Relationship of Transformation Efficiency and Metabolites Induced in Korean Soybean Cotyledons Treated with Sonication

Kitae Song,Won Cheol Yim,Gun-Ho Jung,Sun Lim Kim,Young-Up Kwon,Byung-Moo Lee 韓國作物學會 2013 Korean journal of crop science Vol.58 No.2

The interaction between Agrobacterium and soybean has been studied at the transcriptome level but not at the metabolic level. However, it is necessary to investigate the difference in metabolites between susceptible and non-susceptible cultivars for high efficiency transformation. We investigated the difference in metabolites from sonicated soybean cotyledons of Korean cultivars and Bert cultivar. To identify difference in metabolites, sonicated extracts were analysed by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR/MS). The soybean cultivars were classified by susceptibility using green fluorescent protein expression. We found a difference in metabolites between the high susceptible and low susceptible cultivars. The FT-ICR/MS experimental m/z data of different metabolites were compared with theoretical m/z in KNApSAcK database. The candidate list was made using KNApSAcK and focused on phenolic compounds. These candidate metabolites are speculated to influence factors in the interaction. This list of candidates may be useful to investigate the interaction between Agrobacterium and plants to increase transformation efficiency.

Relationship of Transformation Efficiency and Metabolites Induced in Korean Soybean Cotyledons Treated with Sonication

Song, Kitae,Yim, Won Cheol,Jung, Gun-Ho,Kim, Sun Lim,Kwon, Young-Up,Lee, Byung-Moo The Korean Society of Crop Science 2013 한국작물학회지 Vol.58 No.2

The interaction between Agrobacterium and soybean has been studied at the transcriptome level but not at the metabolic level. However, it is necessary to investigate the difference in metabolites between susceptible and non-susceptible cultivars for high efficiency transformation. We investigated the difference in metabolites from sonicated soybean cotyledons of Korean cultivars and Bert cultivar. To identify difference in metabolites, sonicated extracts were analysed by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR/MS). The soybean cultivars were classified by susceptibility using green fluorescent protein expression. We found a difference in metabolites between the high susceptible and low susceptible cultivars. The FT-ICR/MS experimental m/z data of different metabolites were compared with theoretical m/z in KNApSAcK database. The candidate list was made using KNApSAcK and focused on phenolic compounds. These candidate metabolites are speculated to influence factors in the interaction. This list of candidates may be useful to investigate the interaction between Agrobacterium and plants to increase transformation efficiency.

Differential gene expression in Korean soybean under heat stress condition.

Kitae Song,Gun-Ho Jung,Sun Lim Kim,Young-Up Kwon,Byung-Moo Lee 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07

Soybean is an important crop with useful traits such as the high seed protein and oil contents. Soybean reproduction is sensitive to temperature over 35℃. To obtain database of gene expression profiles, we used soybean cultivars, sensitive and tolerant. RNA sequencing was performed to find differentially expressed genes in two Korean soybean cultivars under heat stress condition. The transcriptomic changes in each cultivar under heat stress. We found 2727 common transcripts in two soybean cultivars under heat stress, and selected 20 transcripts to heat stress response genes. The 20 selected genes were analysed using BLAST2GO and PLANEX. The genes were major factor in co-expression networks. It appears that these 20 genes were mainly attributable to heat stress.

Gene Expression Analysis and Polymorphism Discovery to Investigate Drought Responsive System in Tropical Maize

( Kitae Song ),( Hyo Chul Kim ),( Kyung-hee Kim ),( Jun-cheol Moon ),( Jae Yoon Kim ),( Sang-kyu Lee ),( Byung-moo Lee ) 한국육종학회 2018 Plant Breeding and Biotechnology Vol.6 No.4

Maize has high food and industrial value, whereas has difficulties in research because of their complex and huge size genome. Nested association mapping (NAM) was constructed to better understand maize genetics. However, most studies were conducted using the reference genome B73, and only a few studies were conducted on tropical maize. Ki3, one of the founder lines of the NAM population, is a tropical maize. We analyzed the genetic characteristics of Ki3 by using RNA sequencing and bioinformatics tools for various genetic studies. As results, a total of 30,526 genes were expressed, and expression profile were constructed. A total of 1,558 genes were differentially expressed in response to drought stress, and 513 contigs of them come from de novo assemblies. In addition, high-density polymorphisms including 464,930 single nucleotide polymorphisms (SNPs), 21,872 multiple nucleotide polymorphisms (MNPs) and 93,313 insertions and deletions (InDels) were found compared to reference genome. Among them, 15.0 % of polymorphisms (87,838) were passed non-synonymous test which could alter amino acid sequences. The variants have 66,550 SNPs, 5,853 MNPs, and 14,801 InDels, also proportion of homozygous type was higher than heterozygous. These variants were found in a total of 15,643 genes. Of these genes, 637 genes were found as differentially expressed genes (DEGs) under drought stress. Our results provide a genome-wide analysis of differentially expressed genes and information of variants on expressed genes of tropical maize under drought stress. Further characterization of these changes in genetic regulation and genetic traits will be of great value for improvement of maize genetics.

