Metabolomic Variability of Different Soybean Genotypes: β-Carotene-Enhanced (Glycine max), Wild (Glycine soja), and Hybrid (Glycine max × Glycine soja) Soybeans

Jung, Jung-Won; Park, Soo-Yun; Oh, Sung‐Dug; Jang, Yejin; Suh, Sang-Jae; Park, Soon-Ki; Ha, Sun-Hwa; Park, Sang Un; Kim, Jae Kwang

doi:10.3390/foods10102421

Cited by 9 publications

(14 citation statements)

References 49 publications

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“…34,35 Furthermore, as plants mature, they activate their secondary metabolism, which results in an increase in phytosterols. 20 Therefore, phytosterol, a senescence-related metabolite, was increased in R3−5 stages.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

Metabolite Changes in Soybean (Glycine max) Leaves during the Entire Growth Period

Park,

Lee,

Park

et al. 2023

ACS Omega

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Although soybean (Glycine max) leaves generate building blocks to produce seeds, a comprehensive understanding of the metabolic changes in soybean leaves during the entire growth stages is limited. Here, we investigated the metabolite changes in soybean leaves from five cultivars among four vegetative (V) and eight reproductive (R) stages using metabolite profiling coupled with chemometrics. Principal component analysis (PCA) of all samples showed a clear separation by growth stage. The total amount of monosaccharides and organic acids for energy production were highly detected in the V stage samples, accumulating in concentrations 2.5 and 1.7 times higher than in the R stage samples, respectively. The results of partial least-squares-discriminant analysis (PLS-DA) revealed a clear separation from R1 to R5 by the first PLS, suggesting significant alterations in the metabolic networks up to R5. After flowering, the stage of seed formation, R5, was associated with lower levels of most amino acids and an accumulation of phytosterols. The negative correlation observed between amino acids and phytosterol levels suggests a sophisticated coordination between carbon and nitrogen metabolism in plant, ensuring and supporting optimal growth (r = −0.50085, P = 0.0001). In addition, R-stage samples had decreased monosaccharide levels, indicating redistribution to seeds and senescence-related metabolite changes. Thus, metabolite profiling coupled with chemometrics could be a useful tool for investigating alterations in metabolic networks during various plant growth and development stages. Furthermore, we observed variations in flavonoid contents among the different cultivars. The results could be a basis of further studies on the source−sink interactions in the plant system.

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Section: ■ Results and Discussionmentioning

confidence: 99%

Metabolite Changes in Soybean (Glycine max) Leaves during the Entire Growth Period

Park,

Lee,

Park

et al. 2023

ACS Omega

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“…To date, many studies have explored the molecular mechanisms by using “omics” methods such as transcriptomics ( Lou et al, 2017 ; Yuan et al, 2021 ), proteomics ( Hu et al, 2017 ; Hochholdinger et al, 2018 ), and metabolomics ( Kumar et al, 2017 ; Sharma et al, 2021 ). By comparing the omics expression characteristics between different samples, the genes controlling various phenotypes can be identified ( Jung et al, 2021 ). Previous studies have mostly investigated the effect of a certain gene or enzyme in the nicotine synthesis pathway; however, none of the studies have investigated the key regulatory factors affecting nicotine synthesis and metabolism from the perspective of proteomics ( Wang et al, 2011 ; Yin et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

Proteomics and Co-expression Network Analysis Reveal the Importance of Hub Proteins and Metabolic Pathways in Nicotine Synthesis and Accumulation in Tobacco (Nicotiana tabacum L.)

Duan

et al. 2022

Front. Plant Sci.

