• Korean Journal of Poultry Science
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• v.43 no.4
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• pp.263-272
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• 2016

In this study, we aimed to identify the nonsynonymous single nucleotide polymorphisms (nsSNPs) located in lipid metabolism-related genes because lipids are an important factor affecting the taste and flavor of meat, and they predict the functional consequences. The results showed that we identified 139 common nsSNPs in all five Korean native chicken (KNC) lines from the 81 genes related to lipid metabolism. Furthermore, sorting intolerant from tolerant (SIFT) and polymorphism phenotyping v2 (Polyphen-2) analyses predicted that among the genes, 14 nsSNPs of nine genes might be deleterious. Protein domain prediction of the nine genes revealed that all deleterious nsSNPs identified in this study were located outside the functional domain. This observation suggests that the common deleterious nsSNPs might be dispensable and have a minor effect on the traits of the KNCs.

• Journal of the Korean Data and Information Science Society
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• v.26 no.6
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• pp.1249-1258
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• 2015

DGAT1(diacylglycerol O-acyltransferase1) gene is well known as a major gene of milk production in dairy cattle. This study was conducted to investigate how the DGAT1 gene effect on milk yield was appeared from the genome wide association (GWA) using high density whole genome SNP chip. The data set used in this study consisted of 353 Korean Holstein sires with 50k SNP genotypes and deregressed estimated breeding values of milk yield. After quality control 41,051 SNPs were selected and locations on chromosome were mapped using UMD 3.1. Bayesian regression of BayesB method (pi=0.99) was used to estimate the SNP effects and genomic breeding values. Percentages of variance explained by 1 Mb non-overlapping windows were calculated to detect the QTL region. As the result of this study, top 1 and 3 of 2,516 windows were seen around DGAT1 gene region and 0.51% and 0.48% of genetic variance were explained by these two windows. Although SNPs on the DGAT1 gene region are excluded in commercial 50k SNP chip, the effect of DGAT1 gene seem to be reflected on GWA by the SNPs which are in linkage disequilibrium with DGAT1 gene.

• Korean Journal of Plant Resources
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• v.32 no.4
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• pp.303-311
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• 2019

Various colors of fruit skin and flesh are the most popular commercial criteria for peach classification. In order to breed new red-fleshed peach cultivar, many cross seedlings and generations should be maintained. Therefore it is necessary to develop early selection markers to screen seedlings with target traits to increase breeding efficiency. For the comparison of transcription profiles in peach cultivars differing in flesh color expression, two cDNA libraries were constructed. Differences in gene expression between red-fleshed peach cultivar, 'Josanghyeoldo' and white-fleshed peach cultivar, 'Mibaekdo' were analyzed by next-generation sequencing (NGS). Expressed sequence tag (EST) of clones from the two cultivars were selected for nucleotide sequence determination and homology searches. Putative single nucleotide polymorphisms (SNP) were screened from peach EST contigs by high resolution melting (HRM) analysis displayed specific difference between 8 red-fleshed peach cultivars and 24 white-fleshed peach cultivars. All 72 pairs of SNPs were discriminated and the HRM profiles of amplicons were established. In the study reported here, the development of SNP markers for distinguishing between red and white fleshed peach cultivars by HRM analysis offers the opportunity to use DNA markers. This SNP marker could be useful for peach marker assisted breeding and provide a good reference for relevant research on molecular mechanisms of color variation in peach cultivars.

• 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.

• ETRI Journal
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• v.37 no.2
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• pp.212-221
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• 2015

As the amount of re-sequencing genome data grows, minimizing the execution time of an analysis is required. For this purpose, recent computing systems have been adopting both high-performance coprocessors and host processors. However, there are few applications that efficiently utilize these heterogeneous computing resources. This problem equally refers to the work of single nucleotide polymorphism (SNP) detection, which is one of the bottlenecks in genome data processing. In this paper, we propose a method for speeding up an SNP detection by enhancing the utilization of heterogeneous computing resources often used in recent high-performance computing systems. Through the measurement of workload in the detection procedure, we divide the SNP detection into several task groups suitable for each computing resource. These task groups are scheduled using a window overlapping method. As a result, we improved upon the speedup achieved by previous open source applications by a magnitude of 10.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.5
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• pp.2625-2628
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• 2016

ABCC11 is reported to be associated with breast cancer. However, whether ABCC11 polymorphisms relate to breast cancer risk remains unclear. This study aimed to evaluate any association of a single nucleotide polymorphism (SNP), rs17822931, in ABCC11 with breast cancer in Koreans. Genomic DNA samples of 170 women with breast cancer and 100 controls were assessed for SNP rs17822931 of ABCC11 by single-strand conformation polymorphism (SSCP) and DNA sequencing. A 27-bp deletion (${\Delta}27$) of ABCC11 was analyzed by PCR amplification. The genotype of SNP rs17822931 was confirmed to be AA in all samples from breast cancer patients and ${\Delta}27$ was found in none of the samples. Our finding indicated that the SNP rs17822931 in ABCC11 is not associated with breast cancer. However, this study does provide information on fundamental genetic aspects of ABCC11 with regard to breast cancer risk in Koreans.