Expression of Heat Shock Proteins by Heat Stress in Soybean

( Kitae Song ),( Won Cheol Yim ),( Byung-moo Lee ) 한국육종학회 2017 Plant Breeding and Biotechnology Vol.5 No.4

Heat stress is one of the factors disturb productivity and growth of plants. Many genes including heat shock protein (HSP), heat shock transcription factors (HSF) and chaperones, were identified and characterized in many plants to play role in increased tolerance to abiotic stress. To reveal responsive gene to heat stress, we performed RNA-seq using two Korean soybean varieties under heat stress and normal conditions. The transcripts were analyzed, and we obtained 2,458 genes including 46 co-up regulation and 55 co-down regulated genes in both soybean varieties. We also revealed HSPs, HSFs and chaperones in the differentially expressed genes using BLAST and Pfam analyzation and verified expression changes under heat stress. Finally, we find 68 genes involved in HSP, HSF, chaperones in heat responsive genes associated increasing heat tolerance. As a result, relatively small HSP families were up regulated and continuously expressed in long period heat stress. On the other hand, large molecule HSPs, HSFs and chaperonin did not response to long heat stress. The expression profiling and characterization provide invaluable information to understand heat tolerance of soybean.

Meta-analysis of QTL involved in drought tolerance and grain yield of maize

Kitae Song,Hyochul Kim,Seungho Shin,Kyung-Hee Kim,Jun-Cheol Moon,Jae Yoon Kim,Byung-Moo Lee 한국육종학회 2015 한국육종학회 심포지엄 Vol.2015 No.07

The maize genome is complex with exceeding the levels of intra-specific variation, repetitive DNA content, and allelic content observed between many species. Because of tremendous diversity and variants, maize is considered as a forefront crop development and estimation of molecular markers for agricultural trait in genetics and breeding. Using quantitative trait loci (QTL) and marker assisted breeding (MAS), molecular breeders are able to development of drought tolerance and grain yield in maize genotype. To study QTL congruency, a meta QTL analysis including results from eight-teen QTL publications for grain yield and drought tolerance were considered. Among them, we assembled 420 QTLs for abscisic acid (ABA) concentration, anthesis silking interval (ASI), days to flower, days to silk, ear number, kernel number, grain number and grain yields, involved in drought tolerance and grain yield. The meta QTL analysis revealed significant evidence for linkage of these traits to 39 different segments as candidates regions on maize genome. A total of 571 marker was selected as QTL or integrated QTL markers for narrowing down the QTL region into specific functionally relevant candidates. The results of meta QTL analysis helped to refine the genomic regions of agricultural traits, interest described and provided the closest flanking markers.

Distribution of Genetic Variants in Korean Soybeans

Kitae Song,Jeong Hoon Kim,Gi Yong Yoon,Hyo Chul Kim,Seungho Shin,Won Cheol Yim,Kyung-Hee Kim,Byung-Moo Lee 한국작물학회 2015 Korean journal of crop science Vol.60 No.2

Next generation sequencing technologies provide opportunities to reveal the genetic variants and differentially expressedgenes. The genetic variants are closely relevance to understanding of genes and phenotypic differences related to agronomic characteristics among cultivars. In this study, we conducted RNA-seq using two Korean soybean accessions, including Daewon and Hwangkeum, by using next generation sequencing against Williams 82 genome as reference. A number of variants such assingle nucleotide variants (SNV), multiple nucleotide variants (MNV), insertion/deletion (InDel) and replacement, was 34,411 and 55,544 in Daewon and Hwangkeum, respectively. Among these variants, 9,611 nonsynonymous variants were detected within 4,290 genes in Daewon and 13,225 non-synonymous variants were located on 5,672 genes in Hwangkeum. The distribution of nonsynonymous variants and expression values of genes can serve as invaluable resource for genotyping and study of traits within genes for soybean improvements.

