• Horticultural Science & Technology
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• v.32 no.4
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• pp.535-543
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• 2014

Backcross breeding is the method most commonly used to introgress new traits into elite lines. Conventional backcross breeding requires at least 4-5 generations to recover the genomic background of the recurrent parent. Marker-assisted backcrossing (MABC) represents a new breeding approach that can substantially reduce breeding time and cost. For successful MABC, highly polymorphic markers with known positions in each chromosome are essential. Single nucleotide polymorphism (SNP) markers have many advantages over other marker systems for MABC due to their high abundance and amenability to genotyping automation. To facilitate MABC in hot pepper (Capsicum annuum), we utilized expressed sequence tags (ESTs) to develop SNP markers in this study. For SNP identification, we used Bukang $F_1$-hybrid pepper ESTs to prepare a reference sequence through de novo assembly. We performed large-scale transcriptome sequencing of eight accessions using the Illumina Genome Analyzer (IGA) IIx platform by Solexa, which generated small sequence fragments of about 90-100 bp. By aligning each contig to the reference sequence, 58,151 SNPs were identified. After filtering for polymorphism, segregation ratio, and lack of proximity to other SNPS or exon/intron boundaries, a total of 1,910 putative SNPs were chosen and positioned to a pepper linkage map. We further selected 412 SNPs evenly distributed on each chromosome and primers were designed for high throughput SNP assays and tested using a genetic diversity panel of 27 Capsicum accessions. The SNP markers clearly distinguished each accession. These results suggest that the SNP marker set developed in this study will be valuable for MABC, genetic mapping, and comparative genome analysis.

• Journal of Animal Science and Technology
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• v.55 no.6
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• pp.515-520
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• 2013

Pyruvate kinase M2 (PKM2) is a key regulatory enzyme in the glycolytic pathway. It is one of four pyruvate kinase isoenzymes that widely differ in their occurrence according to tissue type. PKM2 is expressed in differentiated tissues, such as fat tissues, lung, as well as normal proliferating cells, embryonic cells, and tumor cells. The objective of this study was to investigate the association of single nucleotide polymorphisms (SNPs) in the PKM2 gene with meat quality traits in Berkshire pigs. We detected a SNP (g.34341 A>G) in the 3'UTR region of the PKM2 gene in 670 Berkshire pigs through DNA sequencing. Three genotypes, AA, AG, and GG, were found for this SNP, but based on an association analysis with meat quality traits, genotype AA was significantly associated with thicker back fat than genotype GG (p=0.027). Therefore, the g.34341 A>G polymorphism in the 3'UTR region of the porcine PKM2 gene could be applied in pig breeding programs to improve back fat thickness.

• The Korean Journal of Physiology and Pharmacology
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• v.12 no.3
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• pp.125-129
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• 2008

The aim of this study was to determine whether single nucleotide polymorphisms (SNPs) of matrix metallopeptidase 2 (MMP2) are associated with obesity. MMP2 is an enzyme with proteolytic activity against matrix and nonmatrix proteins, particularly basement membrane constituents. To identify the relationship between polymorphisms of MMP2 and overweight/obese, we genotyped 5 SNPs (rs17242319, rs1053605, rs243849, rs2287074, and rs10775332) of the coding region of MMP2 using the Golden Gate assay on an Illumina BeadStation 500 GX. One hundred and forty two overweight/obese ($BMI\;{\ge}\;23$) and 145 normal (BMI 18 to < 23) subjects were analyzed. SNPStats, Haploview, HapAnalyzer, SNPAnalyzer, and Helixtree programs were used for the analysis of genetic data. A linkage disequilibrium (LD) block was discovered among the 5 SNPs selected, including rs17242319, rs1053605, rs243849, and rs2287074. Of the 5 polymorphisms, 2 synonymous SNPs [rs17242319 (Gly226Gly) and rs10775332 (Phe602Phe)] were found significant associations with overweight/obese. Recently, rs1132896 replaced rs17242319 as a new number (SNP database, BUILD 129). In haplotype analysis using Haploview, a haplotype (haplotype: CCCA) containing a meaningful polymorphism (rs17242319) was found to be significantly different. The results suggest that MMP2 may be associated with overweight/obese in Korean population.

