• Molecular & Cellular Toxicology
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• v.2 no.1
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• pp.7-10
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• 2006

We performed comprehensive SNP validation and linkage disequilibrium (LD) analysis of the c-fos induced growth factor (Figf) gene in Korean population. Out of 32 SNPs, only 9 SNPs were polymorphic in Korean population. Validated SNPs formed a single extended haplotype block with strong LD through the entire length of the gene. Tagging SNP analysis picked only 2 SNPs to represent most of the genetic variation information of the Figf gene. Our results demonstrate the utility of LD block and tagging SNP analysis for an efficient way of performing a candidate gene based association study.

• Proceedings of the Korea Information Processing Society Conference
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• 2004.05a
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• pp.993-996
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• 2004

사람들 사이에는 DNA 서열의 변이로 인한 유전적 차이가 있으며, 가끔 이러한 차이가 유전 질병의 원인이 되기도 한다. 일반적으로 DNA에서 가장 잘 알려진 변이가 바로 SNP(Single Nucleotide Polymorphism : 스닙)이다. SNP는 보통 블록단위로 유전되어지며 한쪽 부모로부터 유전되어진 SNP 블록을 SNP 하플로타입이라고 부른다. 생물학 실험을 통하여 추출되어진 결과물은 부모로부터 유전되어진 대립 유전자가 혼합되어진 지노타입(genotype)의 정보이다. 지노타입은 직관적으로 정확한 SNP 하플로타입을 추정하기가 힘들고, 생물학 실험을 통하여 하플로타입(haplotype)을 분석하는데 많은 비용이 들기때문에, 이를 컴퓨터 계산을 통하여 추론하는 연구가 Clark[1]에 의해서 제안되어진 이후 활발하게 진행되고 있다. 본 논문에서는 하플로타입을 효과적으로 추론하기 위해 유전자 알고리즘을 이용한 새로운 방법을 설명하고, 실험 결과를 기존의 연구 결과와 비교 분석한다.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.11
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• pp.1548-1551
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• 2005

The leptin, an anti-obesity protein, is a hormone protein expressed and secreted mainly from adipocyte tissue, and involved in regulation of body weight, food intake and energy metabolism. In an effort to discover polymorphism(s) in genes whose variant(s) might be implicated in phenotypic traits of growth, we have sequenced exons and their boundaries of leptin gene including 1,000 bp upstream of promoter region with twenty-four unrelated Korean cattle. Fifty-seven sequence variants were identified: fourteen in 5' flanking region, twenty-seven in introns, eight in exons, and eight in 3' flanking region. By pair-wise linkage analysis among polymorphisms, ten sets of SNPs were in absolute linkage disequilibrium (LD) (|D'| = 1 and $r^2$ = 1). Among variants identified, thirty-six SNPs were newly identified, and twenty-one SNPs, which were reported in other breeds, were also confirmed in Korean cattle. The allele frequencies of variants were quite different among breeds. The information from SNPs of bovine leptin gene could be useful for further genetic studies of this gene.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.9
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• pp.1240-1244
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• 2006

The complete coding region sequence of the SRY gene in Chinese swamp buffalo was determined by PCR product sequencing. Comparison of swamp and river buffalo SRY gene sequences revealed a single nucleotide polymorphism (SNP, C/G) at the 202 bp site of the coding region. Further, a total of 124 male domestic buffaloes were genotyped at this SNP site using the PCR-SSCP method, and it was found that all Chinese indigenous swamp buffaloes had a guanine (G) at this site, while introduced river buffaloes and crossbred buffaloes showed a cytosine (C). Our findings suggested that this Y-linked SNP displayed type-specific alleles differentiating swamp and river buffaloes, and could be used as an effective marker to detect crossbreeding of swamp buffaloes with introduced river buffaloes in native buffalo populations, and thereby assess genetic diversity status and make proper conservation decisions for indigenous swamp buffaloes. In addition, this SNP can be potentially applied in the study of Asian water buffalo phylogeny from a male perspective.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.1
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• pp.1-6
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• 2007

Leptin is the hormone product of the obese gene and is synthesized and secreted predominantly by white adipocytes and relates to the feedback system that regulates long-term body fat weight and composition. Therefore, the leptin gene could be an excellent candidate gene controlling fat deposition, carcass traits and meat quality in beef cattle. The objective of this study was to evaluate the association of 3 SNPs (A1127T and C1180T in exon 2 and C3100T in exon 3) in the bovine leptin gene with carcass and meat quality traits in Korean cattle. The C1180T SNP was associated with backfat thickness (BF) and marbling score (MS) (p<0.05). Animals with the genotype CC had higher BF than animals with TT genotype and higher MS compared with CT and TT genotypes. No significant associations were observed between the C3100T SNP and any carcass and meat quality traits analyzed. The effect of the A1127T SNP was not analyzed because the TT genotype was not detected and the AT genotype showed only 1.0% frequency. These results suggest that the C1180T SNP of the leptin gene may be useful as a genetic marker for carcass and meat quality traits in Korean cattle.

