• Horticultural Science & Technology
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• v.32 no.1
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• pp.84-90
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• 2014

Berchemia racemosa var. magna is only found in Anmyeon Island of South Korea. Genetic diversity and the spatial genetic structure of B. racemosa var. magna in Anmyeon Island were studied by I-SSR marker system. Fifty I-SSR amplicons were produced from 8 selected primers. We used 13 polymorphic markers to analyze the genetic structure. Distribution of 39 individuals in the study plot($90m{\times}70m$) showed aggregate pattern (aggregation index = 0.706). Total 21 genets were observed from 39 individuals through I-SSR genotyping. Proportion of distinguishable genotype (G/N), genotype diversity (D) and genotype evenness (E) were 53.8%, 0.966 and 0.946, respectively. In spite of the small number and the narrow distribution, Shannon's diversity index (I = 0.598) was relatively high as compared with those of the other plant species. For ex situ genetic conservation of B. racemosa var. magna, the sampling strategy based on spatial autocorrelation using Tanimoto distance is efficient at choosing the conserved individuals with a 6 meter interval between individual trees.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.6
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• pp.2747-2751
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• 2014

Background: DNA repair pathways play a crucial role in maintaining the human genome. Previous studies associated DNA repair gene polymorphisms (XPD Lys751Gln, XRCC1 Arg280His and XRCC1 Arg399Gln) with nasopharyngeal carcinoma. These non-synonymous polymorphisms may alter DNA repair capacity and thus increase or decrease susceptibility. The present study aimed to determine the genotype distribution of XPD codon 751, XRCC1 codon 280 and codon 399 polymorphisms and haplotype associations among NPC cases and controls in the Malaysian population. Materials and Methods: We selected 157 NPC cases and 136 controls from two hospitals in Kuala Lumpur, Malaysia for this study. The polymorphisms studied were genotyped by PCR-RFLP assay and allele and genotype frequenci es, haplotype and linkage disequilibrium were determined using SNPstat software. Results: For the XPD Lys751Gln polymorphism, the frequency of the Lys allele was higher in cases than in controls (94.5% versus 85.0%). For the XRCC1 Arg280His polymorphism, the frequency of Arg allele was 90.0% and 89.0% in cases and controls, respectively and for XRCC1 Arg399Gln the frequency of the Arg allele was 72.0% and 72.8% in cases and controls respectively. All three polymorphisms were in linkage disequilibrium. The odds ratio from haplotype analysis for these three polymorphisms and their association with NPC was 1.93 (95%CI: 0.90-4.16) for haplotype CGC vs AGC allele combinations. The global haplotypte association with NPC gave a p-value of 0.054. Conclusions: Our study provides an estimate of allele and genotype frequencies of XRCC1Arg280His, XRCC1 Arg399Gln and XPD Lys751Gln polymorphisms in the Malaysian population and showed no association with nasopharyngeal cancer.

• The Korean Journal of Physiology and Pharmacology
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• v.12 no.2
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• pp.83-87
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• 2008

The fyn-related kinase (FRK) belongs to the tyrosine kinase family of protein kinases. Recent studies have shown that Frk affects pancreatic beta cell number during embryogenesis and promotes beta cell cytotoxic signals in response to streptozotocin. To investigate the genetic association between FRK polymorphisms and the risk of obesity in Korean population, single nucleotide polymorphisms (SNPs) in the FRK gene region were selected and analyzed. The body mass index (BMI) was calculated, and biochemical data (systolic blood pressure, diastolic blood pressure, hemoglobin A1C, triglyceride, total cholesterol, high density lipoprotein, and low density lipoprotein) of blood sample from each subject were also measured. One hundred fifty five healthy control and 204 overweight/obesity subjects were recruited. Genotype frequencies of six SNPs [rs6568920 (+8391G>A), rs3756772 (+56780A>G), rs3798234 (+75687C>T), rs9384970 (+68506G>A), rs1933739 (+72978G>A), and rs9400883 (+75809A>G)] in the FRK gene were determined by Affymetrix Targeted Genotyping Chip data. According to the classification of Korean Society for the Study of Obesity, control (BMI 18 to < 23) and overweight/obesity (BMI$\geq$23) subjects were recruited. For the analysis of genetic data, EM algorithm, SNPStats, Haploview, HapAnalyzer, SNPAnalyzer, and Helixtree programs were used. Multiple logistic regression analysis (codominant, dominant, and recessive models) was performed. Age and gender as covariates were adjusted. For biochemical data, Student's t test was used. The mean value of BMI in the control and overweigh/obesity groups was 21.1${\pm}$1.2 (mean${\pm}$SD) and 25.6${\pm}$2.0, respectively. All biochemical data of the overweight/obesity group were statistically significance, compared with the control group. Among six SNPs, two linkage disequilibrium (LD) blocks were discovered. One block consisted of rs1933739 and rs9400883, and the other comprised rs3756772 and rs3798234. One SNP (rs9384970, +68506G>A) showed an association with overweight/obesity in the codominant model (p=0.03). Interestingly, the AA genotype distribution in the overweight/obesity group (n=7, 3.5%) was higher than those in the control group (n=1, 0.6%), which is not found in either Japanese or Chinese subjects. Therefore, the AA genotype of rs9384970 may be a risk factor for development of obesity in Korean population. The results suggest that FRK may be associated with overweight/obesity in Korean population.