• Journal of Ginseng Research
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• v.36 no.2
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• pp.176-189
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• 2012

This study examined the effects of Korean red ginseng (KRG) on obese women and aimed to confirm that the effects of KRG on obesity differ dependently on a gene. Fifty obese women were recruited and randomized to receive KRG (n=24) or placebo (n=26) for 8 wk. Measurements of blood pressure, height, weight, waist circumference, waist-hip ratio (WHR), total fat mass, percentage of body fat, resting metabolic rate, basal body temperature, and daily food intake (FI), blood test (serum lipid, liver and renal function), Korean version of obesity-related quality of life scale (KOQOL), and a gene examination were performed. Comparisons of subjects before and after the administration of KRG revealed significant improvements of obesity in terms of weight, body mass index (BMI), WHR, FI, and KOQOL. However, in the comparison between KRG group and placebo group, only KOQOL was significantly different. KRG displayed significant efficacy on BMI and KOQOL in the CT genotype of the G protein beta 3 gene, but not in the CC genotype, on blood sugar test in the Trp64/Arg genotype of the beta 3 adrenergic receptor gene, but not in Trp64/Trp genotype, on KOQOL in the DD genotype of the angiotensin I converting enzyme gene, but not in the ID and DD genotypes. The effects of KRG on obesity were confirmed to some extent. However, a distinct effect compared to placebo was not confirmed. KRG is more effective for improving the secondary issues of the quality of life derived from obesity rather than having direct effects on the obesity-related anthropometric assessment and blood test indices.

• Journal of Korean Society of Forest Science
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• v.95 no.6
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• pp.631-635
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• 2006

Single-strand conformation polymorphism (SSCP) analysis of MD and JWB phytopalsma isolates which amplified PCR products using the R16F2n/R2 phytoplamsa universal primer pair were compared for variations of their nucleotide sequence. The MD and JWB phytoplasmas were clearly distinct each of the band patterns from about 1.2 kb PCR products. To clearly distinct of close SSCP band patterns, the MD and JWB phytoplasma PCR products were mixed and performed to detect their polymorphism. The SSCP band patterns show all of bands of MD and JWB on single lane and easily distinct their each band patterns. The PCR-SSCP analysis was possible to detect of 1.2 kb nucleotide sequence and near close band patterns were easily distinct by mixing two samples.

• Journal of Ginseng Research
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• v.43 no.3
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• pp.482-487
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• 2019

Background: The mixed-cultivation of different Panax ginseng cultivars can cause adverse effects on stability of yield and quality. K-1 is a superior cultivar with good root shape and stronger disease resistance. DNA markers mined from functional genes are clearly desirable for K-1, as they may associate with major traits and can be used for marker-assisted selection to maintain the high quality of Korean ginseng. Methods: Five genes encoding pathogenesis-related (PR) proteins of P. ginseng were amplified and compared for polymorphism mining. Primary, secondary, and tertiary structures of PR5 protein were analyzed by ExPASy-ProtParam, PSSpred, and I-TASSER methods, respectively. A coding single nucleotide polymorphism (SNP)-based specific primer was designed for K-1 by introducing a destabilizing mismatch within the 3' end. Allele-specific polymerase chain reaction (PCR) and real-time allele-specific PCR assays were conducted for molecular discrimination of K-1 from other cultivars and landraces. Results: A coding SNP leading to the modification of amino acid residue from aspartic acid to asparagine was exploited in PR5 gene of K-1 cultivar. Bioinformatics analysis showed that the modification of amino acid residue changed the secondary and tertiary structures of the PR5 protein. Primer KSR was designed for specific discrimination of K-1 from other ginseng cultivars and landraces. The developed real-time allele-specific PCR assay enabled easier automation and accurate genotyping of K-1 from a large number of ginseng samples. Conclusion: The SNP marker and the developed real-time allele-specific PCR assay will be useful not only for marker-assisted selection of K-1 cultivar but also for quality control in breeding and seed programs of P. ginseng.

• Korean Journal of Schizophrenia Research
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• v.23 no.2
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• pp.71-77
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• 2020

Objectives: Tardive dyskinesia (TD) is a movement disorder that is characterized by hyperkinetic movements. Previous studies have suggested that the serotonergic systems are correlated with TD vulnerability. In this study, the association between a single-nucleotide polymorphism (SNP) of the serotonin 1A receptor gene (HTR1A) rs6295 and TD was investigated. Methods: We investigated whether HTR1A rs6295 SNP is associated with antipsychotic-induced TD in 280 Korean patients with schizophrenia. Patients with schizophrenia having TD (n=105) and those without TD (n=175) were matched for their antipsychotic exposures and other relevant variables. The HTR1A rs6295 SNP was analyzed using polymerase chain reaction (PCR)-based methods. Results: There was no significant difference in the distribution of genotypic (χ²=2.70, p=0.26) and allelic (χ²=1.87, p=0.17) frequencies between the patient groups with TD and without TD. There was no significant difference in total abnormal involuntary movement scale score (F=0.39, p=0.68) among the genotype group either. Conclusion: Although there were no differences in genotypic and allelic frequency between patient groups with and without TD, further studies on association of TD with other SNPs of HTRA1 are needed to understand the pathophysiological mechanism of TD.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.5
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• pp.2865-2869
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• 2013

