• Korean Journal of Poultry Science
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• v.45 no.4
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• pp.253-260
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• 2018

The hepatocyte nuclear factor 4 alpha ($HNF4{\alpha}$) gene is related to lipid transport, including abdominal fat and growth, in chickens. Interestingly, the A543G SNP within the $HNF4{\alpha}$ gene has previously been reported to be associated with body weight in both broilers and Korean native chickens (KNCs). However, its exact position within the HNF4 is not yet reported. This study aimed to identify the position of the A543G SNP and to identify additional SNPs that can be used as genetic markers in KNCs. A total of 128 KNCs were used for the sequencing and analysis of these genetic associations. As a result, A543G SNP was located in intron 4 of the $HNF4{\alpha}$ gene; it is reported as rs731246957 in the NCBI database. Fourteen SNPs were detected in the sequenced portion of the $HNF4{\alpha}$ gene; three of these, rs731246957, rs736159604 and new SNP, intron 6 (249), were significantly related with growth in the chickens. In this study, the TT genotype of rs731246957, previously reported as A543G SNP, the GG genotype of rs736159604 and GT of new SNP have are highly associated with body weight from birth to 40 weeks of age in KNCs (P<0.01). These results suggest that rs736159604, rs731246957 and intron 6 (249) SNPs within the $HNF4{\alpha}$ gene could function as growth-related markers in the selective breeding of KNCs.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.5
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• pp.628-635
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• 2018

Objective: To determine the effects of genomic breeding values (GBV) and single nucleotide polymorphisms (SNP) on the total number of piglets born (TNB) in 3 pig breeds (Berkshire, Landrace, and Yorkshire). Methods: After collecting genomic information (Porcine SNP BeadChip) and phenotypic TNB records for each breed, the effects of GBV and SNP were estimated by using single step best linear unbiased prediction (ssBLUP) method. Results: The heritability estimates for TNB in Berkshire, Landrace, and Yorkshire breeds were 0.078, 0.107, and 0.121, respectively. The breeding value estimates for TNB in Berkshire, Landrace, and Yorkshire breeds were in the range of -1.34 to 1.47 heads, -1.79 to 1.87 heads, and -2.60 to 2.94 heads, respectively. Of sows having records for TNB, the reliability of breeding value for individuals with SNP information was higher than that for individuals without SNP information. Distributions of the SNP effects on TNB did not follow gamma distribution. Most SNP effects were near zero. Only a few SNPs had large effects. The numbers of SNPs with absolute value of more than 4 standard deviations in Berkshire, Landrace, and Yorkshire breeds were 11, 8, and 19, respectively. There was no SNP with absolute value of more than 5 standard deviations in Berkshire or Landrace. However, in Yorkshire, four SNPs (ASGA 0089457, ASGA0103374, ALGA0111816, and ALGA0098882) had absolute values of more than 5 standard deviations. Conclusion: There was no common SNP with large effect among breeds. This might be due to the large genetic composition differences and the small size of reference population. For the precise evaluation of genetic performance of individuals using a genomic selection method, it may be necessary to establish the appropriate size of reference population.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.12
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• pp.1703-1709
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• 2008

As genetic markers, single nucleotide polymorphisms (SNP) are very appropriate for the development of genetic tests for economic traits in livestock. Several microsatellite markers have been identified as useful markers for the genetic improvement of Hanwoo. Among those markers, ILSTS035 was recently mapped at a similar position with four SNPs (AH1_11, AH1_9, 31465_446, and 12273_165) in a linkage map of EST-based SNP in BAT6. Among the four SNPs, two SNPs (31465_446 and 12273_165) were analyzed using BLAST at the NCBI web site. The sequences including the 12273_165 SNP were identified at the intron region within the LOC534614 gene on the gene sequence map (Bos taurus NCBI Map view, build 3.1). The LOC534614 gene represents a protein similar to myosin heavy chain, fat skeletal muscle, embryonic isoform 1 in the dog, and myosin_1 (Myosin heavy chain D) in Macaca mulatta. In cattle, the myosin heavy chain was associated with muscle development. The phenotypic data for growth and carcass traits in the 415 animals were analyzed by the mixed ANCOVA (analysis of covariance) linear model using PROC GLM module in SAS v9.1. By the genotyping of Hanwoo individuals (n = 415) to evaluate the association of SNP with growth and carcass traits, it was shown that the 12273_165 SNP region within LOC534614 may be a candidate marker for growth. The results of the statistical analyses suggested that the genotype of the 12273_165 SNP significantly affected birth weight, weight of the cattle at 24 months of age, average daily gain and carcass cold weight (p<0.05). Consequently, the 12273_165 SNP polymorphisms at the LOC534614 gene may be associated with growth in Hanwoo, and functional validation of polymorphisms in LOC534614 should be performed in the future.

