• 원예과학기술지
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• 제31권1호
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• pp.72-79
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• 2013

Inactivation of the gene coding for dihydroflavonol 4-reductase (DFR) is responsible for the color difference between red and yellow onions (Allium cepa L.). Two inactive DFR-A alleles, DFR-$A^{PS}$ and DFR-$A^{DEL}$, were identified in our previous study. A functional marker was developed on the basis of the premature stop codon that inactivated the DFR-$A^{PS}$ allele. A derived cleaved amplified polymorphic sequences (dCAPS) primer was designed to detect the single nucleotide polymorphism, an A/T transition, which produced the premature stop codon. Digested PCR products clearly distinguished the homozygous and heterozygous red $F_2$ individuals. Meanwhile, to develop a molecular marker for detection of the DFR-$A^{DEL}$ allele in which entire DFR-A gene was deleted, genome walking was performed and approximately 3 kb 5' and 3' flanking sequences of the DFR-$A^R$ coding region were obtained. PCR amplification using multiple primers binding to the extended flanking regions showed that more of the extended region of the DFR-A gene was deleted in the DFR-$A^{DEL}$ allele. A dominant simple PCR marker was developed to identify the DFR-$A^{DEL}$ allele using the dissimilar 3' flanking sequences of the DFR-A gene and homologous DFR-B pseudogene. Distribution of the DFR-$A^{PS}$ and DFR-$A^{DEL}$ alleles in yellow onion cultivars bred in Korea and Japan was surveyed using molecular makers developed in this study. Results showed predominant existence of the DFR-$A^{PS}$ allele in yellow onion cultivars.

• 한방비만학회지
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• 제12권2호
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• pp.28-43
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• 2012

Objectives: The aim of the study was to investigate the efficacy of Boiogito for obesity. We examined the efficacy of Boiogito for obese patients and we expected the reaction of Boiogito would vary according to the single nucleotide polymorphism(SNPs). Methods: 111 subjects(body mass index${\geq}25m/kg^2$) were recruited and randomized to receive Boiogito(n=55) or Placebo(n=56) for 8weeks. Anthropometric factors, serum lipid profile, glucose, blood pressure(BP), pulse rate, resting metabolic rate and Korean version of obesity-related quality of life(KOQOL) scale measured at baseline and 8weeks. SNPs(${\beta}3$-adrenergic receptor(ADRB3), G protein ${\beta}3$(GNB3), peroxisome proliferator activated receptor gamma 2 gene(PPAR-${\gamma}2$), uncoupling protein(UCP2)) were conducted at baseline. Adverse reactions and safety outcome variables were also checked during trials. Results: Both groups showed significant improvement on obesity after treatment. Boiogito group decreased triglyceride than did control group and improved KOQOL. Boiogito showed a significant higher efficacy in C/T and T/T genotype of GNB3 gene / in Trp64 and Arg64 genotype of ADRB3 gene / in D/D genotype of UCP2 gene / in Pro/Pro genotype of PPAR-${\gamma}$ gene. Conclusions: Boiogito promoted obesity indexes without severe adverse reactions and proved its safety. Pharmacogenetical studies of Boiogito on obesity could be a effective method for the individualized treatment and prevention of obesity.

• Journal of Platform Technology
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• 제6권4호
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• pp.87-95
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• 2018

개인 전장 유전체 분석 가격의 하락으로 많은 국가들이 10만명에서 100만명까지의 대량 전장 유전체 분석과 엑솜 시퀀싱을 진행하고 있다. 하지만 많은 대형 프로젝트에서 대량의 데이터를 처리할 수 있는 프로그램이나 시스템의 부족으로 많은 비용이 클러스터 구축 및 시스템 구매 비용으로 소비되고 있다. 본 연구에서는 자체 서버나 클러스터 환경을 구축하지 않고도 동시에 수백 개 이상의 전장 유전체 및 엑솜에 대한 단일 염기 다형성(Single Nucleotide Polymorphism; SNP) 분석을 수행할 수 있고, 생물학자들도 쉽게 설치하여 운영할 수 있는 클라이언트 프로그램인 NGSOne을 개발하였다. 대표적인 SNP 분석 도구인 DRAGEN, BWA/GATK 및 Isaac/Strelka2를 선택하여 분석할 수 있고, 3개 툴에서 실행 시간 및 에러의 개수 면에서는 DRAGEN이 가장 좋은 성능을 보였다. 또한 NGSOne은 SNP 분석뿐만 아니라 다양한 분석 도구의 자동적인 실행을 위한 확장이 가능하다.

