• Plant Breeding and Biotechnology
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• v.5 no.4
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• pp.269-281
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• 2017

With the continual development of genetically modified (GM) crops, it has become necessary to develop detailed and effective molecular characterization methods to select candidate events from a large pool of transformation events. Relative to traditional molecular analysis methods such as the polymerase chain reaction (PCR) and Southern blot hybridization, next generation sequencing (NGS) technology for whole-genome sequencing of complex crop genomes had proven comparatively useful for in-depth molecular characterization. In this study, four transformation events, including one in Bacillus thuringiensis (Bt)-resistant rice, one in resveratrol-producing rice, and two in beta-carotene-enhanced soybeans, were selected for molecular characterization. To merge NGS analysis and Southern blot-hybridization results, we confirmed the transgene insertion sites, insertion construction, and insertion numbers of these four transformation events. In addition, the read-coverage depth assessed by NGS analysis for inserted genes might provide consistent results in terms of inserted T-DNA numbers in case of complex insertion structures and highly duplicated donor genomes; however, PCR-based methods can produce incorrect conclusions. Our combined method provides an effective and complete analytical approach for whole-genome visual inspection of transformation events that require biosafety assessment.

• Proceedings of the National Institute of Ecology of the Republic of Korea
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• v.4 no.1
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• pp.16-27
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• 2023

Primary succession on bare rocks is a challenge for invaders, including one of which was plants. The invasion of bare rock by exotic species raises the question of whether their presence hinders or facilitates succession. This study aimed to determine the role of exotic species in primary succession in six overburden (OB) coal mines using a chronosequence approach. Vegetation analysis was undertaken using line transects. Measurements were carried out on the absolute and relative coverage of each species. Native and exotic species were identified and grouped using information from local communities, identification books, and websites. The relationship between time and number of species, time, and relative dominance of exotic and native species was analyzed using Pearson's correlation. Species number and dominance data were analyzed descriptively. The number of native species from the six OB heaps was higher (57) than that from exotic heaps (50). Neither the number of species nor the coverage showed a significant relationship with time. Exotic species predominated throughout the age of the embankment but tended to decrease over time. Temporary dominance by exotic species plays a role in assisting primary succession in the OB. This process might be prolonged without the temporary dominance of exotic species during early primary succession.

• Molecules and Cells
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• v.26 no.3
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• pp.250-257
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• 2008

Microsatellites or simple sequence repeats (SSR) are widely distributed in eukaryotic genomes and are informative genetic markers. Despite many advantages of SSR markers such as a high degree of allelic polymorphisms, co-dominant inheritance, multi-allelism, and genome-wide coverage in various plant species, they also have shortcomings such as low polymorphic rates between genetically close lines, especially in Capsicum annuum. We developed an alternative technique to SSR by normalizing and alternating anchored primers in random amplified microsatellite polymorphisms (RAMP). This technique, designated reverse random amplified microsatellite polymorphism (rRAMP), allows the detection of nucleotide variation in the 3' region flanking an SSR using normalized anchored and random primer combinations. The reproducibility and frequency of polymorphic loci in rRAMP was vigorously enhanced by translocation of the 5' anchor of repeat sequences to the 3' end position and selective use of moderate arbitrary primers. In our study, the PCR banding pattern of rRAMP was highly dependent on the frequency of repeat motifs and primer combinations with random primers. Linkage analysis showed that rRAMP markers were well scattered on an intra-specific pepper map. Based on these results, we suggest that this technique is useful for studying genetic diversity, molecular fingerprinting, and rapidly constructing molecular maps for diverse plant species.

• The Korean Journal of Ecology
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• v.26 no.2
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• pp.71-74
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• 2003

Effects of nitrogen addition on the growth of Indigofera pseudo-tinctoria (Leguminosae) in the waste landfill site was investigated. Nitrogen fertilization in the nitrogen poor soils of waste landfill may influence the growth of nitrogen fixing plants beneficially or detrimentally. When I. pseudo-tinctoria was fertilized with three different levels of nitrogen, the coverage of plants treated with 46 g N/$m^2$ and 460 g N/$m^2$ was significantly less than that of plants treated with 23 g N/$m^2$. The growth rates of plant height treated with 46 g N/$m^2$ and 460 g N/$m^2$ were significantly less than those of plants treated with 23 g N/$m^2$. The growth rates of plant diameter treated with 46 g N/$m^2$ and 460 g N/$m^2$ were significantly less than those of plants treated with 23 g N/$m^2$. Dry weights of whole plants in control sites were higher than those of all the others nitrogen treatment sites. Nodule numbers were higher in control plants than those of plants in all the other nitrogen treatment sites. It is suggested that nitrogen fertilizer addition over 23 g N/$m^2$ affect the growth of some nitrogen fixing plants, such as I. pseudo-tinctoria, negatively.

