• 한국균학회소식:학술대회논문집
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• 2014.10a
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• pp.9-9
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• 2014

Null mutants generated by targeted gene replacement are frequently used to reveal function of the genes in fungi. However, targeted gene deletions may be difficult to obtain or it may not be applicable, such as in the case of redundant or lethal genes. Constitutive expression system could be an alternative to avoid these difficulties and to provide new platform in fungal functional genomics research. Here we developed a novel platform for functional analysis genes in Magnaporthe oryzae by constitutive expression under a strong promoter. Employing a binary vector (pGOF1), carrying $EF1{\beta}$ promoter, we generated a total of 4,432 transformants by Agrobacterium tumefaciens-mediated transformation. We have analyzed a subset of 54 transformants that have the vector inserted in the promoter region of individual genes, at distances ranging from 44 to 1,479 bp. These transformants showed increased transcript levels of the genes that are found immediately adjacent to the vector, compared to those of wild type. Ten transformants showed higher levels of expression relative to the wild type not only in mycelial stage but also during infection-related development. Two transformants that T-DNA was inserted in the promotor regions of putative lethal genes, MoRPT4 and MoDBP5, showed decreased conidiation and pathogenicity, respectively. We also characterized two transformants that T-DNA was inserted in functionally redundant genes encoding alpha-glucosidase and alpha-mannosidase. These transformants also showed decreased mycelial growth and pathogenicity, implying successful application of this platform in functional analysis of the genes. Our data also demonstrated that comparative phenotypic analysis under over-expression and suppression of gene expression could prove a highly efficient system for functional analysis of the genes. Our over-expressed transformants library would be a valuable resource for functional characterization of the redundant or lethal genes in M. oryzae and this system may be applicable in other fungi.

• Animal cells and systems
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• v.16 no.5
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• pp.408-414
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• 2012

To reexamine taxonomic status of endemic Mogera wogura coreana from Korea, we first obtained partial 12S rRNA sequences (893 bp) and complete cytochrome b gene sequences (1140 bp) of this subspecies, and these sequences and partial cytochrome b sequences (402 bp) were compared to the corresponding haplotypes of M. wogura from East Asia, obtained from GenBank. The one of three 12S rRNA haplotypes in M. w. coreana was identical to one 12S rRNA haplotype of M. w. robusta from East Asia: 10 complete and 13 partial cytochrome b haplotypes of M. w. coreana formed a single clade with one complete and four partial cytochrome b haplotypes of M. w. robusta, respectively. We considered that M. w. coreana from Korea is an endemic subspecies with only morphological differences, although it is necessary to reexamine the subspecies status of M. w. coreana. Additionally, in the 12S rRNA and complete cytochrome b sequences, M. wogura from Japan was distinct from the two continental subspecies of M. w. coreana and M. w. robusta with average distances of 1.76 and 5.65%, respectively; insular M. wogura, with within-group distances of 2.09 and 4.38%, respectively, was also genetically more divergent than the mainland M. wogura, with within-group distances of 0.08 and 0.57%, respectively. Thus, we considered that insular M. wogura of Japan dispersed into neighboring East Asian continent, which is opposite to the traditional hypothesis on the origin of Japanese M. wogura.

• Journal of Korean Society of Forest Science
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• v.90 no.1
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• pp.155-160
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• 2001

Changes in genetic diversity after seed-tree practice were simulated in test plantation of tulip tree at Sokdal-ri, Banwol-myon, Hwasung-gun, Kyungki Provence. I-SSR markers were analyzed in a total of 305 tulip trees. A total of 89 amplicon variants were observed by PCR with 9 I-SSR primers. Genetic diversity for 305 trees was relatively high (S. I. =0.4532). Individuals originated from the seed orchards in U.S.A. showed the highest level of genetic diversity (0.4530), those from Anyang showed the medium level (0.4152), and those from Cheonbuk showed the lowest (0.3929). Simulation of seed-tree practice accompanied by 2 consecutive thinnings was performed on the basis of morphological characteristics and planted distances of the individual trees, which left 37 trees as candidates for seed-trees. Decreasing rate of genetic diversity within seed sources was greatest for individuals from Cheonbuk (28.3%), moderate for those from Anyang (16.3%), and smallest for those from U.S.A. (8.0%). In spite of little difference in decreasing rate of individuals for the 3 seed sources (87.5~88.2%), large difference in decreasing rate of genetic diversity within seed sources might be due to difference in number of mother trees for the 3 seed sources. For example, whereas individuals originated from the seed orchard in U.S.A., which showed the smallest decreasing rate of genetic diversity, might be originated from relatively large number of mother trees, those from Anyang and Cheonbuk might be originated from relatively small number of mother trees. Although mean of 17.5% of the genetic diversity within seed sources was decreased through 2 consecutive thinnings, a decrease in genetic diversity for the whole individuals (37 trees) was only 6.1%. This observation suggests that the seed-tree practice on the basis of the criteria established in the present study may not result in great reduction in overall genetic diversity of the progenies.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.54 no.2
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• pp.231-240
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• 2009

