Construction of composite comparative genetic maps for ten legume species

Dongwoon Yu,Chaeyoung Lee,Daejin Hyung,Jinhyun Kim,Yejin Jo,Jusuk Park,Eunji Kwon,Hongkyu Choi 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07

The legume family is the third largest group, including approximately 650 genera and 18,000 species, in the flowering plants and the second important crops to the Poaceae in the agricultural economy. Comparative analysis is a useful tool to understand cross-species genomic structure and alterations during organism’s evolutionary history. In this study, we constructed a composite comparative map of ten legume species, including Medicago truncatula, Medicago sativa, Lens culinaris, Pisum sativum, Lotus japonicus, Cicer arietinum, Vicia faba L, Vigna radiata, Phaseolus vulgaris and Glycine max. Of these species, M. truncatula, which is a representative model system, played a central role to develop the cross-genome amplifiable PCR gene markers for the purpose of transferring them to other related legume species. A total of 108 cross-species core markers were employed to analyze genomic colinearity across this broad array of legume species. The comparative map demonstrates a diverse array of evolutionary events, such as duplications, inversions and reciprocal translocations. It is anticipated that resulting maps would provide a broader insights into the lineage-specific genomic organization of these glalegoid/phaseoloid legumes, which are two clades containing almost all crop legumes of economic importance, and can further used for the molecular breeding through translating genomic information into other orphan legumes.

경제발전에서 제도의 역할

유동운(Dongwoon Yu) 韓國經濟發展學會 2010 經濟發展硏究 Vol.16 No.2

사회가 진보할수록 사람들 사이에 지식은 점점 분산되어 각자가 다른 사람의 지식에 의존하는 정도는 증대한다. 그에 따라 사람들 사이에 비대칭으로 분포되어 있는 지식을 교환하는 일이 경제발전의 중심과제로 들어선다. 경제발전의 요인 가운데에서 인간의 인지능력을 절약시켜주는 제도가 높은 경제성장률로 높은 인당 소득을 가져다주었을 것으로 기대된다. 사람들의 인지능력을 과부하시키는 획일적인 가치와 견해를 강요하는 집단주의문화와 개인의 경제적 자유를 제한하는 정부의 각종 규제는 개인이 인지를 절약하여 거두어들일 수 있는 이득을 고갈시킨다. 인지경제에 들어선 경제가 성장하려면, 집단주의적 신념에서 벗어난 개인주의문화가 확산되어야 할 뿐만 아니라 각종 경제규제의 철폐로 개인의 경제적 자유가 확대될 것이 요구된다. 그리하여 개인은 지식의 정확성을 살리고 동시에 사회는 다양한 지식을 확장시키면서 인지를 절약하는 제도의 뒷받침을 통해 성장의 활로가 찾아지기를 기대한다(JEL: K20, O38). As society advances, knowledge becomes more dispersedly distributed among individuals, which requires him a dependence from others. As a result the main concern for economic growth lies in the exchange of knowledge asymmetrically dispersed among them. Out of the factors which lead to the growth of an economy, institutions that save on cognitive capacity of individual, in particular, individualism and economic freedom brought a high growth rate of the economy and high living standards among the citizens. At present Korean society is embedded with collectivism which enforces individual a uniform value and opinion. Government regulations which restrict individual economic freedom, waste cognitive capacity of individual. For a cognitive economy to grow, individualism freed from collective responsibility needs to expand as well as individual economic freedom needs to develop through deregulation which contributes to save on his scarce cognitive capacity. Economic growth is expected to be found through cognitive economy which requires individual an accuracy of knowledge and society a variety of knowledge.

Cross-family translation of genomic information on abiotic stress-related genes between Arabidopsis and Medicago truncatula

Chaeyoung Lee,Daejin Hyung,Jinhyun Kim,Dongwoon Yu,Jeonghoon Park,Meejin Kim,Hyun-A So,Howon Chung,Youngsoo Chung,Dohoon Kim,Jaehun Lee,Hongkyu Choi 한국육종학회 2012 한국육종학회 심포지엄 Vol.2012 No.07

Cross-species translation of genomic information may play a pivotal role in applying biological knowledge gained from one species to other genomes. Abiotic stress-responsive genes in Arabidopsis have been translated to a legume model system, Medicago truncatula. A total of 1,370 Arabidopsis genes were identified by searching TAIR database, expression profiling data and literatures. For purposes of cross-genome identification of orthologous genes, tBlastX or BlastP were employed between these two model systems. Candidate genes potentially associated with abiotic stress responses were classified into 18 functional criteria and corresponding genomic locations were analyzed by Circos program. To do this, user-friendly bioinformatic analysis platform was established. In order to discover abiotic stress-associated genes, gene network and/or interactome analyses were conducted using a combination of AraNet web-based platform and CytoScape program. As a result, we could identify 240 key genes that appeared to play an important role within central gene networks. We anticipate that these genes may impact molecular breeding programs by developing them into genetic markers and discovering trait-associated nucleotide variations.

