• Molecules and Cells
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• v.27 no.2
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• pp.175-181
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• 2009

The myosin light chain kinase (MYLK) gene encodes both smooth muscle and nonmuscle cell isoforms. Recently, polymorphisms in MYLK have been reported to be associated with several diseases. To examine the genetic effects of polymorphisms on the risk of asthma and related phenotypes, we scrutinized MYLK by re-sequencing/genotyping and statistical analysis in Korean population (n = 1,015). Seventeen common polymorphisms located in or near exons, having pairwise $r^2$ values less than 0.25, were genotyped. Our statistical analysis did not replicate the associations with the risk of asthma and log-transformed total IgE levels observed among African descendant populations. However, two SNPs in intron 16 (+89872C> G and +92263T> C), which were in tight LD (|D'| = 0.99), revealed significant association with log-transformed blood eosinophil level even after correction multiple testing ($P=0.002/P^{corr}=0.01$ and $P=0.002/P^{corr}=0.01$, respectively). The log-transformed blood eosinophil levels were higher in individuals bearing the minor alleles for +89872C> G and +92263T> C than in those bearing other allele. In additional subgroup analysis, the genetic effects of both SNPs were much more apparent among asthmatic patients and atopic asthma patients. Among atopic asthma patients, the log-transformed blood eosinophil levels were proportionally increased by gene-dose dependent manner of in both +89872C> G and +92263T> C(P = 0.0002 and P = 0.00007, respectively). These findings suggest that MYLK polymorphisms might be among the genetic factors underlying differential increases of blood eosinophil levels among asthmatic patients. Further biological and/or functional studies are needed to confirm our results.

• Journal of Mushroom
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• v.19 no.1
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• pp.76-80
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• 2021

To develop a method for the differentiation of Pleurotus ostratus cultivars, the multiplex-simple sequence repeat (SSR) primer set based on the SSRs obtained from whole genomic DNA sequence analysis was designed with two polymerase chain reaction (PCR) primer sets. These SSR primer sets were employed to distinguish 10 cultivars and strains. Twenty polymorphic markers were selected based on the genotyping results. PCR with each primer produced 1-4 distinct bands ranging in size from 150 to 350 bp, which was within the expected range. However, since a sole SSR marker was unable to detect polymorphisms in every cultivar, multiplex PCRs with composite PCR primer sets were employed. The multiplex primer, "166+115," completely discriminated 12 cultivars and strains with 40 loci, which were 12 more than the simple arithmetic addition of each locus of the primers 115 and 166. These results might be useful to provide an efficient method for the differentiation of P. ostreatus cultivars with separate PCRs for the quality control of spawn and protection of breeders' rights.

• Korean Journal of Clinical Laboratory Science
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• v.53 no.1
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• pp.41-48
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• 2021

Essential thrombocythemia (ET) is a clonal bone marrow stem cell disorder, primarily involving the megakaryocytic lineage. The WHO 2016 guidelines include the molecular detection of JAK2, MPL, and CALR mutations as a major diagnostic criterion for ET. This study aimed to determine the frequency of JAK2 V617F, MPL W515L, and CALR mutations in Iraqi Kurdish patients afflicted with ET, and to analyze their clinical and hematological features. A total of 73 Iraqi Kurdish patients with ET were enrolled as subjects, and analysis was achieved utilizing real-time PCR. The frequency of JAK2 V617F, CALR, and MPL W515L mutations was determined to be 50.7%, 22%, and 16.4%, respectively. No statistically significant difference was obtained when considering the age and gender among different genotypes. The JAK2 V617F mutated patients had significantly higher white blood cell counts and hemoglobin levels than the CALR-positive patients (P-value=0.000, 0.007, respectively), MPL W515L-positive patients (P-value=0.000, 0.000, respectively), and triple negative patients (P-value=0.000, 0.000, respectively). Also, the JAK2 V617F mutated patients showed higher platelet count as compared to the MPL W515L-positive patients (P-value=0.02) and triple negative patients (P-value=0.04). Furthermore, significantly lower white blood cell count and hemoglobin levels were associated with CALR positivity (P-value=0.000, 0.01, respectively), MPL W515L-positivity (P-value=0.001, 0.000, respectively), and triple negativity (P-value=0.000, 0.000, respectively), as compared to patients with combined mutations. In conclusion, apart from a relatively high frequency of MPL W515L mutation, our data is comparable to earlier reports, and highlights the importance of genotyping the JAK2 V617F, MPL W515L, and CALR mutations for accurate diagnosis of patients with ET.

• Animal Bioscience
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• v.35 no.12
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• pp.1827-1838
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• 2022

Objective: The semen quality of stallions including sperm motility is an important target of selection as it has a high level of individual variability. However, effects of the molecular architecture of the genome on the mechanisms of sperm formation and their preservation after thawing have been poorly investigated. Here, we conducted a genome-wide association study (GWAS) for the sperm motility of cryopreserved semen in stallions of various breeds. Methods: Semen samples were collected from the stallions of 23 horse breeds. The following semen characteristics were examined: progressive motility (PM), progressive motility after freezing (FPM), and the difference between PM and FPM. The respective DNA samples from these stallions were genotyped using Axiom Equine Genotyping Array. Results: We performed a GWAS search for single nucleotide polymorphism (SNP) markers and potential genes related to motility properties of frozen-thawed semen in the stallions of various breeds. As a result of the GWAS analysis, two SNP markers, rs1141327473 and rs1149048772, were identified that were associated with preservation of the frozen-thawed stallion sperm motility, the relevant putative candidate genes being NME/NM23 family member 8 (NME8), olfactory receptor family 2 subfamily AP member 1 (OR2AP1), and olfactory receptor family 6 subfamily C member 4 (OR6C4). Potential implications of effects of these genes on sperm motility are herein discussed. Conclusion: The GWAS results enabled us to localize novel SNPs and candidate genes for sperm motility in stallions. Implications of the study for horse breeding and genetics are a better understanding of genomic regions and candidate genes underlying stallion sperm quality, and improvement in horse reproduction and breeding techniques. The identified markers and genes for sperm cryotolerance and the respective genomic regions are promising candidates for further studying the biological processes in the formation and function of the stallion reproductive system.