• Journal of Life Science
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• v.30 no.7
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• pp.592-597
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• 2020

Soybean [Glycine max (L.) Merr.] seeds contain an average of 40% protein on a dry weight basis, but they also contain antinutritional elements such as lectin, Kunitz trypsin inhibitor (KTI), and 7S α'- subunit protein. The objective of this research was to develop a new soybean genotype with triple recessive alleles for these elements. Three parents (Gaechuck#2, PI506876, and Le-16) were used to develop the genetic population, and the presence of lectin and KTI protein was detected using Western blot while 7S α' subunit protein was detected using SDS-PAGE. One F₃ plant strain with proper agronomical traits such as type, height, seed quality, and 100-seed weight was selected. The genotype of the developed strain is titilelecgy1cgy1, that is KTI, lectin, and 7S α' subunit protein free. The new strain has a purple flower, determinate growth habit, and light yellow pods at maturity. The seed has a buffer hilum and is yellow in color. The new strain's height was 58 cm compared to the Daewonkong cultivar at 46 cm, and its 100-seed weight was 27.1 g, smaller than the Daewonkong at 29.0 g. This is the first new soybean strain with the titilelecgy1cgy1 genotype, and it can be used to improve yellow soybean cultivars of high quality and function.

• Journal of Life Science
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• v.29 no.7
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• pp.774-778
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• 2019

Soybean [Glycine max (L.) Merr.] is one of the major food sources of protein, oil, carbohydrates, isoflavones, and other nutrients for both humans and animals. However, soybean seeds contain antinutritional factors, such as lectin protein, Kunitz Trypsin Inhibitor (KTI) protein, and stachyose. The objective of this research was to stack recessive alleles for development a triple recessive genotype, titilelers2rs2, with low KTI protein, lectin protein, and stachyose contents. Three parents (Gaechuck#2, PI200508, and 14G20) were used to develop the breeding population. The presence or absence of the lectin and KTI proteins was detected by western blotting. The stachyose content in mature seeds was determined by HPLC. Agronomic traits, such as plant type, plant height, maturity date, lodging, seed quality, and 100-seed weight, were evaluated for the four $F_3$ plant strains. One $F_4$ plant strain with the desired agronomical traits was selected. One new strain with the triple recessive titilelers2rs2 genotype was developed. The plant height of the new strain was 51 cm and the 100-seed weight was 31.0 g. The new strain had a yellow seed coat and yellow hilum. The stachyose content of the new strain was 3.8 g/kg. One strain developed in this research will be used to produce improved yellow soybean cultivars that are free of lectin and KTI proteins and low in stachyose content.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.21 no.1
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• pp.240-246
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• 2020

This study was conducted to develop specific Single Nucleotide Polymorphism (SNP) markers to identify the genetic characteristics and breed of White Hanwoo (WH) using a molecular biological method. SNP genotyping was performed with an Illumina Bovine HD 777K SNP chip using DNA extracted from 48 Hanwoo and 22 WH. The minor allele frequency (MAF) difference of each SNP was calculated and the statistical significance (P-value) of the MAF difference was calculated through Fisher's Exact test (Genotype). SNPs with 100% difference in the MAF difference were selected based on marker selection criteria. The nine SNP markers with genetic differences were selected. The selected markers have different alleles as being Hanwoo- and WH- specific. Therefore, based on these results, it can be concluded that the Hanwoo and WH varieties can be clearly distinguished by using these SNPs. So, the patent of the WH breed identification markers was registered. WH is a breed that shows the characteristics of a Korean native species that is separate from the native Hanwoo. It is expected that genetic characteristics research on the WH can be used to identify the breed and as a knowledge base for enhancing the value of breeding stock.