Predicting family-wide consensus sequence of pre-mRNA splicing signals in legumes and their potential utility as phylogenetic markers

Chaeyoung Lee,Daejin Hyung,Jinhyun Kim,Dongwoon Yu,Jeonghoon Park,Meejin Kim,Hyun-A So,Eunsook Jeong,Howon Chung,Youngsoo Chung,Dohoon Kim,Jaihun Lee,Hongkyu Choi 한국육종학회 2012 한국육종학회 심포지엄 Vol.2012 No.07

For purposes of studying intron structures and predicting consensus splice motifs, a total of 102 legume species were used to isolate introns across the family. Of 196 gene-targeted PCR primer pairs, we successfully amplified 118 intron-containing genes (60.2%) and obtained a total of 1,870 introns with an average size of 143 nucleotides. Species-based compilation of 5’- and 3’-splicing motifs showed lineage-specific conservation in each splicing motif. Compilation of the entire intron set permitted prediction of the consensus sequences of splicing signal motifs in legumes, AYGWGTABABGH and TVNC/TAGGHTV for the 5’- and 3’-splicing motifs, respectively. Interestingly, these consensus motifs are very similar to the corresponding splicing signals of two model systems, Arabidopsis and rice. This result is suggestive of conservation of pre-mRNA splicing mechanisms in higher plants. Multiple alignments of CALTL introns demonstrated that the region from the branch point to 3’ splice site was relatively more conserved than the region from5’ splice site to the branch point. Phylogenetic analysis demonstrated that each of three splicing motifs, 5’-splice sites, 3’-splice sits, and branch site, was relevant to evolutionary divergence of species and phylogenetically informative, suggesting that splice signal sequences would be useful as a potential tool for the molecular phylogenetic analysis.

Development of interactive comparative analysis platform for the legume translational genomics

Daejin Hyung,Chaeyoung Lee,Jinhyun Kim,Dongwoon Yu,Yejin Jo,Jusuk Park,Hongkyu Choi 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07

Comparative analysis is a typically useful tool for translating genomic information from one species to another. However, currently available softwares are relatively difficult to directly use for researchers that are not familiar with use of bioinformatic tools. Therefore, we intended to develop a new platforms and/or interface through which one can use in more comfortable way, based on the concept of interactive comparative analysis. Towards this direction, we, firstly, constructed relational database to store the information on abiotic stress genes identified from multiple plant species using various resources, such as the TAIR (http://www.arabidopsis.org), gene expression profiles and relevant literatures, and linked with comparative analysis interface. For purposes of comparative analysis and identification of synteny blocks, cross-species orthologous genes were determined using a combination of tBlastX and BlastP homology searches. We adapted and developed a Circos-like format to present resulting comparative maps. Users can readily choose analysis parameters, for example individual genes and specific chromosomes for chosen species, in the pane of analysis DB, which is useful feature to avoid complexity of comparative genomic analysis. This DB-associated comparative analysis tool, developed in this study, will be able to provide customer-friendly interface for comparative analysis and extend its utility across a broader range of plant genomes.

Cross-species translation of abiotic stress-responsive genes between Arabidopsis thaliana and Medicago truncatula.

Chaeyoung Lee,Daejin Hyung,Jinhyun Kim,Dongwoon Yu,Yejin Jo,Jusuk Park,Eunji Kwon,Hongkyu Choi 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07

Cross-species translation of genomic information may play a crucial role in applying biological knowledge gained from one species to other genomes. To screen and identify a broad range of abiotic stress-responsive genes, we employed a diverse array of resources, including Arabidopsis databases (http://www.arabidopsis.org), expression profiling data and previously reported literatures. As a result, a total of 1,377 genes were identified and classified into 18 different functional criteria based on biological processes of gene ontology. The gene set was translated into M. truncatula, which is a representative model system in the Fabaceae, by identifying orthologous genes between these two genomes with a combination of tBlastx and BlastP analyses. It is shown that approximately 82% of genes were estimated to be translated between the two genomes below the E-value of 10-30. These orthologous loci were used to construct comparative maps by developing a user-friendly analysis platform, resulting in a total of 52 synteny blocks. Furthermore, to discover central genes by which control responses to the abiotic stresses, a combination of AraNet (http://www.functionanet.org) and the Cytoscape program was used for the gene network analysis. The analysis resulted in the identification of 240 potential key genes. We anticipate that these genes may impact molecular breeding programs by discovering trait-associated SNPs followed by marker development.

Development of interactive comparative analysis platform for translation of genomic information across different plant species

Daejin Hyung,Chaeyoung Lee,Jinhyun Kim,Dongwoon Yu,Yejin Jo,Jusuk Park,Eunji Kwon,Hongkyu Choi 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07

Comparative analysis is a typically useful tool for translating genomic information from one species to another. However, currently available softwares are relatively difficult to directly use for researchers that are not familiar with use of bioinformatic tools. Therefore, we intended to develop a new platforms and/or interface through which one can use in more comfortable way, based on the concept of interactive comparative analysis. Towards this direction, we, firstly, constructed relational database to store the information on abiotic stress genes identified from multiple plant species using various resources, such as the TAIR (http://www.arabidopsis.org), gene expression profiles and relevant literatures, and linked with comparative analysis interface. For purposes of comparative analysis and identification of synteny blocks, cross-species orthologous genes were determined using a combination of tBlastX and BlastP homology searches. We adapted and developed a Circos-like format to present resulting comparative maps. Users can readily choose analysis parameters, for example individual genes and specific chromosomes for chosen species, in the pane of analysis DB, which is useful feature to avoid complexity of comparative genomic analysis. This DB-associated comparative analysis tool, developed in this study, will be able to provide customer-friendly interface for comparative analysis and extend its utility across a broader range of plant genomes.

