Seung Hun Choi

Gene set by de novo assembly of Perilla species and expression profiling between P. frutescens (L.) var. frutescens and var. crispa

Perilla frutescens (L.) Britt. is a self-pollinating annual species and is widely cultivated in China, Korea and Japan as an economic crop and a source of medicine and spices. In this study, we sequenced one cultivar variety (PF98095) of P. frutescens (L.) var. frutescens Britt., which was assembled as reference and other three varieties (PF11109, weedy of var. frutescens, PF06336 and PF06353, cultivars of varieties crispa) in order to carry out comparative expression profiling within cultivar and weedy in varieties frutescens and between varieties frutescens and varieties crispa of cultivar type in P. frutescens. Assembly of PF98095, annotation mapping, DEG (differentially expressed gene) profiling, and comparative analysis were performed. We found that more than 65% of the reads were mapped to the reference of P. frutescens gene set. Moreover, we detected 22,962 DEGs in the weedy variety compared to the cultivar, and also, 22,138 and 23,845 DEGs were identified in two cultivars according to the reference, respectively. The DEGs and functional classification were developed to analyze the differences between weedy and cultivar and between varieties frutescens and varieties crispa of Perilla. Furthermore, candidate genes for the different color and seed size of Perilla were identified that could be further investigated in future study. The herein results may play a significant role, and contribute in functional transcriptome studies of Perilla.

Identification of genetic variations of cultivated and weedy types of Perilla species in Korea and Japan using morphological and SSR markers

To better understand the genetic diversity and relationships of the two cultivated types of Perilla crop and their weedy types in Korea and Japan, we evaluated the genetic variations of 56 accessions by assessing five morphological characteristics and 18 SSR markers. The two cultivated types of var. frutescens and var. crispa were clearly distinguished by seed size, whereas most accessions of cultivated and weedy types of var. crispa cannot be distinguished strictly by seed characteristics. A total of 165 alleles with the SSR analysis were detected with an average number of 9.2 alleles per locus among the 56 Perilla accessions. The number of alleles per locus ranged from two for KWPE-56 and KWPE-39 to 21 for GBPFM-204. Additionally, the genetic diversity of each locus ranged from 0.497 at KWPE-56 and KWPE-39 to 0.959 at GBPFM-204, with an average of 0.692. The average genetic diversity values were 0.549, 0.685, 0.451 and 0.557 for cultivated and weedy types of var. frutescens and for cultivated and weedy types of var. crispa, respectively. The weedy type accessions of var. frutescens and var. crispa evidenced greater variation than the corresponding cultivated type accessions. The accessions of the cultivated and weedy types of var. frutescens and var. crispa from Korea exhibited greater SSR diversity than those of Japan. An UPGMA phylogenetic tree revealed three major groups, which was congruent with their morphological characteristics except for a few odd accessions. SSR markers clarified the genetic relationships between var. frutescens and var. crispa and helped improve our understanding of the genetic diversity of the two cultivated types of P. frutescens and their weedy types in Korea and Japan.

Genetic diversity and population structure in cultivated and weedy types of Perilla in East Asia and other countries as revealed by SSR markers

In this study, 17 simple sequence repeat (SSR) primer sets were used to analyze the genetic diversity, genetic relationships, and population structure among 81 accessions of two cultivated types of Perilla crop and their corresponding weedy types in East Asia and other countries. A total of 166 alleles were identified with an average of 9.8 alleles per locus. The average gene diversity (GD) value was 0.709. The average polymorphic information content (PIC) value was 0.679. The GD of each locus for accessions of cultivated var. frutescens, weedy var. frutescens, cultivated var. crispa, and weedy var. crispa were 0.557, 0.740, 0.429, and 0.509, respectively. Both weedy accessions exhibited higher GD and PIC values than their corresponding cultivated types. The cultivated and weedy types of the Perilla crop had much higher GD and PIC values in East Asia than in other countries. Particularly, in East Asia, the Perilla accessions from China showed higher SSR diversity than those from Korea, Japan, and other countries. Population structure analysis identified three groups, Group I, Group II, and an admixed group. Phylogenetic analysis produced four major clusters, but there was no clear geographic relationship between the two cultivated types of Perilla crop and their weedy types based on their regional distribution. This study demonstrated the utility of SSR analysis for performing genetic and population analysis of cultivated and weedy types of Perilla accessions in East Asia and other countries.

