Gibum Yi | Chungnam National University (original) (raw)

Papers by Gibum Yi

Applied Biological Chemistry

Phytosterols are important structural components of plant cells that affect membrane fluidity, pe... more Phytosterols are important structural components of plant cells that affect membrane fluidity, permeability, and membrane-related metabolic regulation. These compounds, which are abundant in vegetable oils and corn kernel oil, are also beneficial for human health. Cultivation of corn (Zea mays L.) produces huge amounts of cobs as a by-product, but efforts to utilize cobs are still limited. Here, we investigated phytosterol, crude oil, and fatty acid contents in the kernels and cobs of four major corn cultivars in South Korea and explored the potential use of cobs as a source of phytosterols. Total phytosterol levels were two times higher in cobs (68.0–217.1 mg 100 g−1 DW) than in kernels (43.8–89.5 mg 100 g−1 DW) and were highest in the kernels and cobs of Sinhwangok at 60 days after pollination. We showed that not only kernels but also cobs can be a rich source of phytosterols. The results also revealed that the amount of phytosterol is depending on a genetic background as well as ...

Additional file 1: Table S1. Summary of F1 samples and their usage for analysis (DOCX 2531 kb). T... more Additional file 1: Table S1. Summary of F1 samples and their usage for analysis (DOCX 2531 kb). Table S2. Summary of RNA-seq reads. Table S3. Top 5 enriched GO terms of the genes having expression correlation with the phenotypes in F1 hybrids. Table S4. Top 5 enriched GO terms of the genes have expression correlation with the metabolite contents in F1 hybrids. Table S5. Orthologous pair genes and their primers used for qRT-PCR analysis. Figure S1. Leaf shapes of the newly synthesized allodiploid xBrassicoraphanus. Figure S2. Pollen shapes of the newly synthesized allodiploid xBrassicoraphanus. Figure S3. Chromosome numbers for CF, WK, and CWB. 19 chromosomes (univalents) were observed in allodiploid F1 hybrid (C), whereas 10 and 9 chromosome pairs (bivalents) were observed in CF (A) and WK (B), respectively. Chromosome spreads were obtained from pollen mother cells in diakinesis of meiosis. Bars = 10 μm. Figure S4. Concentrations of metabolites for four biological replicates for the...

Strawberry is an important fruit crop and a model for studying non-climacteric fruit ripening. Fr... more Strawberry is an important fruit crop and a model for studying non-climacteric fruit ripening. Fruit ripening and senescence influence strawberry fruit quality and postharvest storability, and have been intensively studied. However, genetic and physiological differences among cultivars preclude consensus understanding of these processes. We therefore performed a meta-analysis by mapping existing transcriptome data to the newly published and improved strawberry reference genome and extracted meta-differentially expressed genes (meta-DEGs) from six cultivars to provide an expanded transcriptomic view of strawberry ripening. We identified cultivar-specific transcriptome changes in anthocyanin biosynthesis-related genes and common changes in cell wall degradation, chlorophyll degradation, and starch metabolism-related genes during ripening. We also identified 483 meta-DEGs enriched in gene ontology categories related to photosynthesis and amino acid and fatty acid biosynthesis that had ...

Applied Biological Chemistry

Purple waxy corn is a good source of antioxidant compounds such as anthocyanins and polyphenols. ... more Purple waxy corn is a good source of antioxidant compounds such as anthocyanins and polyphenols. Promotion of its use requires an appropriate assay to determine antioxidant activity. The aim of this study is to verify compatibility of the antioxidant activity assays by comparing five different assays in daily kernel samples of the fresh purple waxy corn during grain filling. The levels of antioxidants measured by 2,2-diphenyl-1-picrylhydrazyl, ferric reducing antioxidant power, and chemiluminescence showed significant positive correlations with the levels measured by the other assays (r = 0.761–0.893; p 0.699; p

The Korean Journal of Crop Science, 2020

Recently in Korea, soybean harvesting has been delayed due to rainfall during the harvesting seas... more Recently in Korea, soybean harvesting has been delayed due to rainfall during the harvesting season, resulting in a reduction in yield and seed quality. This study was conducted to analyze the changes in yield and seed quality during delayed harvest with rainfall treatment using different harvesting methods, including field harvesting and polyethylene film covering after cutting fully-matured soybean plants (PE covering after cutting), with two major Korean soybean cultivars (Glycine max L), Pungsannamulkong and Daewonkong. The shattering rate of Pungsannamulkong, which is higher than that of Daewonkong, increased up to 41.8% when the harvest was delayed for 40 days without rainfall treatment by harvesting with PE covering after cutting. The weight of 100 seeds tended to decrease slightly as harvesting was delayed. When Daewonkong was harvested using the PE covering after cutting method with rainfall treatment, the yield decreased to the lowest level with a 0.8 kg ha-1 daily reducti...