• YAKHAK HOEJI
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• v.44 no.1
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• pp.80-86
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• 2000

TEA, glibenclamide, L-NAME and SKF 525A-induced contraction were investigated using acetylcholine, sodium nitroprusside (SNP, NO donor) and pinacidil (ATP sensitive $K^{+}$ channel opener) in rat abdominal and thoracic aorta. The relaxant effects of acetylcholine, SNP and pinacidil were not different in the abdominal aorta and in the thoracic aorta. Acetylcholine-induced relaxation was dependent on endothelial cell, but pinacidil was independent endothelia cell. In the presence of TEA, glibenclamide, L-NAME, mepacrine and SKF 525A, acetylcholine and SNP did not change, but pinacidil-induced relaxation was significantly reduced in presence of glibenclamide, which is ATP sensitive $K^{+}$ channel blocker. SKF 525A, which is inhibitor of cytochrome P$_{450}$ dependent epoxygenase, partially inhibited the pinacidil-induced relaxation. These results indicate that the pinacidil-induced relaxation may be mediated by ATP sensitive $K^{+}$ channel and partially by EETs, which is produced by cytochrome P$_{450}$ dependent epoxygenase.enase.

• Development and Reproduction
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• v.1 no.2
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• pp.165-172
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• 1997

the pupose of this study was to investigate the effects of gonadotropin and nitric oxide (NO) on the expression of mouse follicular bad and bax genes that are known induce apoptosis. Large and midium size follicles of immature mice were obtained at 0, 24, and 48 hours time intervals after Pregnant Mare's Serum gonadotropins(PMSG, 5 I.U.) injection. Preovulatory follicles collected at 24 hrs after PMSG injection were cultured with or without various chemicals such as gonadotropin, gonadotropin Releasing hormone(GnRH), testosterone, Sodium nitroprusside (SNP) for 24 hrs at $37^{\circ}C$. After 24 hrs culture, the culture media was used for nitrite assay and total RNA was extracted, subjected to RT-PCT for the analyses of bad and bax expression. We found that expression of bad and bax genes in follicles was markedly reduced before and after in vivo priming with hCG. When the preovulatory follicles were cultured for 24 hrs in culture media with PMSG and hCG, the expression of bad and bax genes was decreased. Moreover, SNP (NO generating agent) can significantly suppress the expression of bad and bax genes in follicles when apoptosis was induced by GnRH agonist and testosterone. At the same time, nitrite production of culture media was increased in GnRH agonist + SNP, testosterone + SNP and SNP treated groups than control group. These data demonstrated for the first time that peptide hormones and NO may play important roles in the regulation of mouse follicular differentiation and may prevent apoptosis via supressing the expression of bad and bax genes.

• Proceedings of the Korean Society of Developmental Biology Conference
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• 2003.10a
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• pp.94-94
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• 2003

Rotavirus는 유아나 어린아이들에게 가장 일반적으로 나타나는 심한 위장염의 원인자이며 설사로 인한 심한 탈수 증세를 일으켜 급속히 성장하는 유아의 균형적인 영양 공급을 방해함으로써 유아들의 발육과 성장 그리고 심하면 생명에 커다란 영향을 미치게 된다. 한편 모유로 키운 유아들은 설사병의 낮은 발병율과 연관이 있었다. 특히 모유의 뮤신 복합체는 rotavirus에 특이적으로 결합하여 항 바이러스활동을 보여주는 것으로 나타났다. 이러한 배경에서 본 연구는 human breast tissue로부터 lactadherin의 cloning 및 sequence 분석을 통하여 유전자의 다양성을 조사하기로 하였다. 한국 여성 9명의 유두 근처 조직에서 lactadherin을 cloning하여 그 sequence를 보고 된 서양여성의 염기서열과 비교 분석결과 여러 곳에서 single nucleotide variation이 발견되었고 본 연구에서 클론한 lactadherin(31bp-1518bp)의 염기서열과 보고된 서양여성 lactadherin gene의 SNP와 비교하였을 때 8개의 SNP중 3부분만이 일치한다는 것을 확인하였다. 또한 같은 조직중 정상 조직과 암 조직 부분에서 각각 lactadherin을 클론하여 염기서열을 비교 분석하였는데 정상 조직에서 2곳의 silent mutation있었고 암조직에서 2곳의 mutation과 1곳의 silent mutation을 발견하였으며 전체 적으로 정상조직과 암 조직 부분에서 lactadherin을 clone하여 염기서열을 분석해본 결과 암조직일수록 유전자의 변이 비율이 높다는 것을 알 수 있었다. 그리고 동일한 염기서열 상에서 많은 변이가 일어났는데 286dp(A->C), 1418dp(G->C)은 mutation이었고 327dp (A->G), 454(C->T)은 silent mutation이었다. 그 외 DNA상에서 여러 부근에 변이가 존재하였는데 이 결과로 보아 coding region에 위치한 cSNP 중 amino acid 변화를 일으켜 protein structure 또는 function에 영향을 줄 수 있는 non-synonymous cSNP 일 것으로 예상되어지며 natural selection의 영향을 받고 있음을 암시하고 있다. 본 연구에서 관찰되어진 각각의 염기 서열의 변이는 한국 사람이 가지는 lactadherin gene의 cSNP의 일부라고 판단하였다.

• BMB Reports
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• v.41 no.4
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• pp.334-337
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• 2008

MCL1 expression has been found to be up-regulated during infection with virulent Mycobacterium tuberculosis. We investigated the genetic polymorphisms in MCL1 as potential candidate gene for a host genetic study of clinical TB infection. We have sequenced exons and their boundaries of MCL1, including the 1.5 kb promoter region, to identify polymorphisms, and eight polymorphisms were identified. The genetic associations of polymorphisms in MCL1 with clinical TB patients (n=486) and normal controls (n=370) were analyzed. Using statistical analyses, one common promoter polymorphism (MCL1-324C>A) which is absolutely linked with three other SNPs in the promoter and 3'UTR regions, were found to be significantly associated with increased risk of clinical TB disease. The frequency of the A-bearing genotype of -324C>A was higher in clinical TB patients than in normal controls (P=0.0008, OR=1.68). Our findings suggest that polymorphisms in MCL1 might be one of genetic factors for the risk of clinical tuberculosis development.