• KOREAN JOURNAL OF CROP SCIENCE
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• v.68 no.3
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• pp.134-146
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• 2023

Phytophthora root rot (PRR) is a major soybean disease caused by an oomycete, Phytophthora sojae. PRR can be severe in poorly drained fields or wet soils. The disease management primarily relies on resistance genes called Rps (resistance to P. sojae). This study aimed to identify resistance loci associated with resistance to P. sojae isolate 40468 in Daepung × CheonAl recombinant inbred line (RIL) population. CheonAl is resistant to the isolate, while Daepung is generally susceptible. We genotyped the parents and RIL population via high-throughput single nucleotide polymorphism genotyping and constructed a set of genetic maps. The presence or absence of resistance to P. sojae was evaluated via hypocotyl inoculation technique, and phenotypic distribution fit to a ratio of 1:1 (R:S) (χ² = 0.57, p = 0.75), indicating single gene mediated inheritance. Single-marker association and the linkage analysis identified a highly significant genomic region of 55.9~56.4 megabase pairs on chromosome 18 that explained ~98% of phenotypic variance. Many previous studies have reported several Rps genes in this region, and also it contains nine genes that are annotated to code leucine-rich repeat or serine/threonine kinase within the approximate 500 kilobase pairs interval based on the reference genome database. CheonAl is the first domestic soybean genotype characterized for resistance against P. sojae isolate 40468. Therefore, CheonAl could be a valuable genetic source for breeding resistance to P. sojae.

• Clinical and Experimental Pediatrics
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• v.51 no.1
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• pp.73-77
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• 2008

Purpose : p16 gene, mapped to the 9p21 chromosomal region, has emerged as a candidate tumor suppressor gene in human neoplasm. It is an inhibitor of cyclin-dependent kinase and inhibits Rb phosphorylation. In a variety of tumors including childhood acute lymphoblastic leukemia (ALL), deletion and/or mutation of the p16 gene has been found. Despite their high frequency, the prognostic importance of p16 alterations is still controversial in ALL and has been reported to be either unfavorable or similar to that of other patients. We studied the correlation between loss of p16 protein confirmed by immunohistochemical staining and clinical outcomes of patients diagnosed as ALL. Methods : We performed an immunohistochemical staining for p16 protein in 74 cases of bone marrow biopsy slide initially diagnosed as ALL between January 1998 and December 2006. We reviewed the clinical manifestations, laboratory findings, treatment outcomes retrospectively. Results : Of 74 slides, 12 were negative for p16 protein. Seven were males and 5 were females with a median age at diagnosis was 5.8 (1.3-18.8) years. Initial WBC were 17,225 $(500-403,300)/{\mu}L$. By immunologic surface marker analysis, 7 patients were early pre-B CALLA (+) and 5 patients were T-cell ALL. Two patients of intermediate risk group had relapsed and died. Three patients had family history of breast cancer. Four patients died and overall survival rates were $53.5{\pm}18.7%$. Conclusion : Loss of p16 protein is supposed to be an independent risk factor of childhood ALL associated with poor outcomes. In clinical setting, the clinician must take into account p16 status, not only at the genomic but also at the protein level. Further clinical experience on thoroughly investigated cases will help a better understanding between p16 status and clinical outcomes.

• Journal of Animal Science and Technology
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• v.49 no.5
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• pp.559-568
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• 2007

Recently, copy number variations (CNV) of genes or genomic segments have been intensively studied and various analysis methods have been developed. In this study, quantitative oligonucleotide ligation assay (qOLA) was applied to investigate CNV of KIT gene in the Landrace breed. A combined assay using qOLA and pyrosequencing, 6 genotype classes, I1/I1 or I3/i (IBe), I1/I2 or I3/IP, I1/I3, I1/IP or I2/i (IBe), I2/I2and I2/IP, were identified from 44 Landrace pigs. Genotype assignment using grouping features of measurements on a scatter plot showed 100% agreement with those using a statistical assignment by PROC FASTCLUS procedure implemented in the SAS package. Two versions (3100 and 3130) of ABI sequencers gave the same genotyping results, indicating there was no influence on qOLA by different versions of instrument, however, the means of standard deviation and coefficient of variation from the qOLA on a ABI 3130 (2.33 and 4.10) was lower than those from the qOLA on a ABI 3100 (2.67 and 4.81). Effect of proteinase K treatment on the PCR product followed by qOLA was very clear because noise peaks were disappeared and the observed ration fit better to the reference ratio corresponding to each genotype.

