• Journal of Plant Biotechnology
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• v.45 no.3
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• pp.242-249
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• 2018

This study was conducted to develop an SNP set that can be useful for marker-assisted breeding (MAB) in watermelon (Citrullus. lanatus L) using Genotyping-by-sequencing (GBS) analysis of 20 commercial elite watermelon inbreds. The result of GBS showed that 77% of approximately 1.1 billion raw reads were mapped on the watermelon genome with an average mapping region of about 4,000 Kb, which indicated genome coverage of 2.3%. After the filtering process, a total of 2,670 SNPs with an average depth of 31.57 and the PIC (Polymorphic Information Content) value of 0.1~0.38 for 20 elite inbreds were obtained. Among those SNPs, 55 SNPs (5 SNPs per chromosome that are equally distributed on each chromosome) were selected. For the understanding genetic relationship of 20 elite inbreds, PCA (Principal Component Analysis) was carried out with 55 SNPs, which resulted in the classification of inbreds into 4 groups based on PC1 (52%) and PC2 (11%), thus causing differentiation between the inbreds. A similar classification pattern for PCA was observed from hierarchical clustering analysis. The SNP set developed in this study has the potential for application to cultivar identification, F1 seed purity test, and marker-assisted backcross (MABC) not only for 20 elite inbreds but also for diverse resources for watermelon breeding.

• Asian-Australasian Journal of Animal Sciences
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• v.24 no.2
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• pp.190-197
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• 2011

The objective of the present study was to elucidate the fundamental mechanism of bovine oviduct epithelial cell (BOEC) co-culture on developmental capacity of bovine IVM/IVF embryos and to determine whether or not melatonin acts as an antioxidant in BOEC culture and subsequent embryo development. These studies examined the effects of melatonin against NO-induced oxidative stress on cell viability, lipid peroxidation (LPO) and the expression of antioxidant genes (CuZnSOD, MnSOD and Catalase) or apoptosis genes (Bcl-2, Caspase-3 and Bax) during BOECs culture. We also evaluated the developmental rates of bovine IVM/IVF embryos with BOEC co-culture, which were pre-treated with melatonin ($1,000\;{\mu}M$) in the presence or absence of sodium nitroprusside (SNP, $1,000\;{\mu}M$) for 24 h. Cell viability in BOECs treated with SNP (50-$2,000\;{\mu}M$) decreased while melatonin addition (1-$1,000\;{\mu}M$) increased viability in a dose-dependent manner. Cell viability in melatonin plus SNP ($1,000\;{\mu}M$) gradually recovered according to increasing melatonin addition (1-$1,000\;{\mu}M$). The LPO products were measured by thiobarbituric acid (TBA) reaction for malondialdehyde (MDA). Addition of melatonin in BOEC culture indicated a dose-dependent decrease of MDA, and in the SNP group among BOECs treated with SNP or melatonin plus SNP groups MDA was significantly increased compared with SNP plus melatonin groups (p<0.05). In expression of apoptosis or antioxidant genes detected by RT-PCR, Bcl-2 and antioxidant genes were detected in melatonin or melatonin plus SNP groups, while Caspase-3 and Bax genes were only found in the SNP group. When bovine IVM/IVF embryos were cultured for 6-7 days under the BOEC co-culture system pre-treated with melatonin in the presence or absence of SNP, the highest developmental ability to blastocysts was obtained in the $1,000\;{\mu}M$ melatonin group. These results suggest that melatonin has an anti-oxidative effect against NO-induced oxidative stress on cell viability of BOECs and on the developmental competence of bovine IVM/IVF embryo co-culture with BOEC.

• Journal of Apiculture
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• v.32 no.3
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• pp.147-154
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• 2017

Honeybees (Apis mellifera) are common pollinators and important insects studied in agriculture, ecology and basic research. Recently, RDA (Rural Development Administration) and YIRI (Yecheon-gun Industrial Insect Research Institute) have been breeding a triple crossbred honey bee named Jangwon, which have the ability to produce superior quality honey. In this study, we identified a single nucleotide polymorphism (SNP) marker in the genome of Jangwon honeybee, particularly, in the paternal line (D line). Initially, we performed Sequence-Based Genotyping (SBG) using the Illumina Hiseq 2500 in 5 honeybee inbred lines; A, C, D, E, and F; and obtained 1,029 SNPs. Seventeen SNPs for each inbred line were generated and selected after further filtering of the SNP dataset. The 17 SNP markers validated by performing TaqMan probe-based real-time PCR and genotyping analysis was conducted. Genotyping analysis of the 5 honeybee inbred lines and one hybrid line, $D{\times}F$, revealed that one set of SNP marker, AmD9, precisely discriminated the inbred line D from the others. Our results suggest that the identified SNP marker, AmD9, is successful in distinguishing the inbred honeybee lines D, and can be directly used for genotyping and breeding applications.