• Plant Breeding and Biotechnology
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• 제6권4호
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• pp.413-425
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• 2018

A previous work developed and identified a new omega-5 gliadin deficient wheat line named O-free by crossing Keumkang and Olgeuru, which is nutritionally quite meaningful in that omega-5 gliadin is one of the known wheat allergens. To verify the characteristics of the O-free, we performed RNA sequencing (RNAseq) analysis of the O-free and the two parent lines (Keumkang and Olgeuru). The results of the similarity analysis with the ESTs for gliadins and glutenins showed that the O-free ESTs had no similarity with the omega-5 gliadin sequences but had similarity to other gliadins and glutenins. Furthermore, mapping results between the raw RNAseq data from the O-free and the omega-5 gliadin sequence showed a clear deletion of the N-terminal sequences which are an important signature of omega-5 gliadin. We also designed specific PCR primers that could identify omega-5 gliadin in the genomic DNA. The results showed that no omega-5 gliadin fragments were detected in the O-free. According to these results, we confirmed that the deficiency of omega-5 gliadin in the O-free is not caused by post-transcriptional or post-translational regulations such as epigenetic phenomena but by a simple deletion in the chromosome. Furthermore, we showed that the low-molecular weight glutenin subunit (LMW-GS) gene in the O-free had a single nucleotide polymorphism (SNP) causing a premature stop codon, resulting in a truncated polypeptide. We expect that the O-free line may serve as an excellent source of wheat that could prevail in the hypo-allergen wheat market, which has recently gained interest world-wide.

• 농업과학연구
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• 제45권4호
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• pp.707-713
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• 2018

This study was done to search for positional candidate genes associated with the back fat thickness trait using a Genome-Wide Association Study (GWAS) in purebred Yorkshires (N = 1755). Genotype and phenotype analyses were done for 1,642 samples. As a result of the associations with back fat thickness using the Gemma program (ver. 0.93), when the genome-wide suggestive threshold was determined using the Bonferroni method ($p=1.61{\times}10^{-5}$), the single nucleotide polymorphism (SNP) markers with suggestive significance were identified in 1 SNP marker on chromosome 2 (MARC0053928; $p=3.65{\times}10^{-6}$), 2 SNP markers on chromosome 14 (ALGA0083078; $p=7.85{\times}10^{-6}$, INRA0048453; $p=1.27{\times}10^{-5}$), and 1 SNP marker on chromosome 18 (ALGA0120564; $p=1.44{\times}10^{-5}$). We could select positional candidate genes (KCNQ1, DOCK1, LOC106506151, and LOC110257583), located close to the SNP markers. Among these, we identified a potassium voltage-gated channel subfamily Q member gene (KCNQ1) and the dedicator of cytokinesis 1 (DOCK1) gene associated with obesity and Type-2 diabetes. The SNPs and haplotypes of the KCNQ1 and DOCK1 genes can contribute to understanding the genetic structure of back fat thickness. Additionally, it may provide basic data regarding marker assisted selection for a meat quality trait in pigs.

• Clinical and Experimental Reproductive Medicine
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• 제46권3호
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• pp.132-139
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• 2019

Objective: Vitamin D-binding protein (VDBP) mediates various biological processes in humans. The goal of this study was to investigate whether VDBP gene polymorphisms could predispose Korean women to endometriosis. Methods: We prospectively enrolled women with endometriosis (n = 16) and healthy controls (n = 16). Total serum 25-hydroxyl vitamin D (25(OH)D) concentrations were measured using an Elecsys vitamin D total kit. Levels of bioavailable and free 25(OH)D were calculated. Concentrations of VDBP were measured using a vitamin D BP Quantikine ELISA kit. DNA was extracted using a DNeasy blood & tissue kit. Two single-nucleotide polymorphisms (SNPs; rs4588 and rs7041) in GC, the gene that codes for VDBP, were analyzed using a TaqMan SNP genotyping assay kit. The functional variant of VDBP was determined based on the results of the two SNPs. Results: Gravidity and parity were significantly lower in the endometriosis patients than in the control group, but serum CA-125 levels and the erythrocyte sedimentation rate were significantly higher. Total serum 25(OH)D levels in the endometriosis patients were significantly lower than in the control group. However, serum bioavailable 25(OH)D, free 25(OH)D, and VDBP levels did not differ significantly between the endometriosis and control groups. The genotypes and allele frequencies of GC were similar in both groups. Conclusion: Korean women with endometriosis had lower total serum 25(OH)D concentrations than controls. Neither serum VDBP concentrations nor polymorphisms in the gene coding for VDBP were associated with endometriosis. Further studies are needed to investigate the pathophysiology and clinical implications of 25(OH)D and VDBP in endometriosis.

• Asian-Australasian Journal of Animal Sciences
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• 제32권7호
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• pp.939-948
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• 2019

