the candidate genes exhibited higher expression levels in samples from vulnerable regions compared with stable regions. These results confirm that the six high temperature-induced genes can be used as diagnostic markers for the identification of populations of A. koreana that are experiencing stress due to the effects of climate change.

• 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.

• Reproductive and Developmental Biology
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• v.37 no.4
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• pp.199-203
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• 2013

This experiment was conducted to investigate the genetic effects of candidate genes on the growth of spleen and liver tissues using dietary Curcuma longa (C. longa) supplementation. Expression analyses of candidate genes regarding animal growth was performed in order to determine the factors affecting the growth related to immune components of Curucumin, Turmerone, and Zingiberene as the bile secretion Paratolyl methyl carbinol (PTMC). The animals were divided into four groups of five chicks supplied with experimental diets of C. longa at 0.25, 0.5 and 1% and controls. The 19 growth-related genes were known to cell maturation, differentiation significant expression patterns in this analysis. Expression of growth response-related genes in chicks supplemented with 1% of C. longa showed better growth performance than chicks with 0.25 and 0.5% in spleen (p<0.05). The IGF1, MSTN, POU1F1, ADCYAP1 gene were known to central roles in mediating gonadotropin function, regulating steroidogenesis and promoting oocyte growth and maturation. Sex steroids, androgen and estrogen can affect sex differentiation and also can affect muscle development. On the other hand, GHSR and FABP3 gene showed significant expression patterns in this analysis. The results would be used as basic information for the variation of growth-related genes expression on the cell growth, sex cell growth, and sex hormones according to dietary supplementation with C. longa in chickens.