Applied Biological Chemistry, 2021

Corn ( Zea mays L.) provides a major source of calories for human consumption and therefore, the ... more Corn ( Zea mays L.) provides a major source of calories for human consumption and therefore, the nutritional components of corn have a large impact on human health. For example, corn kernels contain antioxidants, such as polyphenols (including anthocyanins and other flavonoids) and carotenoids. Such compounds represent useful targets for biofortification breeding. In this study, we used 34 corn inbred lines from three different regions (East Asia, Southern Asia, and subtropical regions) and 11 F 1 hybrids derived from the inbreds to investigate antioxidant activity in yellow corn. We compared different methods for measuring antioxidant activity to test their consistency and to determine whether color could be used as an indicator of antioxidant activity. We also measured carotenoid levels in yellow corn. No difference in antioxidant activity was detected between inbred corn lines from temperate vs. tropical regions. We determined that carotenoid is a major contributor to antioxidant...

ABSTRACT Expressional alteration of duplicated genes after polyploidization is a largely unknown ... more ABSTRACT Expressional alteration of duplicated genes after polyploidization is a largely unknown process. To investigate the polyploidization effect, we performed NGS-associated transcriptome analyses of a synthetic intergeneric hybrid xBrassicoraphanus cv. BB1 and its two representative parents, Brassica rapa accession Chiifu-401-42 and Raphanus sativus accession WG10039. Through de novo assemblies and homology analyses, we obtained 8,367 homologous unigene sets from these three species. Most of unigenes which showed altered expressions were down-regulated in BB1, and 87% of paralogs in BB1 was attuned their expression to the similar level. Considering the mid-parent phenotypes in the hybrid progeny, the global downward attunements of transcriptome might be a causal step to stabilize the coexistence of two distinct genomes in a single organism. These approaches give us more detailed insight into the expressional alteration of each paralogs in BB1, compare to the hybridization based mid-parent value approaches.

Korean Journal of Breeding, 2005

Genes & Genomics

Background Hybridization and polyploidization events are important driving forces in plant evolut... more Background Hybridization and polyploidization events are important driving forces in plant evolution. Allopolyploids formed between different species can be naturally or artificially created but often suffer from genetic instability and infertility in successive generations. xBrassicoraphanus is an intergeneric allopolyploid obtained from a cross between Brassica rapa and Raphanus sativus, providing a useful resource for genetic and genomic study in hybrid species. Objective The current study aims to understand the cause of hybrid sterility and pollen abnormality in different lines of synthetic xBrassicoraphanus from the cytogenetic perspective. Methods Alexander staining was used to assess the pollen viability. Cytogenetic analysis was employed to monitor meiotic chromosome behaviors in pollen mother cells (PMCs). Origins of parental chromosomes in xBrassicoraphanus meiocytes were determined by genome in situ hybridization analysis. Results The xBrassicoraphanus lines BB#4 and BB#6...

Postharvest Biology and Technology

Hybridization and polyploidization are pivotal to plant evolution. Genetic crosses between distan... more Hybridization and polyploidization are pivotal to plant evolution. Genetic crosses between distantly related species rarely occur in nature mainly due to reproductive barriers but how such hurdles can be overcome is largely unknown. xBrassicoraphanus is a fertile intergeneric allopolyploid synthesized between Brassica rapa and Raphanus sativus in the Brassicaceae family. Genomes of B. rapa and R. sativus are diverged enough to suppress synapsis formation between non-homologous progenitor chromosomes during meiosis, and we found that both genomes reside in the single nucleus of xBrassicoraphanus without genome loss or rearrangement. Expressions of syntenic orthologs identified in B. rapa and R. sativus were adjusted to a hybrid nuclear environment of xBrassicoraphanus, which necessitates reconfiguration of transcription network by rewiring cis-trans interactions. B. rapa coding sequences have a higher level of gene-body methylation than R. sativus, and such methylation asymmetry is m...