• Journal of KIISE:Computer Systems and Theory
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• v.35 no.11
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• pp.509-516
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• 2008

The Minimum Letter Flips (MLF) model and the Weighted Minimum Letter Flips (WMLF) model are for solving the haplotype assembly problem. But these two models are effective only when the error rate in SNP fragments is low. In this paper, we first establish a new computational model that employs the related genotype information as an improvement of the WMLF model and show its NP-hardness, and then propose an efficient genetic algorithm to solve the haplotype assembly problem. The results of experiments on random data set and a real data set indicate that the introduction of genotype information to the WMLF model is quite effective in improving the reconstruction rate especially when the error rate in SNP fragments is high. And the results also show that genotype information increases the convergence speed of the genetic algorithm.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.2
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• pp.172-177
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• 2007

Thyroid hormones play an important role in regulating metabolism and can affect homeostasis of fat depots. The gene encoding thyroglobulin (TG), producing the precursor for thyroid hormones, has been proposed as a positional and functional candidate gene for a QTL with an effect on fat deposition. The SNP occurs in the 5' promoter region of the TG gene and is widely used in marker assisted selection (MAS) programs to improve the predictability of marbling level and eating quality in beef cattle. In this study, we identified three SNPs at the 5' promoter region of the TG gene in Korean cattle. Of the three SNPs identified in TG gene, the C257T and A335G were previously unreported new SNPs. The sequence data were submitted to GenBank (GenBank accession number: AY615525). The previously reported C422T SNP showed three genotypes, CC, CT and TT, by digestion with the restriction enzyme MflI using the PCR-RFLP method. A new allelic variant corresponding to the C${\rightarrow}$T and A${\rightarrow}$G mutations at positions 257 and 335, respectively, could be detected by the SSCP analysis. The gene-specific SNP marker association analysis indicated that the C422T SNP marker was significantly associated (p<0.05) with marbling score. Animals with the CC and CT genotypes had higher marbling score than those with the TT genotype. Results from this study suggest that TG gene-specific SNP may be a useful marker for meat quality traits in future MAS programs in Korean cattle.

• The Korean Journal of Physiology and Pharmacology
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• v.1 no.6
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• pp.731-739
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• 1997

The aim of present study is to investigate the effects of cGMP on hyperpolarization activated inward current ($I_f$), pacemaker current of the heart, in rabbit sino-atrial node cells using the whole-cell patch clamp technique. When sodium nitroprusside (SNP, $80{\mu}M$), which is known to activate guanylyl cyclase, was added, $I_f$ amplitude was increased and its activation was accelerated. However, when $I_f$ was prestimulated by isopreterenol (ISO, $1{\mu}M$), SNP reversed the effect of ISO. In the absence of ISO, SNP shifted activation curve rightward. On the contrary in the presence of ISO, SNP shifted activation curve in opposite direction. $8Br-cGMP(100\;{\mu}M)$, more potent PKG activator and worse PDE activator than cGMP, also increased basal $I_f$ but did not reverse stimulatory effect of ISO. It was probable that PKG activation seemed to be involved in SNP-induced basal $I_f$ increase. The fact that SNP inhibited ISO-stimulated $I_f$ suggested cGMP antagonize cAMP action via the activation of PDE. This possibility was supported by experiment using 3-isobutyl-1-methylxanthine (IBMX), non-specific PDE inhibitor. SNP did not affect $I_f$ when $I_f$ was stimulated by $20{\mu}M$ IBMX. Therefore, cGMP reversed the stimulatory effect of cAMP via cAMP breakdown by activating cGMP-stimulated PDE. These results suggest that PKG and PDE are involved in the modulation of $I_f$ by cGMP: PKG may facilitate $I_f$ and cGMP-stimulated PDE can counteract the stimulatory action of cAMP.

• The Korean Journal of Physiology and Pharmacology
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• v.2 no.2
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• pp.225-232
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• 1998