• Korean Journal of Agricultural Science
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• v.36 no.2
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• pp.167-177
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• 2009

This study was conducted to characterize the DGAT1 gene in Korean Holstein dairy cattle population and examine the relationship of DGAT1 polymorphisms with milk yield and milk fat yield for the genetic improvement of Korean Holstein dairy cattle. Results indicated that the 411 bp PCR products were successfully amplified by DGAT1 specific primers. Sequence analysis indicated that the DGTA1 Q allele had AUG (Lysine, K) nucleotide sequences in 216-218 bp and q allele had GCG (Alanine, A) sequences in the same position. Nucleotide sequence homology between the DGAT1 sequences generated in this study showed 100% homology with bovine DGAT1 sequences in the NCBI database. The genotype frequencies of DGAT1 QQ, Qq, and qq were 16.43, 36.43, and 47.14%, respectively, in Korean Holstein dairy cattle population. The observed Q and q allele frequencies were 0.35 and 0.65, respectively. Statistically significant (P<0.05) results were identified for milk yield and milk fat yield for the DGAT1 genotypes. The Qq genotype Holsteins have significantly higher milk yield and milk fat yield than those of the QQ and qq genotype Holsteins(P<0.05).

• Tuberculosis and Respiratory Diseases
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• v.63 no.3
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• pp.235-241
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• 2007

Background: Airway mucus hypersecretion plays an important role in the pathogenesis of asthma, and is associated with the induction of MUC5AC expression in airway secretion. The MUC5AC gene is highly polymorphic; however, there are few studies about the association between the polymorphisms of the MUC5AC gene and asthma susceptibility or asthma phenotypes. We have investigated the association of MUC5AC promoter polymorphisms with the risk of asthma and asthma phenotypes. Methods: We determined the genotypes of the MUC5AC promoter (-1274G>A) in 78 asthma patients and in 78 age, sex-matched control individuals in the Korean population. Genomic DNAs from blood were analyzed by PCR and RFLP (restriction fragment length polymorphism) determination. We examined $FEV_1$, total eosinophil count, serum IgE level, $PC_{20}$ and the presence of atopy (by a skin test) in asthma patients. Results: The mean age of the patients was $47.7{\pm}16.1$ years and 38.5% were men, and the mean $FEV_1$ was $84.4{\pm}22.3%$ of predicted in the asthma patients. The -1274G>A polymorphism of the MUC5AC promoter in asthma patients was not significantly different as compared with normal individuals (GG 57.7%, AG 34.6% and AA 7.7% in asthma patients vs. GG 56.4%, AG 38.5% and AA 5.1% in control subject, p = 0.752, Cod). Several clinical parameters in asthma patients such as $FEV_1$, total eosinophil count, serum IgE level, $PC_{20}$ and the presence of atopy, were not associated with the -1274G>A polymorphism of the MUC5AC promoter. Conclusion: The -1274G>A single nucleotide polymorphism (SNP) frequency of the MUC5AC promoter was not associated with asthma in a Korean population.

• 한국균학회소식:학술대회논문집
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• 2014.05a
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• pp.27-28
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• 2014