Korean Journal of Breeding Science

BMC Plant Biology

Background Heterosis is biologically important but the molecular basis of the phenomenon is poorl... more Background Heterosis is biologically important but the molecular basis of the phenomenon is poorly understood. We characterized intergeneric hybrids between B. rapa cv. Chiifu and R. sativus cv. WK10039 as an extreme example of heterosis. Taking advantage of clear heterosis phenotypes and the genetic distance between parents, we performed transcriptome and metabolite analysis to decipher the molecular basis of heterosis. Results The heterosis was expressed as fresh weight in the field and as inflorescence stem length in the glass house. Flowering time, distributed as a normal segregating population, ranged from the early flowering of one parent to the late flowering of the other, in contrast to the homogeneous flowering time in a typical F1 population, indicating unstable allelic interactions. The transcriptome and metabolome both indicated that sugar metabolism was altered, suggesting that the change in metabolism was linked to the heterosis. Because alleles were not shared between...

Scientific Reports

Pepper (Capsicum annuum L.) fruit is sensitive to temperatures below 10 °C, which severely dimini... more Pepper (Capsicum annuum L.) fruit is sensitive to temperatures below 10 °C, which severely diminish fruit quality during cold chain distribution. Seed browning was a major chilling symptom in 36 genotypes of C. annuum fruit screened after storage at 2 °C for 3 weeks. Among them, pepper fruits of chilling-insensitive ‘UZB-GJG-1999–51’ and -sensitive ‘C00562’ were treated at 2 °C for 0 or 24 h, respectively. Analyses of integrated transcriptome-metabolome and relative gene expression in seeds obtained from the two genotypes were conducted to identify key factors involved in the seed browning induced by chilling. The relative contents of branched-chain amino acids such as leucine, isoleucine, and valine were significantly increased after chilling. Transcriptome identification showed 3,140 differentially expressed genes (log twofold change > 1.0 and FDR-corrected p value

Applied Biological Chemistry

Phytosterols are important structural components of plant cells that affect membrane fluidity, pe... more Phytosterols are important structural components of plant cells that affect membrane fluidity, permeability, and membrane-related metabolic regulation. These compounds, which are abundant in vegetable oils and corn kernel oil, are also beneficial for human health. Cultivation of corn (Zea mays L.) produces huge amounts of cobs as a by-product, but efforts to utilize cobs are still limited. Here, we investigated phytosterol, crude oil, and fatty acid contents in the kernels and cobs of four major corn cultivars in South Korea and explored the potential use of cobs as a source of phytosterols. Total phytosterol levels were two times higher in cobs (68.0–217.1 mg 100 g−1 DW) than in kernels (43.8–89.5 mg 100 g−1 DW) and were highest in the kernels and cobs of Sinhwangok at 60 days after pollination. We showed that not only kernels but also cobs can be a rich source of phytosterols. The results also revealed that the amount of phytosterol is depending on a genetic background as well as ...

Additional file 1: Table S1. Summary of F1 samples and their usage for analysis (DOCX 2531 kb). T... more Additional file 1: Table S1. Summary of F1 samples and their usage for analysis (DOCX 2531 kb). Table S2. Summary of RNA-seq reads. Table S3. Top 5 enriched GO terms of the genes having expression correlation with the phenotypes in F1 hybrids. Table S4. Top 5 enriched GO terms of the genes have expression correlation with the metabolite contents in F1 hybrids. Table S5. Orthologous pair genes and their primers used for qRT-PCR analysis. Figure S1. Leaf shapes of the newly synthesized allodiploid xBrassicoraphanus. Figure S2. Pollen shapes of the newly synthesized allodiploid xBrassicoraphanus. Figure S3. Chromosome numbers for CF, WK, and CWB. 19 chromosomes (univalents) were observed in allodiploid F1 hybrid (C), whereas 10 and 9 chromosome pairs (bivalents) were observed in CF (A) and WK (B), respectively. Chromosome spreads were obtained from pollen mother cells in diakinesis of meiosis. Bars = 10 μm. Figure S4. Concentrations of metabolites for four biological replicates for the...