To investigate the possible involvement of outward potassium ($K^+$) currents in nitric oxide-induced relaxation in intestinal smooth muscle, we used whole-cell patch clamp technique in freshly dispersed guinea-pig ileum longitudinal smooth muscle cells. When cells were held at -60 mV and depolarized from -40 mV to -50 mV in 10 mV increments, sustained outward $K^+$ currents were evoked. The outward $K^+$ currents were markedly increased by the addition of 10 ${\mu}M$ sodium nitroprusside (SNP). 10 ${\mu}M$ S-nitroso-N-acetylpenicillamine (SNAP) and 1 mM 8-Bromo-cyclic GMP (8-Br-cGMP) also showed a similar effect to that of SNP. 1 mM tetraethylammonium (TEA) significantly reduced depolarization-activated outward $K^+$ currents. SNP-enhanced outward $K^+$ currents were blocked by the application of TEA. High EGTA containing pipette solution (10 mM) reduced the control currents and also inhibited the SNP-enhanced outward $K^+$ currents. 5 mM 4-aminopyridine (4-AP) significantly reduced the control currents but showed no effect on SNP-enhanced outward $K^+$ currents. 0.3 ${\mu}M$ apamin and 10 ${\mu}M$ glibenclamide showed no effect on SNP-enhanced outward $K^+$ currents. 10 ${\mu}M$ 1H-[1,2,4]oxadiazolo [4,3-a]quinoxaline-1-one (ODQ), a specific inhibitor of soluble guanylate cyclase, significantly blocked SNP-enhanced $K^+$ currents. We conclude that NO donors activate the $Ca^{2+}-activated$ $K^+$ channels in guinea-pig ileal smooth muscle via activation of guanylate cyclase.

• Journal of the Korea Society of Computer and Information
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• v.17 no.11
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• pp.141-148
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• 2012

The advance of technologies for human genome makes it possible that the analysis of association between genetic variants and diseases and the application of the results to predict risk or susceptibility to them. Many of those studies carried out in case-control study. For quantitative traits, statistical analysis methods are applied to find single nucleotide polymorphisms (SNP) relevant to the diseases and consider them one by one. In this study, we presented methods to select informative single nucleotide polymorphisms and predict risk for quantitative traits and compared their performance. We adopted two SNP selection methods: one considering single SNP only and the other of all possible pairs of SNPs.

• Journal of Environmental Science International
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• v.20 no.12
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• pp.1509-1519
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• 2011

The protective effect of nitric oxide (NO) on the antioxidant system under paraquat(PQ) stress was investigated in leaves of 8-week-old lettuce (Lactuca sativa L.) plants. PQ stress caused a decrease of leaf growth including leaf length, width and weight. Application of NO donor, sodium nitroprusside (SNP), significantly alleviated PQ stress induced growth suppression. SNP permitted the survival of more green leaf tissue preventing chlorophyll content reduction and of higher quantum yield for photosystem II than in non-treated controls under PQ exposure, suggesting that NO has protective effect on chloroplast membrane in lettuce leaves. Flavonoids and anthocyanin were significantly accumulated in the leaves upon PQ exposure. However, the rapid increase of these compounds was alleviated in the SNP treated leaves. PQ treatment resulted in lipid peroxidation and induced accumulation of hydrogen peroxide ($H_2O_2$) in the leaves, while SNP prevented PQ induced increase in malondialdehyde (MDA) and $H_2O_2$. These results demonstrate that SNP serves as an antioxidant agent able to scavenge $H_2O_2$ to protect plant cells from oxidative damage. The activities of two antioxidant enzymes that scavenge reactive oxygen species, superoxide dismutase (SOD) and catalase (CAT) in lettuce leaves in the presence of NO donor under PQ stress were higher than those under PQ stress alone. Application of 2-(4-carboxyphenyl)-4, 4, 5, 5-tetramethylimidazoline-1-oxyl-3-oxide (PTIO), a specific NO scavenger, to the lettuce leaves arrested SNP mediated protective effect on leaf growth, photosynthetic pigment and antioxidant systems. However, PTIO had little effect on lettuce leaves under PQ stress compared with that of PQ stress alone. The obtained data suggest that the damage caused by PQ stress is in part due to increased generation of active oxygen by maintaining increased antioxidant enzyme activities and SNP protects plants from oxidative stress. From these results it is suggested that NO might act as a signal in activating active oxygen scavenging system that protects plants from oxidative damage induced by PQ stress and thus confer PQ tolerance.

• Journal of Ginseng Research
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• v.35 no.4
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• pp.504-513
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• 2011

In order to develop a novel system for the discrimination of five ginseng cultivars (Panax ginseng Meyer), single nucleotide polymorphism (SNP) genotyping assays with real-time polymerase chain reaction were conducted. Nucleotide substitution in gDNA library clones of P. ginseng cv. Yunpoong was targeted for the SNP genotyping assay. From these SNP sites, a set of modified SNP specific fluorescence probes (PGP74, PGP110, and PGP130) and novel primer sets have been developed to distinguish among five ginseng cultivars. The combination of the SNP type of the five cultivars, Chungpoong, Yunpoong, Gopoong, Kumpoong, and Sunpoong, was identified as 'ATA', 'GCC', 'GTA', 'GCA', and 'ACC', respectively. This study represents the first report of the identification of ginseng cultivars by fluorescence probes. An SNP genotyping assay using fluorescence probes could prove useful for the identification of ginseng cultivars and ginseng seed management systems and guarantee the purity of ginseng seed.