• Journal of KIISE:Computer Systems and Theory
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• v.34 no.7
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• pp.276-281
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• 2007

In this paper, we use Support Vector Machine to predict the susceptibility of chronic hepatitis from single nucleotide polymorphism data. Our data set consists of SNP data for 328 patients based on 28 SNPs and patients classes(chronic hepatitis, healthy). We use leave-one-out cross validation method for estimation of the accuracy. The experimental results show that SVM with SNP is capable of classifying the SNP data successfully for chronic hepatitis susceptibility with accuracy value of 67.1%. The accuracy of all SNPs with health related feature(sex, age) is improved more than 7%(accuracy 74.9%). This result shows that the accuracy of predicting susceptibility can be improved with health related features. With more SNPs and other health related features, SVM prediction of SNP data is a potential tool for chronic hepatitis susceptibility.

• BMB Reports
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• v.41 no.1
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• pp.29-34
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• 2008

The aim of this study was to determine whether single nucleotide polymorphisms (SNP) in the beef cattle adipocyte fatty-acid binding protein 3 and 4 (FABP3 and FABP4) genes are associated with carcass weight (CW) and back fat thickness (BF) of beef cattle. By direct DNA sequencing in 24 unrelated Korean native cattle, we identified 20 SNPs in FABP3 and FABP4. Among them, 10 polymorphic sites were selected for genotyping in our beef cattle. We performed SNP, haplotype and linkage disequilibrium studies on 419 Korean native cattle with the 10 SNPs in the FABP genes. Statistical analysis revealed that 220A>G (I74V) and 348+303T>C polymorphisms in FABP4 showed putative associations with BF traits (P=0.02 and 0.01, respectively). Our findings suggest that the polymorphisms in FABP4 may play a role in determining one of the important genetic factors that influence BF in beef cattle.

• Korean Journal of Poultry Science
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• v.45 no.4
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• pp.291-298
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• 2018

TBC1D1 gene has known functional effects on body energy homeostasis and glucose uptake pathway in skeletal muscle tissue. This biological function is reported to have significant effects on traits of growth and meat quality in chicken. In this study, we focused on two single nucleotide polymorphisms (SNPs) (g.70179137A>G and g.70175861T>C) identified through SNP annotation information of Korean native chicken and previous literature for TBC1D1 in chicken. Association of SNPs in TBC1D1 with growth and serum clinical-chemical traits were evaluated. A total of 584 male and female birds from five Korean native chicken lines were used in the study. The SNP1 (g.70179137A>G) is located in intron 11 and SNP2 (g.70175861T>C) is a non-synonymous missense mutation in exon 10, responsible for the amino acid change from Methionine to Valine. The A allele of SNP1 and T allele of SNP2 had the highest allele frequencies. Both SNPs indicated moderate polymorphism information content values (0.25

• Journal of Microbiology
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• v.35 no.2
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• pp.152-157
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• 1997

