• The Korean Journal of Applied Statistics
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• v.21 no.1
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• pp.53-63
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• 2008

It is commonly believed that disease of human or economic traits of livestock are caused not by single gene acting alone, but by multiple genes interacting with one an-other. This issue is difficult due to the limitations of parametric statistical method like as logistic regression for detection of gene effects that are dependent solely on interactions with other genes and with environmental exposures. Multifactor dimensionality reduction (MDR) nonparametric statistical method, to improve the identification of single nucleotide polymorphism (SNP) associated with the Hanwoo(Korean cattle) carcass cold weight, is applied and compared with ANOVA results.

• Horticultural Science & Technology
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• v.28 no.4
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• pp.627-637
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• 2010

The consumption of tomato has greatly increased recently in Korea, and a large number of tomato cultivars are commercially available in the market. However, identification of tomato cultivars by morphological traits is extremely difficult because of the narrow genetic diversity of breeding lines. Therefore, it is necessary to develop molecular markers for cultivar identification in tomato. In this study, we surveyed single nucleotide polymorphism (SNP), and developed SNP marker sets for tomato cultivar identification. SNP markers were developed based on conserved ortholog set II (COSII) and intron-based markers derived from pepper EST sequences, and marker polymorphism was tested using high-resolution melting (HRM) analysis. A total of 628 primer sets was tested, and 417 primer sets amplifying single bands were selected. Of the 417 primer sets, 70 primer sets showing HRM polymorphism among 4 inbred lines were selected. Eleven markers were selected from the 70 primer sets and subjected to cultivar identification analysis. Thirty two commercial tomato cultivars were successfully identified using the marker set.

• 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.

• Journal of Plant Biotechnology
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• v.43 no.1
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• pp.1-11
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• 2016

Single nucleotide polymorphism (SNP) is an abundant form of genetic variation within individuals of species. DNA polymorphism can arise throughout the whole genome at different frequencies in different species. SNP may cause phenotypic diversity among individuals, such as individuals with different color of plants or fruits, fruit size, ripening, flowering time adaptation, quality of crops, grain yields, or tolerance to various abiotic and biotic factors. SNP may result in changes in amino acids in the exon of a gene (asynonymous). SNP can also be silent (present in coding region but synonymous). It may simply occur in the noncoding regions without having any effect. SNP may influence the promoter activity for gene expression and finally produce functional protein through transcription. Therefore, the identification of functional SNP in genes and analysis of their effects on phenotype may lead to better understanding of their impact on gene function for varietal improvement. In this mini-review, we focused on evidences revealing the role of functional SNPs in genes and their phenotypic effects for the purpose of crop improvements.

• Journal of the Korean Society of Tobacco Science
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• v.30 no.2
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• pp.85-93
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• 2008

This report describes a set of seven informative single-nucleotide polymorphisms (SNPs) and one insertion-deletion (INDEL) distributed over 24 cultivars that can be used for tobacco (Nicotiana tabacum L.) cultivar identification. We analyzed 163,000 genomic DNA sequences downloaded from Tobacco Genome Initiative database and assembled 31,370 contigs and 60,000 singletons. Using relatively long contigs, we designed primer sets for PCR amplification. We amplified 61 loci from 24 cultivars and sequenced the PCR products. We found seven significant SNPs and one INDEL among the sequences and we classified the 24 cultivars into 10 groups. SNP frequency of tobacco, 1/8,380 bp, was very low in comparison with those of other plant species, between 1/46 bp and 1/336 bp. For exact identification of tobacco cultivars, many more SNP markers should be developed. This study is the first attempt to identify tobacco cultivars using SNP markers.

• Communications for Statistical Applications and Methods
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• v.16 no.1
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• pp.67-74
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• 2009

In order to make the high quality Korean cattle, it has been identified the gene markers which influence to various economic traits. To identify statistically significances among SNP markers, Lee et. al. (2008b) identified SNP(19_1)$^*$SNP(28_2) marker was an important marker in LMA(longissimus muscle dorsi area). In addition, CWT(carcass cold weight) and ADG(average daily gain) are applied for expanded multifactor dimensionality reduction (expanded MDR) method from the comprehensive economic traits. The results showed that SNP(19_1)$^*$SNP(28_2) interaction marker was good and a very meaningful for economic traits.

• Bulletin of the Korean Chemical Society
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• v.31 no.7
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• pp.1902-1906
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• 2010

A microchip electrophoresis (ME) method was developed using a programmed field strength gradients (PFSG) for the single nucleotide polymorphism (SNP) based fast identification of cattle breeds. Four different Korean cattle (Hanwoo) and Holstein SNP markers amplified by allele-specific polymerase chain reaction were separated in a glass microchip filled with 0.5% poly(ethyleneoxide) ($M_r$ = 8 000 000) by PFSG as follows: 750 V/cm for 0 - 14 s, 166.7 V/cm for 14 - 31 s, 83.3 V/cm for 31 - 46 s, and 750 V/cm for 46 - 100 s. The cattle breeds were clearly distinguished within 45 s. The ME-PFSG method was 7 times and 5 times faster than the constant electric field ME method and the capillary electrophoresis- PFSG method, respectively, with a high resolving power ($R_s$ = 5.05 - 9.98). The proposed methodology could be a powerful tool for the fast and simultaneous determination of SNP markers for various cattle breeds with high accuracy.

• Communications for Statistical Applications and Methods
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• v.15 no.2
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• pp.265-271
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• 2008

It is commonly believed that diseases of human or economic traits of livestock are caused not by single genes acting alone, but multiple genes interacting with one another. This issue is difficult due to the limitations of parametric-statistic methods of gene effects. So we introduce multifactor-dimensionality reduction(MDR) as a methods for reducing the dimensionality of multilocus information. The MDR method is nonparametric (i. e., no hypothesis about the value of a statistical parameter is made), model free (i. e., it assumes no particular inheritance model) and is directly applicable to case-control studies. Application of the MDR method revealed the best model with an interaction effect between the SNPs, SNP1 and SNP3, while only one main effect of SNP1 was statistically significant for LMA (p < 0.01) under a general linear mixed model.

• BMB Reports
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• v.37 no.3
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• pp.269-274
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• 2004

DNA polymerases without the 3' exonuclease function ($exo^-$ pol) have been widely used in sequencing and SNP genotyping. As a major player that expedited the coming of the postgenomic era, $exo^-$ polymerases worked remarkably well in the Human Genome Sequencing Project. However, it has become a challenge for this class of polymerases to efficiently screen the large number of SNPs that are found in the human genome. For more than three decades it has been recognized that polymerase fidelity varied according to the presence of proofreading activity that is mediated by its internal 3' exonuclease. Polymerases with proofreading function are famous for their high fidelity in DNA replication both in vivo and in vitro, but this well-known class of polymerases has been almost completely neglected in genetic analysis in the postgenomic era. We speculate that $exo^+$ polymerases may exhibit higher nucleotide identification ability when compared to $exo^-$ polymerases for an in vitro genetic analysis. With the application of $exo^+$ polymerases in SNP assays, a novel mechanism for the maintenance of DNA replication, the on/off switch, was discovered. Two new SNP assays have been developed to carry out genome-wide genotyping, taking advantage of the enzymatic properties of $exo^+$ polymerases. Furthermore, the on/off switch mechanism embodies a powerful nucleotide identification ability, which can be used to discriminate the bases that are upstream of the 3' terminus, and thus defines a new concept in de novo sequencing technology. Application of $exo^+$ polymerases to genetic analysis, and especially SNP assays, will greatly accelerate the pace to personalized medicine.

• 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.