• Molecules and Cells
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• v.27 no.2
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• pp.205-209
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• 2009

The loci of the 5S and 45S rRNA genes were localized on chromosomes in five species of Capsicum, namely, annuum, chacoense, frutescens, baccatum, and chinense by FISH. The 5S rDNA was localized to the distal region of one chromosome in all species observed. The number of 45S rDNA loci varied among species; one in annuum, two in chacoense and frutescens, and chinense, and four in baccatum, with the exceptions that 'CM334' of annuum had three loci and 'tabasco' of frutescens gad one locus. 'CM334'-derived BAC clones, 384B09 and 365P05, were screened with 5S rDNA as a probe, and BACs 278M03 and 262A23 were screened with 25S rDNA as a probe. Both ends of these BAC clones were sequenced. FISH with these BAC probes on pachytenes from 'CM334' plant showed one 5S rDNA locus and three 45S rDNA loci, consistent with the patterns on the somatic chromosomes. The 5S rDNA probe was also applied on extended DNA fibers to reveal that its coverage measured as long as 0.439 Mb in the pepper genome. FISH techniques applied on somatic and meiotic chromosomes and fibers have been established for chili to provide valuable information about the copy number variation of 45S rDNA and the actual physical size of the 5S rDNA in chili.

• Nuclear Engineering and Technology
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• v.41 no.6
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• pp.849-858
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• 2009

Risk caused by safety-critical instrumentation and control (I&C) systems considerably affects overall plant risk. As digitalization of safety-critical systems in nuclear power plants progresses, a risk model of a digitalized safety system is required and must be included in a plant safety model in order to assess this risk effect on the plant. Unique features of a digital system cause some challenges in risk modeling. This article aims at providing an overview of the issues related to the development of a static fault-tree-based risk model. We categorize the complicated issues of digital system probabilistic risk assessment (PRA) into four groups based on their characteristics: hardware module issues, software issues, system issues, and safety function issues. Quantification of the effect of these issues dominates the quality of a developed risk model. Recent research activities for addressing various issues, such as the modeling framework of a software-based system, the software failure probability and the fault coverage of a self monitoring mechanism, are discussed. Although these issues are interrelated and affect each other, the categorized and systematic approach suggested here will provide a proper insight for analyzing risk from a digital system.

• The Korean Journal of Ecology
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• v.22 no.5
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• pp.277-285
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• 1999

To develop a better restoration technique for altering urban planted forest to more natural forest, the changes of flora, vegetation structure and woody plant growth in the early stage after lumbering only Populus albaglandulosa of the tree layer were studied in Chungdam Park, Chungdam-dong, Kangnam-gu, Seoul for two years (from 1997 to 1998). The results were as follow. First, in the year after lumbering, the species changes occurred not in woody plants but in herbs, which increased by 44%. Three species including Viola verecunda disappeared, and 15 species including ruderals such as Metaplexis japonica and introduced species such as Erechtites hieracifolia appeared newly. Second, lumbering caused the coverages of Quercus aliena, Q. mongolica, Q. acutissima and Sorbus alnifolia in the subtree, or shrub layer, to be increased abruptly. The coverage of Lespedeza bicolor was affected by neighboring plants. Third, in the herb layer the coverage of Artemisia keiskeana was conspicuously increased but those of the others were not. Fourth, by ridding the upper layer canopy, Quercus' growth rates were increased highly. Rates of DBH growth of Q. aliena, Q. mongolica and Q. dentata were increased to 53.0%, 22.9% and 8% in the experimental area, and 23.1%, 8.3% and 6.1% in the control area, respectively, during two growing seasons (from May 11, 1997 to October 27, 1998). The ratios of twig biomasses of the previous year to the next year were 100:565 in Q. aliena, 100:197 in Q. mongolica and 100:644 in Q. dentata in the experimental area. There were also growth ratios of 100:117 in Q. aliena, 100:100 in Q. mongolica and 100:42 in Q. dentata in the control area, respectively. The growth rate increases of Q. aliena and Q. dentata were thus conspicuous in twig rather than in trunk, but that of Q. mongolica was vice versa.