Infection of human fibroblast (HF) cells with human cytomegalovirus (HCMV) result in changes in the intracellular level of second messengers. Since nitric oxide (NO) production has been known to be related with other second messengers, it is probable that HCMV infection of HF cells may involve NO. To test this possibility, the amount of NO was measured following ogenous addition of NO generators such as sodium nitroprusside (SNP) or S-nitroso-N-a-cetylpenicillamine (SNAP) immediately after HCMV infection, however, inhibited virus multiplication. Furthermore, immunoblot experiment using monoclonal antibody to HCMV major immediate early (MIE) proteins or CAT assay using pCMVIE/CAT (plasmid containing CAT gene driven by HCMV MIE promoter) revealed that SNP or SNAP blocked the MIE gene expression. SNP was more effective than SNAP in hibiting HCMV multiplication or MIE gene expression. SNP produced more NO than SNAP in inhibiting HCMV multiplication or MIE gene expression. SNP produced more NO than SNAP. Although the mechanism for the inhibition of HCMV multiplication and MIE gene expression by NO is still elusive some correlation with NO-mediated inhibition of HCMV-induced increase in cytosolic free Ca$\^$2+/ concentration ([Ca$\^$2+/]) was observed. The increase of [Ca$\^$2+/] following HCMV infection was inhibited by SNP, and less effectively by SNAP. Raising [Ca$\^$2+/ with bromo-A23187 partially reversed the SNP block of MIE gene expression. Thus, there appear to e some relationships among NO. [Ca$\^$2+/], and HCMV MIE gene expression.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.3
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• pp.309-313
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• 2008

The insulin-like growth factor binding protein 3 (IGFBP3) has been investigated as a candidate gene for growth promoting effects in beef cattle and a modulator of IGF bioactivity. Previously, we have reported twenty two sequence variants discovered in Korean native cattle (Hanwoo). In this study, we examined the association between gene-specific polymorphisms of IGFBP3 and cold carcass weight (CW) and marbling score (MS) among Korean native cattle. Among twenty two polymorphisms, four common polymorphic sites (-854G>C, -100G>A, +421G>T and +3863C>A) were genotyped in our beef cattle (n = 437). Statistical analysis revealed that one common polymorphism in the promoter region (-854G>C) showed putative associations with MS (p = 0.03). IGFBP3 variation/haplotype information analyzed in this study will provide valuable information into strategies for the production of a commercial line of beef cattle.

• BMB Reports
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• v.46 no.6
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• pp.305-309
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• 2013

The determination of relatedness between individuals in a family is crucial in analysis of common complex diseases. We present a method to infer close inter-familial relationships based on SNP genotyping data and provide the relationship coefficient of kinship in Korean families. We obtained blood samples from 43 Korean individuals in two families. SNP data was obtained using the Affymetrix Genome-wide Human SNP array 6.0 and the Illumina Human 1M-Duo chip. To measure the kinship coefficient with the SNP genotyping data, we considered all possible pairs of individuals in each family. The genetic distance between two individuals in a pair was determined using the allele sharing distance method. The results show that genetic distance is proportional to the kinship coefficient and that a close degree of kinship can be confirmed with SNP genotyping data. This study represents the first attempt to identify the genetic distance between very closely related individuals.

• The Korean Journal of Physiology and Pharmacology
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• v.2 no.4
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• pp.471-477
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• 1998

Cyclosporin A (CsA), a widely used immunosuppressant, is well known to cause nephrotoxicity and hypertension as major side effects. The present study was aimed at investigating the effects of CsA-pretreatment on the activities of cytosolic guanylate cyclase (cGC) in relation to the alteration of relaxant responses in the rat thoracic aorta. CsA $(10\;{\mu}M)-preincubation$ for 90 min significantly attenuated the vasodilatation induced by sodium nitroprusside (SNP), a cytosolic guanylate cyclase activator, shifting the dose-response curve to the right. The increase in cGMP contents induced by SNP was markedly attenuated by CsA. SNP ($1\;{\mu}M{\sim}\;mM$) increased the cGC activity dose-dependently, and the increase was completely abolished by CsA. CsA attenuated the SNP-induced cGC activation dose-dependently. The abolishing effect of CsA-pretreatment on the SNP-induced cGC activation was not affected by washing the preparation, suggesting that the inhibition is irreversible. When CsA was added simultaneously with SNP, cGC activation was not attenuated. 1-(5-isoquinolinylsulfonyl)-2-methyl piperazine (H-7), a protein kinase C (PKC) inhibitor, decreased SNP-induced cGC activation and blocked the CsA-attenuation of cGC activation. These results suggest that CsA directly inhibits cGC participating in the CsA-induced impairment of vasodilatation, and that PKC is involved in the inhibitory action of CsA on cGC.