Objective: Extension and Agouti loci play a key role for proportions of eumelanin and pheomelanin in determining coat color in several species, including goat. Mongolian goats exhibit diverse types of coat color phenotypes. In this study, investigation of the melanocortin 1 receptor (MC1R) coding region in different coat colors in Mongolian goats was performed to ascertain the presence of the extension allele. Methods: A total of 105 goat samples representing three goat breeds were collected for this study from middle Mongolia. A 938 base pair (bp) long coding region of the MC1R gene was sequenced for three different breeds with different coat colors (Gobi Gurwan Saikhan: complete black, Zalaa Jinstiin Tsagaan: complete white, Mongolian native goat: admixture of different of coat colors). The genotypes of these goats were obtained from analyzing and comparing the sequencing results. Results: A total of seven haplotypes defined by five substitution were identified. The five single nucleotide polymorphisms included two synonymous mutations (c.183C>T and c.489G>A) and three missense (non-synonymous) mutations (c.676A>G, c.748T>G, and c.770T>A). Comparison of genotypes frequencies of two common missense mutions using chi-sqaure ($x^2$) test revealed significant differences between coat color groups (p<0.001). A logistic regression analysis additionally suggested highly significant association between genotypes and variation of black versus white uniform combination. Alternatively, most investigated goats (60.4%) belonged to H2 (TGAGT) haplotype. Conclusion: According to the findings obtained in this study on the investigated coat colors, mutations in MC1R gene may have the crucial role for determining eumelanin and pheomelanin phenotypes. Due to the complication of coat color phenotype, more detailed investigation needed.

• The Plant Pathology Journal
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• 제37권2호
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• pp.194-199
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• 2021

Blackleg is a serious disease in Brassica plants, causing moderate to severe yield losses in rapeseed worldwide. Although China has not suffered from this disease yet (more aggressive Leptosphaeria maculans is not present yet), it is crucial to take provisions in breeding for disease resistance to have excellent blackleg-resistant cultivars already in the fields or in the breeding pipeline. The most efficient strategy for controlling this disease is breeding plants with identified resistance genes. We selected 135 rapeseed accessions in Sichuan, including 30 parental materials and 105 hybrids, and we determined their glucosinolate and erucic acid content and confirmed 17 double-low materials. A recently developed single-nucleotide polymorphism (SNP) marker, SNP_208, was used to genotype allelic Rlm1/rlm1 on chromosome A07, and 87 AvrLm1-resistant materials. Combined with the above-mentioned seed quality data, we identified 11 AvrLm1-resistant double-low rapeseed accessions, including nine parental materials and two hybrids. This study lays the foundation of specific R gene-oriented breeding, in the case that the aggressive Leptosphaeria maculans invades and establishes in China in the future and a robust and less labor consuming method to identify resistance in canola germplasm.

• Journal of Genetic Medicine
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• 제18권2호
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• pp.110-116
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• 2021

Microdeletions of chromosome 22q11.2 are one of the most common microdeletions occurring in humans, and is known to be associated with a wide range of highly variable features. These deletions occur within a cluster of low copy repeats (LCRs) in 22q11.2, referred to as LCR22 A-H. DiGeorge (DGS)/velocardiofacial syndrome is the most prevalent form of a 22q11.2 deletions, caused by mainly proximal deletions between LCR22 A and D. As deletions of distal portion to the DGS deleted regions has been extensively studied, the recurrent distal 22q11.2 microdeletions distinct from DGS has been suggested as several clinical entities according to the various in size and position of the deletions on LCRs. We report a case of long-term follow-up of a female diagnosed with a 22q11.2 distal deletion syndrome, identified a deletion of 1.9 Mb at 22q11.21q11.23 (chr22: 21,798,906-23,653,963) using single nucleotide polymorphism array. This region was categorized as distal deletion type of 22q11.2, involving LCR22 D-F. She was born as a preterm, low birth weight to healthy non-consanguineous Korean parents. She showed developmental delay, growth retardation, dysmorphic facial features, and mild skeletal deformities. The patient underwent a growth hormone administration due to growth impairment without catch-up growth. While a height gain was noted, she had become overweight and was subsequently diagnosed with pre-diabetes. Our case could help broaden the genetic and clinical spectrum of 22q11.2 distal deletions.

• Genomics & Informatics
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• 제20권1호
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• pp.4.1-4.8
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• 2022

Loss of heterozygosity (LOH) is a genomic aberration. In some cases, LOH can be generated without changing the copy number, which is called copy-neutral LOH (CN-LOH). CN-LOH frequently occurs in various human diseases, including cancer. However, the biological and clinical implications of CN-LOH for human diseases have not been well studied. In this study, we compared the performance of CN-LOH determination using three commonly used tools. For an objective comparison, we analyzed CN-LOH profiles from single-nucleotide polymorphism array data from 10 colon adenocarcinoma patients, which were used as the reference for comparison with the CN-LOHs obtained through whole-exome sequencing (WES) data of the same patients using three different analysis tools (FACETS, Nexus, and Sequenza). The majority of the CN-LOHs identified from the WES data were consistent with the reference data. However, some of the CN-LOHs identified from the WES data were not consistent between the three tools, and the consistency with the reference CN-LOH profile was also different. The Jaccard index of the CN-LOHs using FACETS (0.84 ± 0.29; mean value, 0.73) was significantly higher than that of Nexus (0.55 ± 0.29; mean value, 0.50; p = 0.02) or Sequenza (0 ± 0.41; mean value, 0.34; p = 0.04). FACETS showed the highest area under the curve value. Taken together, of the three CN-LOH analysis tools, FACETS showed the best performance in identifying CN-LOHs from The Cancer Genome Atlas colon adenocarcinoma WES data. Our results will be helpful in exploring the biological or clinical implications of CN-LOH for human diseases.