• Journal of Preventive Medicine and Public Health
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• v.55 no.3
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• pp.280-288
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• 2022

Objectives: One of the most widely used pesticides today is chlorpyrifos (CPF). Cytochrome P450 (CYP)2B6, the most prominent catalyst in CPF bioactivation, is highly polymorphic. The objective of our study was to evaluate the role of CYP2B6^*6, which contains both 516G>T and 785A>G polymorphisms, in CPF toxicity, as represented by the concentration of 3,5,6-trichloro-2-pyridinol (TCPy), among vegetable farmers in Central Java, Indonesia, where CPF has been commonly used. Methods: A cross-sectional study was conducted among 132 vegetable farmers. Individual socio-demographic and occupational characteristics, as determinants of TCPy levels, were obtained using a structured interviewer-administered questionnaire and subsequently used to estimate the cumulative exposure level (CEL). TCPy levels were detected with liquid chromatography-mass spectrometry. CYP2B6^*6 gene polymorphisms were analyzed using a TaqMan^® SNP Genotyping Assay and Sanger sequencing. Linear regression analysis was performed to analyze the association between TCPy, as a biomarker of CPF exposure, and its determinants. Results: The prevalence of CYP2B6^*6 polymorphisms was 31% for ^*1/^*1, 51% for ^*1/^*6, and 18% for ^*6/^*6. TCPy concentrations were higher among participants with CYP2B6^*1/^*1 than among those with ^*1/^*6 or ^*6/^*6 genotypes. CYP2B6^*6 gene polymorphisms, smoking, CEL, body mass index, and spraying time were retained in the final linear regression model as determinants of TCPy. Conclusions: The results suggest that CYP2B6^*6 gene polymorphisms may play an important role in influencing susceptibility to CPF exposure. CYP2B6^*6 gene polymorphisms together with CEL, smoking habits, body mass index, and spraying time were the determinants of urinary TCPy concentrations, as a biomarker of CPF toxicity.

• Journal of Life Science
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• v.30 no.3
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• pp.230-238
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• 2020

Carcass traits are the most economically important traits in Hanwoo (Korean cattle). Recently, the development of the field of genomics has made it possible to identify DNA markers for the genetic evaluation of carcass and meat quality traits in beef cattle. The objective of this study was to assess the genetic effects of single nucleotide polymorphism (SNP) markers related to carcass traits by field evaluations in a commercial Hanwoo population. We evaluated 15 SNP markers (TG g.371T>C, APM1 g.1454G>A, FABP4 g.2834C>G, FABP4 g.3533T>A, FABP4 g.3691G>A, SCD g.10153A>G, SCD g.10329T >C, CPE g.601T>C, EDG1 g.166A>G, NPY g.4271T>C, GPD1 g.2766C>T, PDE1B g.17122A>G, PDE1B g.17507A>C, TNNT1 g.6650C>T, and RORC g.20152A>G) related to carcass traits in Hanwoo. Genotyping of these SNP markers was performed using PCR-RFLP analysis in Hanwoo steers (n = 1,536) to evaluate their association with carcass traits. Seven SNPs, APM1 g.1454G>, FABP4 g.3691G>A, SCD g.10153A>G, CPE g.601T>C, PDE1B g.17122A>G, TNNT1 g.6650C>T, and RORC g.20152A>G, were significantly associated with carcass traits such as marbling score (MS), backfat thickness (BF), musculus longissimus dorsi area (LDA), carcass weight (CW), meat grade (MG), meat color (MC), and maturity score (MA). The results suggest that these SNPs may be used as DNA markers for the selection of Hanwoo with higher meat quality.

• Journal of Korean Society of Forest Science
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• v.112 no.2
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• pp.157-172
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• 2023

Controlled pollination (CP) is an important method in tree breeding programs because CP quickly generates desirable genotypes and rapidly maximizes genetic gains. However, few studies have evaluated the efficiency and success rate of CP in the breeding program of Pinus densiflora. To evaluate CP and the management of control pollinated progenies, we used 159 individuals in CB2 × KW40 or KW40 × CB2 populations that were established in 2015. After genotyping microsatellite loci, we estimated whether the number of primers was sufficient or not. Then, we performed pedigree analysis. The result showed that the number of primers was sufficient. By pedigree analysis, we found out that 60 of 159 individuals had been generated by the mating between CB2 and KW40. In the maternity analysis, there was evidence to indicate the possibility of management problems. Therefore, we excluded 54 individuals and repeated the pedigree analysis. In the second analysis, 47 of 105 individuals were generated by the mating between CB2 and KW40. To increase the efficiency of CP in tree breeding programs, several precautions are required. It is necessary to identify the exact clone names of the mother and father trees. In addition, CP processes should be performed properly, including deciding on the schedule of CP and the isolation of female strobili or flowers. Finally, the monitoring of hybrid progenies management after mating is important. Molecular markers should be used to identify the clone names of the mother and father trees and for monitoring post hoc management. This study provides a reference for tree breeding programs for the future control pollination of pine species.