• Asian-Australasian Journal of Animal Sciences
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• v.24 no.11
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• pp.1504-1513
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• 2011

It is important to identify genetic interactions related to human diseases or animal traits. Many linear statistical models have been reported but they did not consider genetic interactions. Genotype matrix mapping (GMM) has been developed to identify genetic interactions. This study uses the GMM method to detect superior SNP combinations of the CCDC158 gene that influences average daily gain, marbling score, cold carcass weight and longissimus muscle dorsi area traits in Hanwoo. We evaluated the statistical significance of the major SNP combinations selected by implementing the permutation test of the F-measure. The effect of g.34425+102 A>T (AA), g.8778G>A (GG) and g.4102+36T>G (GT) SNP combinations produced higher performance of average daily gain, marbling score, cold carcass weight and the longissimus muscle dorsi area traits than the effect of a single SNP. GMM is a fast and reliable method for multiple SNP analysis with potential application in marker-assisted selection. GMM may prospectively be used for genetic assessment of quantitative traits after further development.

• Asian-Australasian Journal of Animal Sciences
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• v.23 no.7
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• pp.833-847
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• 2010

In the past decade, there have been many advances in whole-genome sequencing in domestic animals, as well as the development of "next-generation" sequencing technologies and high-throughput genotyping platforms. Consequently, these advances have led to the creation of the high-density SNP array as a state-of-the-art tool for genetics and genomics analyses of domestic animals. The emergence and utilization of SNP arrays will have significant impacts not only on the scale, speed, and expense of SNP genotyping, but also on theoretical and applied studies of quantitative genetics, population genetics and molecular evolution. The most promising applications in agriculture could be genome-wide association studies (GWAS) and genomic selection for the improvement of economically important traits. However, some challenges still face these applications, such as incorporating linkage disequilibrium (LD) information from HapMap projects, data storage, and especially appropriate statistical analyses on the high-dimensional, structured genomics data. More efforts are still needed to make better use of the high-density SNP arrays in both academic studies and industrial applications.

• The Korean Journal of Malacology
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• v.30 no.3
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• pp.197-210
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• 2014

Single nucleotide polymorphisms (SNPs) are widely acknowledged as the marker of choice for many genetic and genomic applications because they show co-dominant inheritance, are highly abundant across genomes and are suitable for high-throughput genotyping. Here we evaluated the applicability of SNP markers developed from Crassostrea gigas and C. virginica expressed sequence tags (ESTs) in closely related Crassostrea and Ostrea species. A total of 213 putative interspecific level SNPs were identified from re-sequencing data in six amplicons, yielding on average of one interspecific level SNP per seven bp. High polymorphism levels were observed and the high success rate of transferability show that genic EST-derived SNP markers provide an efficient method for rapid marker development and SNP discovery in closely related oyster species. The six EST-SNP markers identified here will provide useful molecular tools for addressing questions in molecular ecology and evolution studies including for stock analysis (pedigree monitoring) in related oyster taxa.

• The Korean Journal of Physiology and Pharmacology
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• v.7 no.2
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• pp.73-77
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• 2003

The effects of nitric oxide on the vestibular function recovery following unilateral labyrinthectomy (UL) were studied. Sprague-Dawley male rats, treated with nitric oxide liberating agent sodium nitroprusside (SNP) and NOS inhibitor $N^G$-nitro-L-arginine methyl ester (L-NAME), were subjected to destruction of the unilateral vestibular apparatus, and then spontaneous nystagmus was observed in the rat. To explore the effects of nitric oxide on the neuronal excitability, whole cell patch clamp technique was applied on isolated medial vestibular nuclear neurons. The frequency of spontaneous nystagmus in SNP treated rats was lesser than that of spontaneous nystagmus in control animals. In contrast, pre-UL treatment with L-NAME resulted in a significant increase in spontaneous nystagmus frequency. In addition, SNP increased the frequency of spontaneous action potential in isolated medial vestibular nuclear neurons. Potassium currents of the vestibular nuclear neurons were inhibited by SNP. After blockade of calcium dependent potassium currents by high EGTA (11 mM) in a pipette solution, SNP did not inhibit outward potassium currents. 1H-[1,2,4] oxadiazolo [4,3-a] quinozalin-1-one (ODQ), a specific inhibitor of soluble guanylyl cyclase, inhibited the effects of SNP on the spontaneous firing and the potassium current. These results suggest that nitric oxide after unilateral labyrinthectomy would help to facilitate vestibular compensation by inhibiting calcium-dependent potassium currents through increasing intracellular cGMP, and consequently would increase excitability in ipsilateral vestibular nuclear neurons.

• Korean Journal of Veterinary Service
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• v.42 no.4
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• pp.217-225
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• 2019

To detect Single nucleotide polymorphisms (SNP) markers associated with Bovine viral diarrhea virus (BVDV) and Bovine respiratory syncytial virus (BRSV) S/P ratio in Korean Holstein dairy cattle, Genome-wide association study (GWAS) was performed using Illumina BovineSNP50 Beadchip. The number of phenotype data and genotype data were 107, and 294. respectively. Phenotype data were collected for four periods (0 week, 1 week, 4 week, 24 week) after having vaccinated (0 week no vaccinated period). A total of 36,257 SNPs was remained after quality control had been done by PLINK. The result of GWAS showed 6 SNP markers (BTB-01704243, BTB-01594395, ARS-BFGL-NGS-118070, ARS-BFGL-NGS-111365, BTA-65410-no-rs, Hapmap38331-BTA-61256) under BVDV and 4 SNP markers (ARS-BFGL-NGS-109861, Hapmap53701-rs29017064, ARS-BFGL-NGS-71055, BTA-11232-no-rs) under BRSV. And also, 10 candidate genes found through 10 SNP markers (TBX18, CEP162, PAFAH1B1, METTL16, BRCA1, RND2, POLK, ENSBTAG00000051724, ADAM18, NRG3).