• 한국균학회소식:학술대회논문집
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• 2015.05a
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• pp.28-28
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• 2015

Clubroot disease caused by Plasmodiophora brassicae induces severe losses of cruciferous vegetables worldwide. To control clubroot of Chinese cabbage, many CR (clubroot resistance) F1 hybrid cultivars have been bred and released in Korea, China and Japan. In this study, we determined the race of P. brassicae 12 field isolates, which collected from 10 regions in Korea, using Williams' differential varieties including two cabbage ('Jersey Queen', 'Badger Shipper') and two rutabaga ('Laurentian', 'Whilhelmsburger'). By Williams' differential varieties, 12 clubroot pathogens were assigned into one (GN2), two (HS and YC), two (HN1 and HN2), three (DJ, KS and SS) and four (GS, GN1, JS and PC) isolates for races 1, 2, 4, 5 and 9, respectively. In addition, the degree of resistance of 45 CR cultivars that were from Korea, China and Japan was tested with the 12 isolates. The 45 CR cultivars of Chinese cabbage were differentiated into three genotypes according to their resistance responses. Even though the 12 P. brassicae isolates were same race by Williams' differential varieties, three CR genotypes showed different resistance response to the isolates. These results indicate that races of P. brassicae by Williams' differentials were not related with resistance of CR cultivars, and three CR genotypes represented qualitative resistance to the P. brassicae isolates. CR genotype I including 'CR-Cheongrok' showed resistance to GN1, GN2, JS, GS, HS, DJ and KS isolates and susceptibility to YC, PC, HN1, HN2 and SS isolates. And CR genotype II such as 'Hangkunjongbyungdaebaekchae' was resistant to GN1, GN2, JS, GS, HS, YC, PC and HN1 and susceptible to DJ, KS, SS and HN2. CR genotype III including 'Chunhajangkun' and 'Akimeki' represented resistance to 10 isolates except for SS and HN2 isolates. Based on these results, we selected 'CR-Cheongrok', 'Hangkunjongbyungdaebaekchae', and 'Chunhajangkun' as a representative cultivar of three CR genotypes and 'Norangkimjang' as a susceptible cultivar. Furthermore, we investigated the resistance of 15 lines of Chinese cabbage, which were provided by seed companies, to 11 isolates except for HN1 of P. brassicae. The results showed that three lines were susceptible to all the tested isolates, whereas five, four, and three lines represented the similar responses corresponding to the CR genotypes I, II, and III, respectively; there is no line of Chinese cabbage showing different resistance patterns compared to three CR genotypes. In particular, line 'SS001' showing resistance responses of CR genotype II was a parent of 'Saerona' that have been commercialized as a CR $F_1$ cultivar of Chinese cabbage. Together, we divided 12 isolates of P. brassicae into 4 races, designated by wild type, mutant type 1, mutant type 2, and mutant type 3. Wild type including GN1, GN2, JS, GS, and HS isolates of P. brassicae was not able to infect all the cultivars of three CR genotypes, whereas, mutant type 3 such as SS and HN2 isolates developed severe clubroot disease on all the CR genotype cultivars. To mutant type 1 including DJ and KS isolates, CR genotypes I, II and III were resistant, susceptible and resistant, respectively. In contrast, to mutant type 2 including YC, PS, and HN1 isolates, CR genotypes I, II and III showed susceptibility, resistance and resistance, respectively. Taken together, our results provide the extended knowledge of classification of P. brassicae races, which is useful information for the breeding of resistant crops, with a suggestion that 'Norangkimjang', 'CR-Cheongrok', 'Saerona' and 'Chunhajangkun' cultivars of Chinese cabbage could be used as new race differentials of P. brassicae for clubroot disease assay.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.4
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• pp.1797-1802
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• 2014