Hepatitis B virus (HBV) infection can become chronic and if left untreated can progress to hepatocellular carcinoma (HCC).Thailand is endemic for HBV and HCC is one of the top five cancers, causing deaths among Thai HBV-infected males. A single nucleotide polymorphism (SNP) at the KIF1B gene locus, rs17401966, has been shown to be strongly associated with the development of HBV-related HCC. However, there are no Thai data on genotypic distribution and allele frequencies of rs17401966. Thai HBV patients seropositive for HBsAg (n=398) were therefore divided into two groups: a case group (chronic HBV with HCC; n=202) and a control group (HBV carriers without HCC; n=196). rs17401966 was amplified by polymerase chain reaction (PCR) and analyzed by direct nucleotide sequencing. The genotypic distribution of rs174019660 for homozygous major genotype (AA), heterozygous minor genotype (AG) and homozygous minor genotype (GG) in the case group was 49.5% (n=100), 40.1% (n=81) and 10.4% (n=21), respectively, and in controls was 49.5% (n=97), 42.3% (n=83) and 8.2% (n=16). Binary logistic regression showed that rs17401966 was not statistically associated with the risk of HCC development in Thai chronic HBV patients (p-value=0.998, OR=1.00 and 95% CI=0.68-1.48). In conclusion, the KIF1B gene SNP (rs174019660) investigated in this study showed no significant association with HBV-related HCC in Thai patients infected with HBV, indicating that there must be other mechanisms or pathways involved in the development of HCC.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.8
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• pp.1065-1070
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• 2006

The avian uncoupling protein (avUCP) is a member of the mitochondrial transporter superfamily that uncouples proton entry in the mitochondrial matrix from ATP synthesis. The sequencing analysis method was used to identify nucleotide polymorphisms within the avUCP gene in Korean native chicken (KNC). This study identified ten single nucleotide polymorphisms (SNPs) in the avUCP gene. We analyzed the SNPs of the avUCP gene to investigate whether polymorphism in the gene might be responsible for quantitative variations in economic traits in KNC. Three significant polymorphic sites for economic traits were avUCP C+282T (mean body weight, p<0.05), avUCP C+433T (daily percent lay, p<0.05), and avUCP T+1316C (daily percent lay, p<0.05). The frequency of each SNP was 0.125 (C+282T in avUCP gene exon 1 region), 0.150 (C+433T in avUCP gene intron 1 region), and 0.15 (T+1316C in avUCP gene exon 3 region), respectively. Among the identified SNPs, one pair of SNPs (genotype CC, C+282T and TT, avUCP C+433T) showed the highest daily percent lay (p<0.05) and mean body weight (p<0.05) and the frequency was 0.067. This study of the avUCP gene could be useful for genetic studies of this gene and selection on economic traits for KNC.

• The Korean Journal of Mycology
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• v.49 no.1
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• pp.33-44
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• 2021

Lentinula edodes (Berk.) Pegler, the most produced mushroom in the world, is an edible mushroom with very high nutritional and pharmacological value. Currently, interest in the protection of genetic resources is increasing worldwide, and securing the distinction between new cultivars is very important. Therefore, the development of efficient molecular markers that can discriminate between L. edodes cultivars is required. In this study, we developed cleaved amplified polymorphic sequence (CAPS) markers for the identification of L. edodes cultivars (Sanbaekhyang and Sulbaekhyang). These markers were developed from whole genome sequencing data from L. edodes monokaryon strain B17 and resequencing data from 40 cultivars. A nucleotide deletion existed in scaffold 19 POS 214449 in Sanbaekhyang (GT→G), and a single nucleotide polymorphism changed in scaffold 7 POS 215801 in Sulbaekhyang (G→A). The restriction enzymes Hha I and HpyCH4IV distinguished Sanbaekhyang and Sulbaekhyang, respectively, from other cultivars. Thus, we developed two CAPS markers for the identification of the L. edodes cultivars Sanbaekhyang and Sulbaekhyang.