• Journal of the Korean Data and Information Science Society
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• v.20 no.1
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• pp.171-178
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• 2009

In order to make the high quality Korean cattle, it has been identified the gene which influence to various economic characters. In this paper, we introduce Restricted Partition Method for gene-gene interaction analysis. Further, economic traits, longissimus muscle dorsi area (LMA), carcass cold weight (CWT) and average daily gain (ADG) are applied with Restricted Partition Method (RPM). The SNP (19_1)$^*$SNP (28_2) was selected and was best marker on Single nucleotide polymorphisms (SNPs). It also influenced SNP (19_1)$^*$SNP (28_2) was an very important marker for economic character and to make the thing know it became.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.8
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• pp.1065-1070
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• 2006

The avian uncoupling protein (avUCP) is a member of the mitochondrial transporter superfamily that uncouples proton entry in the mitochondrial matrix from ATP synthesis. The sequencing analysis method was used to identify nucleotide polymorphisms within the avUCP gene in Korean native chicken (KNC). This study identified ten single nucleotide polymorphisms (SNPs) in the avUCP gene. We analyzed the SNPs of the avUCP gene to investigate whether polymorphism in the gene might be responsible for quantitative variations in economic traits in KNC. Three significant polymorphic sites for economic traits were avUCP C+282T (mean body weight, p<0.05), avUCP C+433T (daily percent lay, p<0.05), and avUCP T+1316C (daily percent lay, p<0.05). The frequency of each SNP was 0.125 (C+282T in avUCP gene exon 1 region), 0.150 (C+433T in avUCP gene intron 1 region), and 0.15 (T+1316C in avUCP gene exon 3 region), respectively. Among the identified SNPs, one pair of SNPs (genotype CC, C+282T and TT, avUCP C+433T) showed the highest daily percent lay (p<0.05) and mean body weight (p<0.05) and the frequency was 0.067. This study of the avUCP gene could be useful for genetic studies of this gene and selection on economic traits for KNC.

• Journal of Life Science
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• v.24 no.11
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• pp.1168-1173
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• 2014

The homogentisate 1,2-dioxygenase (HGD) gene, which consists of 14 exons and spans approximately 42630bp on Bos taurus autosome 1 (BTA 1), is one of the six enzymes required for catabolism of the aromatic amino acids tyrosine and phenylalanine. It has been reported that BTA1 harbors quantitative trait loci that effect marbling score (MS), carcass weight (CW), and longissimus muscle area (LMA) in cattle. The aim of this study was to identify the single nucleotide polymorphisms (SNPs) in the HGD gene and to analyze their association with economic traits in Korean cattle (Hanwoo). Genetic polymorphisms were screened by direct sequencing, which detected 10 SNPs (T11187C, T11301A, T11398G, G29833A, G34256T, G34257C, T34284C, T42333G, T42348C, and T42468C). Six polymorphic sites were selected for genotyping, and economic traits were analyzed using a general linear model in Korean cattle (n=90). The observed genotype frequencies for G34256T were 0.5843(GG), 0.3708(GT), and 0.0449(TT). In addition, 0.3596(GG), 0.3708(GC), and 0.2697(CC) were observed for the G34257C mutation. Statistical association analysis revealed that G34256T polymorphisms were significantly associated with MS, and G34257C polymorphisms were significantly associated with MS and LMA (p<0.05). Further study is needed in order to use the genetic variant as a marker for marker-assisted selection in Korean cattle.

• Journal of Plant Biotechnology
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• v.44 no.2
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• pp.135-141
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• 2017

Cudrania tricuspidata Bureau is a widely used medicinal perennial woody plant. For conservation and germplasm utilization of the plant, it is imperative to obtaining information regarding the genetic diversity of the plant populations. Although C. tricuspidata is an important medicinal plant registered in South Korea, no molecular markers are currently available to distinguish Korean-specific ecotypes from other ecotypes of different countries. In this study, we developed single nucleotide polymorphism (SNP) markers derived from chloroplast genomic sequences to identify distinct Korean-specific ecotypes of C. tricuspidata via the amplification refractory mutation system (ARMS)-PCR analyses. Molecular authentication of twelve C. tricuspidata ecotypes from different regions was performed, using DNA sequences in the trnL-F chloroplast intergenic region. The SNP markers developed in this study are useful for rapidly identifying specific C. tricuspidata ecotypes from different regions.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.12
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• pp.1674-1680
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• 2012

The purpose of this study was to detect significant SNPs for blood components that were related to immunity using high single nucleotide polymorphism (SNP) density panels in a Korean native pig (KNP)${\times}$Yorkshire (YK) cross population. A reciprocal design of KNP${\times}$YK produced 249 $F_2$ individuals that were genotyped for a total of 46,865 available SNPs in the Illumina porcine 60K beadchip. To perform whole genome association analysis (WGA), phenotypes were regressed on each SNP under a simple linear regression model after adjustment for sex and slaughter age. To set up a significance threshold, 0.1% point-wise p value from F distribution was used for each SNP test. Among the significant SNPs for a trait, the best set of SNP markers were determined using a stepwise regression procedure with the rates of inclusion and exclusion of each SNP out of the model at 0.001 level. A total of 54 SNPs were detected; 10, 6, 4, 4, 5, 4, 5, 10, and 6 SNPs for neutrophil, lymphocyte, monocyte, eosinophil, basophil, atypical lymph, immuno-globulin, insulin, and insulin-like growth factor-I, respectively. Each set of significant SNPs per trait explained 24 to 42% of phenotypic variance. Several pleiotropic SNPs were detected on SSCs 4, 13, 14 and 15.