동해안 마을어장의 변동과 별신굿의 사회적 기능

송기태(Song, Kitae) 목포대학교 도서문화연구소 2014 島嶼文化 Vol.0 No.43

본 연구에서는 동해안 마을어장이 근대 이후 변동을 맞이해 온 과정을 주목하고 그 과정에서 빚어진 갈등과 분쟁이 현재까지도 여파를 미치고 있음을 확인하였다. 그리고 동해안에서 왕성하게 전승되는 별신굿이 마을어장을 둘러싼 어촌사회의 이해관계 속에서 존재하고, 별신굿을 통해 다양한 갈등요소들이 해소되거나 조정되고 있음을 파악하였다. 별신굿이 공고하게 전승될 수 있는 기반으로 어촌계를 주목하고, 그 어촌계가 소득을 창출하는 마을어장과 별신굿의 관계를 파악하였다. 마을어장과 별신굿이 직접적으로 관계가 없을 것 같지만, 마을어장이 별신굿의 재정적 근원이 되는 점에서 밀접한 관련이 있다고 할 수 있다. 마을어장을 둘러싼 어촌사회의 변동은 어촌계의 수익이 창출되고 강화되는 과정으로 진행되고 있다. 20세기 제주 해녀들이 동해안으로 진출하면서 주민들과 해녀는 갈등과 타협을 도모하면서 마을어장을 이용하는 주체로 공존하고 있다. 또 미역밭 곽주들이 사유하던 어장은 1960년대에 총유화 되면서 어촌사회의 갈등요인이 되었고, 동시대에 등장한 어촌계는 어촌의 공동체적 질서를 재편하였다. 이제 마을어장은 어촌계에서 점유하고 해녀들은 고용되어 일을 하는 공간이 되었다. 그리고 경작 기술이 발달하면서 전복 등을 자연양식하면서 새로운 수익을 창출하고 있다. 어장을 총유화하여 어촌계에서 이용하고 바다경작을 확대하여 수익을 증대시키고 있는 것이다. 이러한 수익은 모두 어촌계로 귀속되는데 ‘어촌계와 곽주의 문제’, ‘어촌계와 해녀의 문제’, ‘어촌계원과 비계원의 문제’ 등이 걸려있기 때문에 어촌계의 수익을 어촌계원들이 그대로 배분하기에는 윤리적․사회적 반발이 존재한다. 이러한 어촌사회의 복잡한 이해관계 속에서 별신굿이 존재한다. 별신굿은 마을어장을 둘러싼 어촌사회의 갈등을 해소하고 조정하는 데 기능을 발휘하고 있다. 마을어장의 수익을 오로지 어촌계원들이 나누어 갖는다면 어촌사회의 갈등이 부각될 수밖에 없지만, 그 일부를 마을의 공동체의례 비용으로 사용함으로써 효율적으로 갈등을 잠재우고 있는 것이다. 그래서 불만이 있을 수 있는 해녀들도 어장 행사료를 풍어굿 경비라고 생각하는 것이다. 마을어장에서 거두어들인 수익을 별신굿을 통해 베풂으로서 사회적 갈등까지 조정해냈다고 할 수 있다.