A total of 26 Korean elite soybean cultivars including 21 certified cultivars was assessed to evaluate genetic diversity and to analyze relationship among them based on 15 SSR markers. Fifteen SSR markers generated a total of 201 alleles. Average number of alleles per SSR marker was 13.4 with a range from 8 to 19. Genetic diversity of 26 cultivars estimated by PIC value ranged from 0.782 to 0.931 with an average of 0.874. PIC value of Satt197 was the highest with 0.931 and Satt141 was the lowest with 0.782 among 15 SSR markers. Cluster analysis based on genetic distances classified 26 soybean cultivars into 3 clusters. Cluster I, II and III included 2, 7 and 17 cultivars, respectively. Average genetic diversity within clusters was 0.769 with a range from 0.720 to 0.799. Average genetic diversity between clusters was 0.813 with a range from 0.725 to 0.857. Genetic diversity was higher between clusters than within clusters. Genetic relationship among clusters was near between I and II, and I and III and far between II and III cluster. All of 26 Korean elite soybean cultivars could be identified by using any of 5 combinations of 2 SSR markers with higher PIC value, i.e, $Satt197+Sat_088$, Satt197+Satt245, $Sat_088+Sat_-036$, $Sat_088+Satt245$ and Satt185+Satt245.

• Korean Journal of Veterinary Research
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• v.33 no.1
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• pp.43-51
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• 1993

Mitochondrial DNA(mt DNA) of Mammalian is the circular one which the 16.5K base pairs and show the maternal inheritance. Evolutional speed of nucleotide sequence is very fast. So that polymorphic analysis of mt DNA provide the useful informations to investigate the genetic relations of interspecies. Authors trials were focussed to compare with the polymorphic differences of mitochondrial DNA between Jindo and Japanese mongrel dogs. DNA was extracted from bloods of 21 head of Jindo dogs and 20 head of Japanese dogs and isolated using 10 kinds of restriction endonucleases(Apa I, BamH I, Bgl II, EcoR I, EcoR V, Hinc II. Hind III, Pst I, Sty I, Xba I) and then separated by the agarose gel electrophoresis. After sourthern blotting hybridization was completed using the mtDNA of Japanese mongrel dogs as a probe. Autoradiography was used to compare the polymorphism of mtDNA both dogs. The results obtained were as follows; 1. mt DNA of Jindo dog showed polymorphism resulting cleavage with four kinds of restriction endonuclease, Apa I, EcoR V, Hinc II, Sty I. While in the Japanese mongrel dogs observed the polymorphism in the five kinds of restriction endonuclease supplemented with EcoR I. 2. Compared with both dogs the frequency differences of DNA polymorphism were recognized in the specific restriction endonuclease Apa I. Consequently in the restriction endonuclease Apa I both dogs classified with three types as A, B, C however in the Jindo dogs frequency of C type was 71.5 percent but in Japanese mongrel dogs observed 45 percent in the A type. 3. DNA polymorphism obtained from the use of five kinds of restriction endonuclease were classified with seven types. In Jindo dogs frequency was highest in the type 6 as 71.4 percent but in the Japanese mongrel dogs showed 35 percent in the type 5. 4. Genetic distances calculated by NEI method showed 0.0089 in Jindo dogs and was 0.0094 in the Japanese mongrel dogs.

• Geophysics and Geophysical Exploration
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• v.9 no.1
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• pp.93-101
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• 2006

In this study, we propose a joint inversion method, using genetic algorithms, to determine the shear-wave velocity structure of deep sedimentary layers from receiver functions and surface-wave phase velocity. Numerical experiments with synthetic data indicate that the proposed method can avoid the trade-off between shear-wave velocity and thickness that arises when inverting the receiver function only, and the uncertainty in deep structure from surface-wave phase velocity inversion alone. We apply the method to receiver functions obtained from earthquake records with epicentral distances of about 100 km, and Rayleigh-wave phase velocities obtained from a microtremor array survey in the Kanto Plain, Japan. The estimated subsurface structure is in good agreement with the previous results of seismic refraction surveys and deep borehole data.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.8
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• pp.1063-1072
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• 2012