• Journal of Plant Biotechnology
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• v.45 no.2
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• pp.102-109
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• 2018

Thistle is a perennial plant that is widely used for medicinal purposes. Information on the genetic diversity of thistle populations are great important for their conservation and germ plasmic utilization. Although thistle is an important medicinal plant species registered in South Korea, no molecular markers are currently available to distinguish them from other similar species from different countries. In this study, we developed single nucleotide polymorphism (SNP) markers derived from the nuclear ribosomal DNA internal transcribed spacer (ITS) regions of genomic sequences to identify distinct Korean-specific thistle species via an amplification refractory mutation system (ARMS)-PCR and high resolution melting (HRM) curve analyses. We performed molecular authentication of four different kinds of thistle species from different regions using DNA sequences in the ITS intergenic region. We also developed a quantitative PCR assay using species-specific ITS primers, which allowed us to estimate the ratio of Korean-specific thistle species using varying ratios of mixed genomic DNA templates from the two species. The SNP markers developed in this study are useful for rapidly identifying specific thistle species from different countries.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.9
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• pp.1235-1243
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• 2015

The goat Capra hircus is one of several economically important livestock in China. Advances in molecular genetics have led to the identification of several single nucleotide variation markers associated with genes affecting economic traits. Validation of single nucleotide variations in a whole-transcriptome sequencing is critical for understanding the information of molecular genetics. In this paper, we aim to develop a large amount of convinced single nucleotide polymorphisms (SNPs) for Cashmere goat through transcriptome sequencing. In this study, the transcriptomes of Cashmere goat skin at four stages were measured using RNA-sequencing and 90% to 92% unique-mapped-reads were obtained from total-mapped-reads. A total of 56,231 putative SNPs distributed among 10,057 genes were identified. The average minor allele frequency of total SNPs was 18%. GO and KEGG pathway analysis were conducted to analyze the genes containing SNPs. Our follow up biological validation revealed that 64% of SNPs were true SNPs. Our results show that RNA-sequencing is a fast and efficient method for identification of a large number of SNPs. This work provides significant genetic resources for further research on Cashmere goats, especially for the high density linkage map construction and genome-wide association studies.

• Journal of Life Science
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• v.18 no.6
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• pp.770-775
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• 2008

Several studies reported quantitative trait loci (QTL) for meat quality on porcine chromosome 2. For application of the chromosomal information to pig industry through using DNA technology, single nucleotide polymorphism (SNP) markers are developed by comparative re-sequencing of polymerase chain reaction (PCR) products of 13 candidate genes. A total of 34 SNPs were identified in 11 PCR products, an average of one SNP in every 296 bp.PCR restriction fragment length polymorphism (RFLP) assays were developed for 11 SNPs and used to genotype four commercial pig populations in Korea. The SNP markers were used to map candidate genes in QTL and to clarify the relevance of SNP and quantitative traits.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.15
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• pp.6211-6217
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• 2014

Previous genome-wide association studies (GWAS) have implicated several single nucleotide polymorphisms (SNPs) in the AT-rich interactive domain 5B (ARID5B) gene with childhood acute lymphoblastic leukemia (ALL). However, replicated studies reported some inconsistent results in different populations. Using meta-analysis, we here aimed to clarify the nature of the genetic risks contributed by the two polymorphisms (rs10994982, rs7089424) for developing childhood ALL. Through searches of PubMed, EMBASE, and manually searching relevant references, a total of 14 articles with 16 independent studies were included. Odds ratios (ORs) with 95% confidence intervals (95%CI) were calculated to assess the associations. Both SNPs rs10994982 and rs7089424 showed significant associations with childhood ALL risk in all genetic models after Bonferroni correction. Furthermore, subtype analyses of B-lineage ALL provided strong evidence that SNP rs10994982 is highly associated with the risk of developing B-hyperdiploid ALL. These results indicate that SNPs rs10994982 and rs7089424 are indeed significantly associated with increased risk of childhood ALL.

• Proceedings of the KIEE Conference
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• 2004.07c
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• pp.2128-2130
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• 2004

High throughput analysis using a DNA chip microarray is powerful tool in the post genome era. Less labor-intensive and lower cost-performance is required. Thus, this paper aims to develop the multi-channel type label-free DNA chip and detect SNP (Single nucleotide polymorphisms). At first, we fabricated a high integrated type DNA chip array by lithography technology. Various probe DNAs were immobilized on the microelectrode array. We succeeded to discriminate of DNA hybridization between target DNA and mismatched DNA on microarray after immobilization of a various probe DNA and hybridization of label-free target DNA on the electrodes simultaneously. This method is based on redox of an electrochemical ligand.