Strawberry is an important fruit crop and a model for studying non-climacteric fruit ripening. Fr... more Strawberry is an important fruit crop and a model for studying non-climacteric fruit ripening. Fruit ripening and senescence influence strawberry fruit quality and postharvest storability, and have been intensively studied. However, genetic and physiological differences among cultivars preclude consensus understanding of these processes. We therefore performed a meta-analysis by mapping existing transcriptome data to the newly published and improved strawberry reference genome and extracted meta-differentially expressed genes (meta-DEGs) from six cultivars to provide an expanded transcriptomic view of strawberry ripening. We identified cultivar-specific transcriptome changes in anthocyanin biosynthesis-related genes and common changes in cell wall degradation, chlorophyll degradation, and starch metabolism-related genes during ripening. We also identified 483 meta-DEGs enriched in gene ontology categories related to photosynthesis and amino acid and fatty acid biosynthesis that had ...

Applied Biological Chemistry

Purple waxy corn is a good source of antioxidant compounds such as anthocyanins and polyphenols. ... more Purple waxy corn is a good source of antioxidant compounds such as anthocyanins and polyphenols. Promotion of its use requires an appropriate assay to determine antioxidant activity. The aim of this study is to verify compatibility of the antioxidant activity assays by comparing five different assays in daily kernel samples of the fresh purple waxy corn during grain filling. The levels of antioxidants measured by 2,2-diphenyl-1-picrylhydrazyl, ferric reducing antioxidant power, and chemiluminescence showed significant positive correlations with the levels measured by the other assays (r = 0.761–0.893; p 0.699; p

The Korean Journal of Crop Science, 2020

Recently in Korea, soybean harvesting has been delayed due to rainfall during the harvesting seas... more Recently in Korea, soybean harvesting has been delayed due to rainfall during the harvesting season, resulting in a reduction in yield and seed quality. This study was conducted to analyze the changes in yield and seed quality during delayed harvest with rainfall treatment using different harvesting methods, including field harvesting and polyethylene film covering after cutting fully-matured soybean plants (PE covering after cutting), with two major Korean soybean cultivars (Glycine max L), Pungsannamulkong and Daewonkong. The shattering rate of Pungsannamulkong, which is higher than that of Daewonkong, increased up to 41.8% when the harvest was delayed for 40 days without rainfall treatment by harvesting with PE covering after cutting. The weight of 100 seeds tended to decrease slightly as harvesting was delayed. When Daewonkong was harvested using the PE covering after cutting method with rainfall treatment, the yield decreased to the lowest level with a 0.8 kg ha-1 daily reducti...

Applied Biological Chemistry, 2021

Corn ( Zea mays L.) provides a major source of calories for human consumption and therefore, the ... more Corn ( Zea mays L.) provides a major source of calories for human consumption and therefore, the nutritional components of corn have a large impact on human health. For example, corn kernels contain antioxidants, such as polyphenols (including anthocyanins and other flavonoids) and carotenoids. Such compounds represent useful targets for biofortification breeding. In this study, we used 34 corn inbred lines from three different regions (East Asia, Southern Asia, and subtropical regions) and 11 F 1 hybrids derived from the inbreds to investigate antioxidant activity in yellow corn. We compared different methods for measuring antioxidant activity to test their consistency and to determine whether color could be used as an indicator of antioxidant activity. We also measured carotenoid levels in yellow corn. No difference in antioxidant activity was detected between inbred corn lines from temperate vs. tropical regions. We determined that carotenoid is a major contributor to antioxidant...

ABSTRACT Expressional alteration of duplicated genes after polyploidization is a largely unknown ... more ABSTRACT Expressional alteration of duplicated genes after polyploidization is a largely unknown process. To investigate the polyploidization effect, we performed NGS-associated transcriptome analyses of a synthetic intergeneric hybrid xBrassicoraphanus cv. BB1 and its two representative parents, Brassica rapa accession Chiifu-401-42 and Raphanus sativus accession WG10039. Through de novo assemblies and homology analyses, we obtained 8,367 homologous unigene sets from these three species. Most of unigenes which showed altered expressions were down-regulated in BB1, and 87% of paralogs in BB1 was attuned their expression to the similar level. Considering the mid-parent phenotypes in the hybrid progeny, the global downward attunements of transcriptome might be a causal step to stabilize the coexistence of two distinct genomes in a single organism. These approaches give us more detailed insight into the expressional alteration of each paralogs in BB1, compare to the hybridization based mid-parent value approaches.