Quantitative Wind Risk Assessment for Low and Mid-Rise Apartment Buildings Based on a Probabilistic Model

This study develops a risk assessment model and evaluates wind risk to predict typhoon-induced damage. A wind risk assessment model was developed using the convolution of a wind hazard model and a wind fragility model, and both models were developed using the Monte Carlo simulation based on probability theory. Wind risk was quantitatively evaluated using the window system and part of the exterior materials installed in low and mid-rise apartments. Wind risk was compared according to regional (namely Busan, Daegu, Daejeon, and Seoul), geomorphological (namely topographic factor and exposure category), and morphological factors of buildings (height, roof tilt angle, and number of housing units) in order to evaluate relative influence. By employing the risk assessment model this study compared 432 wind risks and found that the most influential factor was exposure category, followed by the topographic coefficient, building height, target site of assessment, roof tilt angle, and number of housing units (in that order). The wind risk assessment model in this study could be used as basic data for the estimation of damage driven by wind and for the establishment of damage reduction measures, combined with the economic value of apartment buildings′ exterior materials and interior contents.

Fragility Assessment of Vinyl Greenhouses and Livestock Sheds Subjected to Volcanic Ash Fall Hazards

In this study, fragility functions are developed to estimate expected volcanic ash damage to vinyl greenhouses and livestock sheds among common agricultural facilities in South Korea. The fragility functions are derived through the FOSM (first-order second-moment) analytical approach based on the thickness distribution of volcanic ash observed in the 1980 eruption of Mt. Saint Helens in the USA and on agricultural facility codes and specifications in South Korea. In this study, the volcanic ash fragility functions evaluated represent the conditional probability of failure of vinyl greenhouses and livestock sheds over the full range of volcanic ash loads. For the evaluation, 4 types (i.e., automated, single span, tree crop, and double span types) of multi-hazard resisting vinyl greenhouses and 3 types (i.e., standard, coastal, and mountain types) of livestock sheds conventionally utilized in South Korea are considered. All volcanic ash fragility functions estimated in this study are fitted using parameters of the lognormal CDF (cumulative distribution function), and the obtained parameters are compiled into a database for use in the future. The volcanic ash fragility functions developed in this study are intended to be used to evaluate potential risks and losses from volcanic eruptions around the Korean Peninsula.

Assessment of Extreme Wind Risk for Window Systems in Apartment Buildings Based on Probabilistic Model

In this study, a coupled probabilistic framework is developed to assess wind risk on apartment buildings by using the convolution of wind hazard and fragility functions. In this framework, typhoon induced extreme wind is estimated by applying the developed Monte Carlo simulation model to the climatological data of typhoons affecting Korean peninsular from 1951 to 2013. The Monte Carlo simulation technique is also used to assess wind fragility function for 4 different damage states by comparing the probability distributions of the window systems resistance performance and wind load. Wind hazard and fragility functions are modeled by the Weibull and lognormal probability distributions based on simulated wind speeds and failure probabilities. The modeled functions are convoluted to obtain the wind risk for the different damage levels. The developed probabilistic framework clearly shows that wind risk are influenced by various important characteristics of terrain and apartment building such as location of building, exposure category, topographic condition, roof angle, height of building, etc. The risk model presented in this paper can be used as tools to predict economic loss estimation and to establish wind risk mitigation plan for the existing building inventory.

Fragility Assessment of Agricultural Facilities Subjected to Volcanic Ash Fall Hazards

Abstract This paper presents findings from the assessment of the volcanic ash fragility for multi-hazard resisting vinyl greenhouse and livestock shed among the agricultural facilities. The volcanic ash fragility was evaluated by using a combination of the FOSM (first-order second-moment) method, available statistics of volcanic load, facility specifications, and building code. In this study, the evaluated volcanic ash fragilities represent the conditional probability of failure of the agricultural facilities over the full range of volcanic ash loads. For the evaluation, 6 types(ie., 2 single span, 2 tree crop, and 2 double span types) of multi-hazard resisting vinyl greenhouses and 3 types(ie., standard, coast, and mountain types) of livestock sheds are considered. All volcanic ash fragilities estimated in this study were fitted by using parameters of the GEV(generalized extreme value) distribution function, and the obtained parameters were complied into a database to be used in future. The volcanic ash fragilities obtained in this study are planning to be used to evaluate risk by volcanic ash when Mt. Baekdu erupts.