Beauveria bassiana (Cordycipitaceae, Hypocreales, Ascomycota) is an anamorphic fungus having a potential to be used as a biological control agent because it parasitizes a wide range of arthropod hosts including termites, aphids, beetles and many other insects. A number of bioactive secondary metabolites (SMs) have been isolated from B. bassiana and functionally verified. Among them, beauvericin and bassianolide are cyclic depsipeptides with antibiotic and insecticidal effects belonging to the enniatin family. Non-ribosomal peptide synthetases (NRPSs) play a crucial role in the synthesis of these secondary metabolites. NRPSs are modularly organized multienzyme complexes in which each module is responsible for the elongation of proteinogenic and non-protein amino acids, as well as carboxyl and hydroxyacids. A minimum of three domains are necessary for one NRPS elongation module: an adenylation (A) domain for substrate recognition and activation; a tholation (T) domain that tethers the growing peptide chain and the incoming aminoacyl unit; and a condensation (C) domain to catalyze peptide bond formation. Some of the optional domains include epimerization (E), heterocyclization (Cy) and oxidation (Ox) domains, which may modify the enzyme-bound precursors or intermediates. In the present study, we analyzed genomes of B. bassiana and its allied species in Hypocreales to verify the distribution of NRPS-encoding genes involving biosynthesis of beauvericin and bassianolide, and to unveil the evolutionary processes of the gene clusters. Initially, we retrieved completely or partially assembled genomic sequences of fungal species belonging to Hypocreales from public databases. SM biosynthesizing genes were predicted from the selected genomes using antiSMASH program. Adenylation (A) domains were extracted from the predicted NRPS, NRPS-like and NRPS-PKS hybrid genes, and used them to construct a phylogenetic tree. Based on the preliminary results of SM biosynthetic gene prediction in B. bassiana, we analyzed the conserved gene orders of beauvericin and bassianolide biosynthetic gene clusters among the hypocrealean fungi. Reciprocal best blast hit (RBH) approach was performed to identify the regions orthologous to the biosynthetic gene cluster in the selected fungal genomes. A clear recombination pattern was recognized in the inferred A-domain tree in which A-domains in the 1st and 2nd modules of beauvericin and bassianolide synthetases were grouped in CYCLO and EAS clades, respectively, suggesting that two modules of each synthetase have evolved independently. In addition, inferred topologies were congruent with the species phylogeny of Cordycipitaceae, indicating that the gene fusion event have occurred before the species divergence. Beauvericin and bassianolide synthetases turned out to possess identical domain organization as C-A-T-C-A-NM-T-T-C. We also predicted precursors of beauvericin and bassianolide synthetases based on the extracted signature residues in A-domain core motifs. The result showed that the A-domains in the 1st module of both synthetases select D-2-hydroxyisovalerate (D-Hiv), while A-domains in the 2nd modules specifically activate L-phenylalanine (Phe) in beauvericin synthetase and leucine (Leu) in bassianolide synthetase. antiSMASH ver. 2.0 predicted 15 genes in the beauvericin biosynthetic gene cluster of the B. bassiana genome dispersed across a total length of approximately 50kb. The beauvericin biosynthetic gene cluster contains beauvericin synthetase as well as kivr gene encoding NADPH-dependent ketoisovalerate reductase which is necessary to convert 2-ketoisovalarate to D-Hiv and a gene encoding a putative Gal4-like transcriptional regulator. Our syntenic comparison showed that species in Cordycipitaceae have almost conserved beauvericin biosynthetic gene cluster although the gene order and direction were sometimes variable. It is intriguing that there is no region orthologous to beauvericin synthetase gene in Cordyceps militaris genome. It is likely that beauvericin synthetase was present in common ancestor of Cordycipitaceae but selective gene loss has occurred in several species including C. militaris. Putative bassianolide biosynthetic gene cluster consisted of 16 genes including bassianolide synthetase, cytochrome P450 monooxygenase, and putative Gal4-like transcriptional regulator genes. Our synteny analysis found that only B. bassiana possessed a bassianolide synthetase gene among the studied fungi. This result is consistent with the groupings in A-domain tree in which bassianolide synthetase gene found in B. bassiana was not grouped with NRPS genes predicted in other species. We hypothesized that bassianolide biosynthesizing cluster genes in B. bassiana are possibly acquired by horizontal gene transfer (HGT) from distantly related fungi. The present study showed that B. bassiana is the only species capable of producing both beauvericin and bassianolide. This property led to B. bassiana infect multiple hosts and to be a potential biological control agent against agricultural pests.

• Journal of The Korean Society of Inherited Metabolic disease
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• v.16 no.2
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• pp.93-101
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• 2016

Purpose: McArdle disease, glycogen storage disease type V (GSD V), is one of the most common adolescent-onset glycogen storage diseases. It is caused by recessive mutations in PYGM encoding myophosphorylase, which is critical to glycogen metabolism. Since only a few korean patients have been reported, we will observe the clinical and genetic features of three korean patients with McArdle disease. Methods: We retrospectively reviewed the medical records of three patients with genetically confirmed McArdle disease, including the results of forearm ischemic exercise test, electromyogram, nerve conduction velocity, muscle biopsy, and PYGM analysis in peripheral leukocytes. Results: All three cases were males and their age of symptom onset was 12, 5, 14 years old, respectively. A high basal level of serum creatine kinase was noted in all three patients. They experienced the recurrent episodes of rhabdomyolysis, but second wind phenomenon was not definite. In muscle biopsy, subsarcolemmal space vacuoles including periodic acid schiff stained materials were found in two patients, while no evidence of glycogen storage disease was found in the other. A total of five different mutations, $p.Arg50^*$, p.Trp798Arg, $p.Arg50^*$, p.Glu779del, $p.Asp511Thrfs^*28$ and p.Phe710del, were found in three patients. Avoidance of isometric exercise, aerobic exercise and glucose intake before each exercise were recommended for all patients. Conclusion: The three Korean patients with McArdle disease showed the typical manifestations of the condition. The most mutations were private. Therefore, identification of more cases with long-term follow-up will be required to understand the clinical and genetic features of this disease among Korean population.