Korean Journal of Breeding, 2005

Genes & Genomics

Background Hybridization and polyploidization events are important driving forces in plant evolut... more Background Hybridization and polyploidization events are important driving forces in plant evolution. Allopolyploids formed between different species can be naturally or artificially created but often suffer from genetic instability and infertility in successive generations. xBrassicoraphanus is an intergeneric allopolyploid obtained from a cross between Brassica rapa and Raphanus sativus, providing a useful resource for genetic and genomic study in hybrid species. Objective The current study aims to understand the cause of hybrid sterility and pollen abnormality in different lines of synthetic xBrassicoraphanus from the cytogenetic perspective. Methods Alexander staining was used to assess the pollen viability. Cytogenetic analysis was employed to monitor meiotic chromosome behaviors in pollen mother cells (PMCs). Origins of parental chromosomes in xBrassicoraphanus meiocytes were determined by genome in situ hybridization analysis. Results The xBrassicoraphanus lines BB#4 and BB#6...

Postharvest Biology and Technology

Hybridization and polyploidization are pivotal to plant evolution. Genetic crosses between distan... more Hybridization and polyploidization are pivotal to plant evolution. Genetic crosses between distantly related species rarely occur in nature mainly due to reproductive barriers but how such hurdles can be overcome is largely unknown. xBrassicoraphanus is a fertile intergeneric allopolyploid synthesized between Brassica rapa and Raphanus sativus in the Brassicaceae family. Genomes of B. rapa and R. sativus are diverged enough to suppress synapsis formation between non-homologous progenitor chromosomes during meiosis, and we found that both genomes reside in the single nucleus of xBrassicoraphanus without genome loss or rearrangement. Expressions of syntenic orthologs identified in B. rapa and R. sativus were adjusted to a hybrid nuclear environment of xBrassicoraphanus, which necessitates reconfiguration of transcription network by rewiring cis-trans interactions. B. rapa coding sequences have a higher level of gene-body methylation than R. sativus, and such methylation asymmetry is m...

Korean Journal of Breeding Science

BMC Plant Biology

Background Heterosis is biologically important but the molecular basis of the phenomenon is poorl... more Background Heterosis is biologically important but the molecular basis of the phenomenon is poorly understood. We characterized intergeneric hybrids between B. rapa cv. Chiifu and R. sativus cv. WK10039 as an extreme example of heterosis. Taking advantage of clear heterosis phenotypes and the genetic distance between parents, we performed transcriptome and metabolite analysis to decipher the molecular basis of heterosis. Results The heterosis was expressed as fresh weight in the field and as inflorescence stem length in the glass house. Flowering time, distributed as a normal segregating population, ranged from the early flowering of one parent to the late flowering of the other, in contrast to the homogeneous flowering time in a typical F1 population, indicating unstable allelic interactions. The transcriptome and metabolome both indicated that sugar metabolism was altered, suggesting that the change in metabolism was linked to the heterosis. Because alleles were not shared between...

Scientific Reports

Pepper (Capsicum annuum L.) fruit is sensitive to temperatures below 10 °C, which severely dimini... more Pepper (Capsicum annuum L.) fruit is sensitive to temperatures below 10 °C, which severely diminish fruit quality during cold chain distribution. Seed browning was a major chilling symptom in 36 genotypes of C. annuum fruit screened after storage at 2 °C for 3 weeks. Among them, pepper fruits of chilling-insensitive ‘UZB-GJG-1999–51’ and -sensitive ‘C00562’ were treated at 2 °C for 0 or 24 h, respectively. Analyses of integrated transcriptome-metabolome and relative gene expression in seeds obtained from the two genotypes were conducted to identify key factors involved in the seed browning induced by chilling. The relative contents of branched-chain amino acids such as leucine, isoleucine, and valine were significantly increased after chilling. Transcriptome identification showed 3,140 differentially expressed genes (log twofold change > 1.0 and FDR-corrected p value