씻김굿 무구(巫具)의 기능과 극적 의례성

송기태(Song Kitae) 한국무속학회 2007 한국무속학 Vol.0 No.15

본 논문에서는 무구의 신성 획득과 발현 과정을 점검하고, 무구를 통한 굿의 극적 의례화에 주목하고 있다. 굿판에서 사용되는 무구 중에는 현장에서 제작되는 것도 있고, 지속적으로 사용되는 것이 있다. 현장에서 제작되는 것은 대부분 생활용품을 활용하거나 구입해 온 종이나 천을 이용해 의례에 적합하게 만드는데, 해당 굿판에서만 사용된다. 이에 비해 지속적으로 사용되는 것은 현장에서 구입하거나 제작하지 않고 본래의 형태를 유지한 상태에서 여타의 굿판에서 지속적으로 활용된다. 이러한 양상은 무구가 일시적인 신성을 획득하는지, 아니면 지속적으로 신성을 유지하는지를 구분하는 기준이 된다. 지속적으로 사용되는 무구는 무녀가 지참하고 다니는데, 이들 무구는 일정한 권위를 획득하고 있으면서 다차원의 존재를 교접시키는 데 사용된다. 그리고 일회성 무구는 본래의 형태에 일정한 변형을 가함으로써 일시적인 신성이 획득되고 굿이 끝난 후 소각된다. 무구의 구성 크게 3가지로 구분할 수 있다. 굿의 개별절차를 넘나들면서 중복 사용되는 무구와 개별 절차에만 사용되는 무구, 여러 절차에 걸쳐 사용되면서 다른 무구들과 결합되어 사용되는 무구가 있다. 지전은 여러 절차에 걸쳐 중복 사용되는데, 이것은 구체적인 신격을 상징하거나 신적 권위를 상징하지 않는, 축원을 위한 무구이기 때문에 의례 절차를 뛰어넘어 사용될 수 있는 것으로 해석된다. 그리고 손대와 정쇠, 바라, 고깔 등은 개별 절차에 국한되어 사용되는 것이면서 직간접적으로 신격과 관련된다. 결과적으로 조상신과 가택신에 대한 의례에서는 신격과 관련된 무구가 사용되지 않는데, 이것은 마래에 이미 조상신과 가택신이 좌정해 있는 것과 관련되어 별도의 무구가 필요하지 않은 것으로 해석될 수 있다. 그리고 중반부에서 넋은 다른 여타의 무구들이 결합되어 사용된다. 여기서 넋은 망자를 대상으로 하는 개별 절차마다 사용되는데, 각 절차를 거치면서 질적으로 변화된 신성으로 볼 수 있다. 씻김굿의 중반부는 극적 짜임새를 갖는다. 중반부의 굿거리가 단절, 풀이, 씻김, 닦음 등의 상징적 절차를 통해 망자의 인격 전환과 저승 이동을 보여주는데, 이러한 특징을 극적 의례성이라고 할 수 있다. 극적 의례성은 굿판의 맥락과 소통하면서 굿판의 흐름과 조응한다. 따라서 무구는 무당의 굿 진행과 수용자의 대응을 읽어낼 수 있는 표지라고 할 수 있다. The focus of this study is to investigate the process of acquisition of divinity and manifestation of shamanic materials and to observe the theoretical formalization through the shamanic materials. Among the shamanic materials that are used at the Gut (trans.exorcism), some of them are made at the site and the others are used repeatedly. The ones made at the site are made appropriate for the ceremony using paper or fabric mostly using household goods or buying them and are used for the one particular Gut. In contrast, the ones used repeatedly are not bought or made at the site but used constantly in other sites of Gut maintaining the original form. This aspect is the standard for classifyingif the shamanic material acquires temporary divinity or it maintains the divinity constantly. The shamanic materials that are used repeatedly arecarried by the female shaman and they acquire uniformed authority and at the same time, are used for interconnecting existences of multiple dimensions. The temporary shamanic materials are incinerated after the Gut when the temporary divinity is acquiredthrough giving specific modifications to the original form. If we look at the phases of the shamanic materials that are fundamental to the construction of the Gut, it could be classified into three phases. They are the shamanic materialsused repeatedly frequenting the individual process of the Gut and ones used incorporated to other shamanic materials through many processes. The paper money is used repeatedly in many processes and since this is just the shamanic material for invocation which does not represent the specific divinity or divine authority, it could be interpreted to be used regardless of the ceremonial procedures. Moreover, the shaman wand, spirits, small gong and peaked hatare used for individual procedures and at the same time directly and indirectly related to divinity. In conclusion, in the ceremony for divinity of ancestors and houses, the shamanic materials related to divinity are not used and this could be interpreted as lack of necessity of separateshamanic materials which the divinity of ancestors and houses are related to their original site. Also, in the middle part, ‘the spirit’ is used incorporated to other shamanic materials. The spirit, here, is used in individual procedures that are subjected to the dead which in each procedures hierophanized of the divinity that are transformed in quality. The middle part of the Sitgimgut (trans. shaman ritual for cleaning dead person's soul) has a dramatic structure. The materials of the Gut in the middle part show the personality transformation and transfer to the Hades through the symbolic procedures of disconnection, clarification, cleansing, and polish. And this characteristic is the theoretical formalization. The theoretical formalization corresponds to the flow of the Gut communicating with the context of the Gut. Therefore, the shamanic materials are the marks that could read the process of the Gut and the reaction of the recipient.

Gene expression analysis based on de novo assembly in wheat RNA-sequencing

Won Cheol Yim,KiTae Song,Byung-Moo Lee 한국육종학회 2012 한국육종학회 심포지엄 Vol.2012 No.07

Wheat is the third largest crop in the world behind corn and rice. Wheat is grown over a wide range of environments, and an essential source of carbohydrates. However, the genomics of wheat, a non-model species, is still challenging despite of corn and rice was done. The recent advent of RNA-Sequencing, a massively parallel sequencing method for genome and transcriptome analysis, provides opportunity to identify gene discovery and molecular mechanisms of cellular processes. We performed a RNA-Seq experiment to find differentially expressed genes under high temperature condition. More than 344 million shot reads were generated using Illumina HiSeq technology. A comprehensive and integrated 285,324 transcripts were assembled via Trinity by combining tentative consensus sequences. Transcripts annotated by BLAST2Go and differently expressed transcripts were analyzed. A total of 208 up-regulated and 182 down-regulated transcripts were found that involve in plastid, starch and sucrose metabolism, glycerolipid metabolism and glycerolipid and dicarboxylate metabolism. Our results demonstrate that RNA-Seq can be successfully used for gene identification, transcript profiling in wheat. Furthermore these sequences will provide valuable resources for wheat researchers.