• Journal of Embryo Transfer
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• v.31 no.3
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• pp.227-233
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• 2016

This study was conducted to analyze the effect of single nucleotide polymorphisms (SNPs) on the equine chromosomes (ECA) 3 for the body conformations of 12 month of age in Jeju crossbred (Jeju horses ${\times}$ Thoroughbred). A total of 199 Jeju crossbred horse samples were obtained from the National Institute of Subtropical Livestock Research Institute for this study. To correctly estimate the body conformations, we measured thirteen elements relevant to the body conformation such as body weight, wither height, body length for all the 199 horses at 12 month of age. Furthermore, all the horses were genotyped using four SNPs including the BIEC2-808466, BIEC2-808543, BIEC2-808967, BIEC2-809370, of which genomic coordinates range approximately from 105.1Mbp to 110 Mbp in the ECA3. For the phenotypic data sets, the average body weight was $193.7{\pm}24.5kg$ and the height was $124.5{\pm}4.0cm$. As for the genotypic data, the miner allele frequencies of the SNPs were shown to be varied from 0.01 to 0.291. Using the phenotypic and genotypic data sets, analysis of covariance was performed to find any association between those SNP genotypes and body conformations, using year of birth, month of birth, sex, and parity as the covariance components. The result showed that alternative genotypes in the BIEC2-808967 and BIEC2-809370 SNPs were significantly associated with the body length (P<0.05) and the wither height (P<0.05) respectively in the Jeju crossbred horses. Therefore, it is estimated that there are significant associations in the body conformation of 12 month of age of Jeju crossbred for those two SNPs used in this study.

• Korean Journal of Poultry Science
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• v.45 no.3
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• pp.229-236
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• 2018

The aim of this study was to evaluate the genetic diversity and relationships of Ogye populations in Korea. A total of 243 genomic DNA samples from 6 Ogye population (Yeonsan Ogye; YSO, Animal Genetic Resources Research Center Ogye; ARO, Chungbuk Ogye; CBO, Chungnam Ogye; CNO, Gyeongbuk Ogye; GBO, Seoul National University Ogye; SUO) and 3 introduced chicken breeds (Rhode Island Red; RIR, White Leghorn; LG, Cornish; CN) were used. Sizes of 25 microsatellite markers were decided using GeneMapper Software(v 5.0) after analyzing ABI 3130XL. A total of 153 alleles were observed and the range was 2 to 10 per each locus. The mean of expected and observed heterozygosity and PIC (Polymorphism Information Content) value was 0.53, 0.50, 0.46 respectively. The lowest genetic distance (0.073) was observed between YSO and SUO, and the highest distance (0.937) between the RIR and CBO. The results of clustering analysis suggested 3 clusters (${\Delta}K=7.96$). Excluding GBO population, 5 Ogye populations (YSO, ARO, CBO, CNO, SUO) were grouped in same cluster with high genetic uniformity (0.990, 0.979, 0.989, 0.994, 0.985 respectively). But GBO population was grouped in cluster 1 with low genetic uniformity (0.340). The results of this study can be use to basic data for the genetic evaluation and management of Ogye populations in Korea.

• Clinical and Experimental Pediatrics
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• v.45 no.7
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• pp.884-890
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• 2002

Purpose : Henoch-Schonlein purpura(HSP) nephritis has been reported to vary from 25 to 50% among HSP patients and is a common cause of chronic glomerulonephritis in children. In our study, we evaluated the distribution and the association of the Insertion/Deletion(I/D) polymorphism of angiotensin converting enzyme(ACE) gene with clinical manifestations, particularly proteinuria in children with HSP nephritis, compared with that in HSP. Methods : ACE gene polymorphism was determined in children with HSP nephritis(n=33) and HSP(n=28) who were diagnosed in Busan Paik hospital from January 1996 to June 2001. The I/D polymorphism of ACE gene was determined by PCR amplication of genomic DNA. Results : The ACE I/D genotype frequency was DD : 25%, ID : 50%, II : 25% in HSP and DD : 24 %, ID : 46%, II : 30% in HSP nephritis, there was no significant difference in the genotype and allele frequencies between two groups. When statistical analysis was done according to the presence of D allele, the amount of 24-hour urinary protein excretion and the incidence of moderate to heavy proteinuria(>$500mg/m^2/day$) at onset and last follow-up were higher in DD/ID genotype than in those in II genotype, but these differences were not statistically significant. Conclusion : We suggest a lack of association between I/D polymorphism of ACE gene and clinical manifestations in children with HSP nephritis. However, further follow-up studies based on a sufficient number of patients and long term follow up periods are necessary to confirm the role of I/D polymorphism of ACE gene in children with HSP nephritis.