Effective population size ($N_e$) is an important measure to understand population structure and genetic variability in animal species. The objective of this study was to estimate $N_e$ in Sapsaree dogs using the information of rate of inbreeding and genomic data that were obtained from pedigree and the Illumina CanineSNP20 (20K) and CanineHD (170K) beadchips, respectively. Three SNP panels, i.e. Sap134 (20K), Sap60 (170K), and Sap183 (the combined panel from the 20K and 170K), were used to genotype 134, 60, and 183 animal samples, respectively. The $N_e$ estimates based on inbreeding rate ranged from 16 to 51 about five to 13 generations ago. With the use of SNP genotypes, two methods were applied for $N_e$ estimation, i.e. pair-wise $r^2$ values using a simple expectation of distance and $r^2$ values under a non-linear regression with respective distances assuming a finite population size. The average pair-wise $N_e$ estimates across generations using the pairs of SNPs that were located within 5 Mb in the Sap134, Sap60, and Sap183 panels, were 1,486, 1,025 and 1,293, respectively. Under the non-linear regression method, the average $N_e$ estimates were 1,601, 528, and 1,129 for the respective panels. Also, the point estimates of past $N_e$ at 5, 20, and 50 generations ago ranged between 64 to 75, 245 to 286, and 573 to 646, respectively, indicating a significant $N_e$ reduction in the last several generations. These results suggest a strong necessity for minimizing inbreeding through the application of genomic selection or other breeding strategies to increase $N_e$, so as to maintain genetic variation and to avoid future bottlenecks in the Sapsaree population.

• Korean Journal of Microbiology
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• v.46 no.3
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• pp.296-302
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• 2010

Microcystis (Cyanobacteria, Chroococcales) is one of the green tide-causing organisms in freshwaters, and some species produce microcystin that is hepatotoxin. In the aspects of freshwater quality controls and health concerns, therefore it is necessary to manage the harmful organisms. In the present study, RNA polymerase beta subunit (rpoB) gene sequences of Microcystis were determined and characterized in order to use a potential marker for the molecular detections of the species. Microcystis rpoB showed high divergences of DNA similarity and genetic distances when compared with those of 16S rRNA, and the molecular differences were statistically significant (Student t-test, p<0.05). Parsimony analyses showed the rpoB gene evolves more than 2-fold faster than 16S rRNA. In addition, phylogeny of the rpoB gene separated each M. aeruginosa strain more clearly compared with a 16S rRNA tree. This study found that the order Chroococcales, including Microcystis, has approximately two rRNA operons and single copy of the rpoB gene in their chromosomes. These results suggest that the rpoB gene is a useful marker for the molecular phylogenetics and the detection of Microcystis.

• Mycobiology
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• v.46 no.4
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• pp.421-428
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• 2018

The white button mushroom (Agaricus bisporus) is one of the most widely cultivated species of edible mushroom. Despite its economic importance, relatively little is known about the genetic diversity of this species. Illumina paired-end sequencing produced 43,871,558 clean reads and 69,174 contigs were generated from five offspring. These contigs were subsequently assembled into 57,594 unigenes. The unigenes were annotated with reference genome in which 6,559 unigenes were associated with clusters, indicating orthologous genes. Gene ontology classification assigned many unigenes. Based on genome data of the five offspring, 44 polymorphic simple sequence repeat (SSR) markers were developed. The major allele frequency ranged from 0.42 to 0.92. The number of genotypes and the number of alleles ranged from 1 to 4, and from 2 to 4, respectively. The observed heterozygosity and the expected heterozygosity ranged from 0.00 to 1.00, and from 0.15 to 0.64, respectively. The polymorphic information content value ranged from 0.14 to 0.57. The genetic distances and UPGMA clustering discriminated offspring strains. The SSR markers developed in this study can be applied in polymorphism analyses of button mushroom and for cultivar discrimination.

• Journal of the Earthquake Engineering Society of Korea
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• v.7 no.5
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• pp.93-102
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• 2003

An optimal design method for hybrid structural control system of building structures subject to earthquake excitation is presented in this paper. Designing a hybrid structural control system may be defined as a process that optimizes the capacities and configuration of passive and active control systems as well as structural members. The optimal design proceeds by formulating the optimization problem via a multi-stage goal programming technique and, then, by finding reasonable solution to the optimization problem by means of a goal-updating genetic algorithm. In the multi-stage goal programming, design targets(or goals) are at first selected too correspond too several stages and the objective function is th n defined as the sum of the normalized distances between these design goals and each of the physical values, that is, the inter-story drifts and the capacities of the control system. Finally, the goal-updating genetic algorithm searches for optimal solutions satisfying each stage of design goals and, if a solution exists, the levels of design goals are consecutively updated to approach the global optimal solution closest too the higher level of desired goals. The process of the integrated optimization design is illustrated by a numerical simulation of a nine-story building structure subject to earthquake excitation. The effectiveness of the proposed method is demonstrated by comparing the optimally designed results with those of a hybrid structural control system where structural members, passive and active control systems are uniformly distributed.