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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.
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.
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.
Predicting consensus sequence of pre-mRNA splicing signals in legume family
Chaeyoung Lee,Jin-Hyun Kim,Joo-Seok Park,Hong-kyu Choi 한국육종학회 2015 한국육종학회 심포지엄 Vol.2015 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.
Characteristics of Heat Waves From a Disaster Perspective
Kim, Do-Woo,Kwon, Chaeyoung,Kim, Jineun,Lee, Jong-Seol The Korean Society for Preventive Medicine 2020 Journal of Preventive Medicine and Public Health Vol.53 No.1
In September 2018, heat waves were declared to be a type of natural disaster by the Framework Act on the Management of Disasters and Safety. The present study examined the characteristics of heat waves from the perspectives of meteorological phenomena and health damage. The government's efforts to minimize the damages incurred by heat waves are summarized chronologically. Furthermore, various issues pertaining to heat waves that are being raised in our society despite the government's efforts are summarized by analyzing big data derived from reported news and academic articles.
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.
Chaeyoung Lee,Daejin Hyung,Jinhyun Kim,Yejin Jo,Jusuk Park,Dongwoon Yu,Hongkyu Choi 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 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 140 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.
Association of Mahogany/Attractin Gene (ATRN) with Porcine Growth and Fat
Kim, Jong Bok,Zeng, Zhao Xun,Nam, Yu Jin,Kim, Younyoung,Yang, Shi Liu,Wu, Xiaolin,Lee, Chaeyoung Asian Australasian Association of Animal Productio 2005 Animal Bioscience Vol.18 No.10
Associations of restriction fragment length polymorphism in porcine attractin (ATRN) gene with average daily gain (ADG), live weight (LWT) and back fat thickness (BFT) were studied with one exotic composition population (Xianghuang) and three local breeds (Ningxing, Shaziling and Daweizi) in China. Two types of alleles were detected; one with the band size of 700 bp (A) and the other with the band size of 450 and 250 bp (B), and their genotypes were classified as AA, AB and BB. Polymorphisms were observed in the exotic breed, but not in the three local breeds. Individuals with the genotype BB showed larger ADG and LWT than those with AA in Xianghuang population (p<0.05). The breed specific effects of the porcine attractin gene in this study implied that identification of the polymorphisms and determination of genetic effects on phenotypes should be performed in the target populations.