Genetic map construction of model legume, Medicago truncatula, and analysis of genomic co-linearity with M. sativa

Chaeyoung Lee,Daejin Hyung,Jinhyun Kim,Dongwoon Yu,Jeonghoon Park,Meejin Kim,Hyun-A So,Eunsook Jeong,Howon Chung,Youngsoo Chung,Dohoon Kim,Jaihun Lee,Hongkyu Choi 한국육종학회 2012 한국육종학회 심포지엄 Vol.2012 No.07

A core genetic map of the legume Medicago truncatula has been established by analyzing the segregation of 288 sequence-characterized genetic markers in an F2 population composed of 93 individuals. These molecular markers correspond to 141 ESTs, 80 BAC end sequence-tags, and 67 resistance gene analogs, covering 513 cM. In the case of EST-based markers we used an intron-targeted marker strategy, with primers designed to anneal in conserved exon regions and amplify across intron regions. Polymorphisms were significantly more frequent in intron vs exon regions, thus providing an efficient mechanism to map transcribed genes. Genetic and cytogenetic analysis produced eight well-resolved linkage groups, which have been previously correlated with eight chromosomes by means of FISH with mapped BAC clones. We anticipated that mapping of conserved coding regions would have utility for comparative mapping among legumes; thus 60 of the EST-based primer pairs were designed to amplify orthologous sequences across a range of legume species. As an initial test of this strategy, we used primers designed against M. truncatula exon sequences to rapidly map genes in Medicago sativa. The resulting comparative map, which includes 68 bridging markers, indicates that the two Medicago genomes are highly similar, and establishes the basis for a “Medicago” composite map.

1980년대 이후 우리나라 등록 제초제의 제반 특성별 현황

유진상(JinSang Yu),임태헌(TaeHeon Lim),최성환(SungHwan Choi),이동운(DongWoon Lee) 한국잡초학회·한국잔디학회 2020 Weed & Turfgrass Science Vol.9 No.1

우리나라에서 제초제의 공급은 1955년부터 시작하여 1970년대이후로 증가하고 있다. 본 조사는 1980년대 이후 우리나라에 등록된 제초제들의 일반적 현황(등록 품목, 독성별 구분, 제형별 구분, 성분별 구분)을 알아보기 위하여 수행하였다. 1982년이후 제초제 등록 품목수는 2014년을 정점으로 감소하는 경향이었다. 등록된 제초제의 85.3%가 저독성이었으며 2010년대 이후 등록된 제초제의 86.1%는 어독성 3급이었고, 1.9%만 어독성 1급이었다. 등록 된 제초제들의 제형별 구성은 1990년대 9종에서 2010년대 17종으로 다양성이 증가하였다. 1980년대 이후 등록된 제초제들의 18가지 제형들중 우점순위는 입제, 유제, 액제, 액상수화제 순이었는데 이들 네 제형의 점유비율은 76.2%였다. 등록 제초제들의 계통별 구성은 년대기별로 다양화되었으나 등록 품목수가 가장 많은 계통은 1990년대 이후 sulfonylurea계통이 가장 많았으며 두 번째는 chloroacetamide계통이었다. 전체 등록 제초제의 계통들 중 상위 3개 계통의 점유 비율은 년대기별로 감소하는 경향이었으나 평균 점유비율은 39.3%로 높았다. In Korea, the supply of herbicides began in 1955 and has increased since the 1970s. This study was conducted to find out the general status of herbicides registered in Korea since the 1980s (registration items, toxicity, formulation, and chemical component). Since 1982, the number of herbicide-registered items has declined since peaking in 2014. 85.3% of the registered herbicides were low toxicity, 86.1% of the herbicides registered since the 2010s were fish toxicity Ⅲ, and only 1.9% were fish toxicity Ⅰ. The formulation composition of registered herbicides increased from 9 in the 1990s to 17 in the 2010s. Among the 18 formulations of herbicides registered since the 1980s, the top priority was granules, emulsifible concentrate, soluble concentrate and suspension concentrate. The composition of registered herbicides varied according to the chronological age, but the sulfonylurea was the largest and the second was the chloroacetamide since the 1990s. The share of the top three lines of all herbicide lines declined by age, but the average share was high at 39.3%.

1980년대 이후 우리나라에 등록 된 살균제와 살충제의 독성, 제형 및 계통별 현황

유진상(Jin-sang Yu),임태헌(Tae Heon Lim),이동운(DongWoon Lee) 한국농약과학회 2020 농약과학회지 Vol.24 No.1