• Korean Journal of Environmental Biology
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• v.38 no.1
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• pp.197-205
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• 2020

With the purpose of designing companion planting of groundcover plants for ornamental uses, this study identified the yearly growth characteristics of nine species of different life forms, analyzed the coverage characteristics of individual plants, and suggested combinations of plants suitable for each life form. Polygonatum odoratum var. pluriflorum, Liriope platyphylla and Hosta capitata, as short-grained plants that can grow to more than 20 cm, tended to grow for 60 days after planting in April and maintain their shape thereafter. Their aerial parts started to wither and enter dormancy after September. Saxifraga stolonifera, Dianthus chinensis and Sedum middendorffianum tended to continuously grow until September after planting in April and their growth declined after September. Lysimachia nummularia, as a creeping plant that grows creeping on the ground, started to show a rapid growth three months after planting. Sedum sarmentosum grew slowly until August and the aerial parts started to wither from September when the temperature decreases. The coverage characteristics of these nine species that grow differently after companion planting were surveyed and the growth of Sedum sarmentosum showed the highest number of companions. It was found that Hosta capitata can be companion planted with Sedum middendorffianum, Saxifraga stolonifera, and Lysimachia nummularia. These results indicate that among different shoot growth types species propagated with their stems creeping on the ground or those that can grow vegetatively with non-rhizome parts are more suitable for companion planting with others than those of which rhizomes branch.

• Journal of Ecology and Environment
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• v.33 no.4
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• pp.377-389
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• 2010

Understanding the factors relevant to endangerment and the patterns of habitat locations in relation to protected areas is critically important for the conservation of rare species. Although 64 plant species have recently been listed as endangered species in Korea, this information has, until now, not been available, making appropriate management and conservation strategies impossible to devise. Thus, we collected information on potentially threatening factors, as well as information on the locations in which these species were observed. The potentially threatening factors were classified into seven categories. National parks, provincial parks, ecosystem conservation areas, and wetland conservation areas were defined as protected conservation areas. Korean digital elevation model data, along with the maps of all protected areas were combined with the maps of endangered plant species, and analyzed via Geographic Information Systems (GIS). Excluding the category of "small population", endangered plant species in Korea were associated more frequently with extrinsic factors than intrinsic factors. Considering land surface only, all conservation areas in Korea totaled 4.9% of the land, far lower than International Union for Conservation of Nature and Natural Resources (IUCN)'s 10% coverage target. At the species level, 69% of the endangered plant species were detected in conservation areas, mostly in national parks. However, this result demonstrates that 31% of endangered species inhabit areas outside the conservation zones. Furthermore, at the habitat level, a large proportion of endangered species were found to reside in unprotected areas, revealing "gaps" in protected land. In the face of rapid environmental changes such as population increases, urbanization, and climate changes, converting these gap areas to endangered species' habitats, or at least including them in habitat networks, will help to perpetuate the existence of endangered species.

• Journal of Wetlands Research
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• v.25 no.3
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• pp.184-195
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• 2023

To develop an effective management plan for Ambrosia trifida L., an invasive alien plant in Korea, we assessed the potential of Ophraella communa LeSage as a biological control agent. This involved investigating the host specificity of the herbivore Ophraella communa LeSage, its annual travel distance, and the impact of this insect on the fitness of Ambrosia trifida L. We confirmed the host plant preference of Ophraella communa LeSage. The travel distance of this insect was determined by monitoring its appearance in selected Ambrosia trifida L. communities without these insects at distances of 10, 20, 30, and 100 meters, based on the locations where the presence of Ophraella communa LeSage was observed. The growth, reproductive, and physiological responses of Ambrosia trifida L. were measured according to feeding by Ophraella communa LeSage. As a result, Ophraella communa LeSage fed on only three taxa and moved short distances within a radius of 30 m per year from the host. The feeding behavior of the herbivore had a negative impact on the growth, reproductive, and physiological responses of Ambrosia trifida L. And the plant's growth and reproduction improved with increasing distance from the herbivore. Furthermore, the introduction of herbivores was able to control over 90% of Ambrosia trifida L. when the coverage of the Ambrosia trifida L. group was below 50%. However, the effectiveness of the removal decreased when the coverage exceeded 90%. These results are likely to be utilized by Ophraella communa LeSage as an ecological control agent. It is advantageous to introduce them in spring (May) when the coverage is low to maximize the effectiveness of control.