Background: The prostaglandin-endoperoxide synthase 2 (PTGS2) and phospholipase A2 group IIA (PLA2G2A) genes encode enzymes that are involved in arachidonic acid and prostaglandin biosynthesis. Dysregulation of both genes is associated with inflammation and carcinogenesis, including esophageal squamous cell carcinoma (ESCC). We therefore hypothesized that there is an association between single nucleotide polymorphisms (SNPs) in these genes and susceptibility to ESCC. Methods: We performed a gene-wide tag SNP-based association study to examine the association of SNPs in PTGS2 and PLA2G2A with ESCC in 269 patients and 269 healthy controls from Taihangshan Mountain, Henan and Hebei Provinces, the rural area of China which has the highest incidence of esophageal cancer in the world. Thirteen tag SNPs in PLA2G2A and 4 functional SNPs in PTGS2 were selected and genotyped using a high-throughput Mass Array genotyping platform. Results: We found a modest increased risk of ESCC in subjects with the PTGS2 rs12042763 AA genotype (OR=1.23; 95% CI, 1.00-3.04) compared with genotype GG. For PLA2G2A, a decreased risk of ESCC was observed in subjects with the rs11677 CT (OR=0.51, 95%CI, 0.29-0.85) or TT genotype (OR=0.51, 95%CI, 0.17-0.96) or the T carriers (CT+TT) (OR=0.52, 95%CI, 0.31-0.85) when compared with the CC genotype. Also for PLA2G2A, rs2236771 C allele carriers were more frequent in the control group (P=0.02). Subjects with the GC (OR=0.55, 95%CI, 0.33-0.93) or CC genotype (OR=0.38, 95% CI, 0.16-0.94) or the C carriers (GC+CC) (OR=0.52, 95%CI, 0.32-0.85) showed a negative association with ESCC susceptibility. Conclusions: Our results suggest that PTGS2 and PLA2G2A gene polymorphisms may modify the risk of ESCC development.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.59 no.3
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• pp.319-324
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• 2014

Soybean (Glycine max (L.) Merr.) is an important crop for protein, oil, carbohydrates, isoflavones, and many other nutrients to humans and animals. But, antinutritional factors in the raw mature soybean are exist. Raffinose and stachyose are main antinutritional factors in soybean seed. Both raffinose and stachyose are carbohydrates, belonging to the raffinose family of oligosaccharides (RFOs). RFOs are not readily digested in humans and cause flatulence or diarrhea. The objective of this research is to obtain the information on raffinose and stachyose content according to genotype and environment. A total of twenty two soybean genotypes (11 cultivars, 3 germplasms and 8 breeding lines) were selected. Each genotype was grown in the field for two years with two replications and harvested in bulk at natural maturity for two years. Content of raffinose and stachyose was detected by HPLC. The raffinose content (g/kg) of 22 genotypes was $2.68{\pm}0.21-5.87{\pm}2.43$ in year 1 and was $3.24{\pm}0.37-9.05{\pm}0.16$ in year 2. The stachyose content (g/kg) was $4.23{\pm}0.98-27.68{\pm}9.90$ at year 1 and was $5.11{\pm}1.09-25.32{\pm}0.35$ in year 2. Genotype and environment have highly significant effects on raffinose and stachyose content. Three genotypes (Da-7, 116-13, and RS-78) have low stachyose content at 5% significant level in two years. A positive correlation ($R^2=0.1985^*$) between raffinose and stachyose was observed in year 2. These informations are valuable in soybean genetics and breeding program related with raffinose and stachyose content.

• Journal of Animal Science and Technology
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• v.53 no.6
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• pp.511-516
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• 2011

Fas gene known to associate with intramuscular fat content in Korean cattle was selected for DNA marker development. Fas (APO-1, CD95), a member of the tumor necrosis factor (TNF) receptor superfamily, is a cell membrane protein that mediates apoptosis (programmed cell death). We discovered single nucleotide polymorphisms (SNPs) within Fas gene in order to develop novel DNA markers at genomic level. Of this gene to search for SNP, sequences of whole exon and 1kb range of both front and back of the gene using 24 cattle were determined by direct-sequencing methods. As a result, 16 SNPs in exon, 37 SNPs in intron and 2 SNPs in promoter region, a total of 55 SNPs were discovered. In these SNPs, thirty-one common polymorphic sites were selected considering their allele frequencies, haplotype-tagging status and Linkage Disequilibrium (LD) for genotyping in larger-scale subjects. Selected SNPs were confirmed genotype through SNaPshot method (n=274) and were examined for possible genetic association of Fas polymorphisms with carcass weight (CWT), eye muscle area (EMA), and backfat thickness (BF). So, the SNP have been identified significant g.-12T>G, g.1112T>G and g.32548T>C. These results suggest that polymorphism of Fas gene was associated with meat quality traits in Hanwoo.