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Nicotine is a unique alkaloid present in tobacco that is widely used in cigarettes and in the agricultural, chemical, and pharmaceutical industries. However, the research on nicotine is mostly limited to its synthesis pathways, and only a few studies have explored the effects of other metabolic pathways on nicotine precursors. Regulating the nicotine content in tobacco can greatly promoting the application of nicotine in other fields. In this study, we performed global data-independent acquisition proteomics analysis of four tobacco varieties. Of the four varieties, one had high nicotine content and three had a low nicotine content. A total of 31,259 distinct peptides and 6,018 proteins across two samples were identified. A total of 45 differentially expressed proteins (DEPs) co-existed in the three comparison groups and were mainly involved in the transport and metallic processes of the substances. Most DEPs were enriched in the biosynthesis of secondary metals, glutathione metabolism, carbon metabolism, and glycolysis/gluconeogenesis. In addition, the weighted gene co-expression network analysis identified an expression module closely related to the nicotine content (Brown, r = 0.74, P = 0.006). Gene Ontology annotation and Kyoto Encyclopaedia of Genes and Genomes enrichment analysis showed that the module proteins were mainly involved in the synthesis and metabolism of nicotine precursors such as arginine, ornithine aspartate, proline, and glutathione. The increased levels of these precursors lead to the synthesis and accumulation of nicotine in plants. More importantly, these proteins regulate nicotine synthesis by affecting the formation of putrescine, which is the core intermediate product in nicotine anabolism. Our results provide a reference for tobacco variety selection with a suitable nicotine content and regulation of the nicotine content. Additionally, the results highlight the importance of other precursor metabolism in nicotine synthesis.

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“…Hybridization may occur with (allopolyploidization) or without (homoploid hybridization) a concomitant increase in ploidy level. Both outcomes involve the merger of genomes from each parental species, causing major disruptions at every level of an organism's cellular biology: genomic (McClintock, 1984; Qin et al, 2016), transcriptomic (Cox et al, 2014; Depotter et al, 2021; McElroy et al, 2017; Yoo et al, 2013), proteomic (Holá et al, 2017; Koh et al, 2012; Ueno et al, 2019) and metabolomic (Jung et al, 2021; Zhang et al, 2019). However, successful adaptation to these challenges can confer new advantages on the hybrid, due to intergenomic heterosis (hybrid vigour) and enhanced genomic redundancy (Adams & Wendel, 2005; Baranwal et al, 2012; Fujimoto et al, 2018; Gu et al, 2003).…”

Section: Introductionmentioning

confidence: 99%

“…hybridization) a concomitant increase in ploidy level. Both outcomes involve the merger of genomes from each parental species, causing major disruptions at every level of an organism's cellular biology: genomic (McClintock, 1984;Qin et al, 2016), transcriptomic (Cox et al, 2014;Depotter et al, 2021;McElroy et al, 2017;Yoo et al, 2013), proteomic (Holá et al, 2017;Koh et al, 2012;Ueno et al, 2019) and metabolomic (Jung et al, 2021;.…”

mentioning

confidence: 99%

Cross‐kingdom transcriptomic trends in the evolution of hybrid gene expression

Behling

Winter

Ganley

et al. 2022

J of Evolutionary Biology

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Hybridization is a route to speciation that occurs widely across the eukaryote tree of life. The success of allopolyploids (hybrid species with increased ploidy) and homoploid hybrids (with unchanged ploidy) is well documented. However, their formation and establishment is not straightforward, with a suite of near‐instantaneous and longer term biological repercussions faced by the new species. Central to these challenges is the rewiring of gene regulatory networks following the merger of distinct genomes inherited from both parental species. Research on the evolution of hybrid gene expression has largely involved studies on a single hybrid species or a few gene families. Here, we present the first standardized transcriptome‐wide study exploring the fates of genes following hybridization across three kingdoms: animals, plants and fungi. Within each kingdom, we pair an allopolyploid system with a closely related homoploid hybrid to decouple the influence of increased ploidy from genome merger. Genome merger, not changes in ploidy, has the greatest effect on posthybridization expression patterns across all study systems. Strikingly, we find that differentially expressed genes in parent species preferentially switch to more similar expression in hybrids across all kingdoms, likely as a consequence of regulatory trans‐acting cross‐talk within the hybrid nucleus. We also highlight the prevalence of gene loss or silencing among extremely differentially expressed genes in hybrid species across all kingdoms. These shared patterns suggest that the evolutionary process of hybridization leads to common high‐level expression outcomes, regardless of the particular species or kingdom.

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Metabolomic Variability of Different Soybean Genotypes: β-Carotene-Enhanced (Glycine max), Wild (Glycine soja), and Hybrid (Glycine max × Glycine soja) Soybeans

Cited by 9 publications

References 49 publications

Metabolite Changes in Soybean (Glycine max) Leaves during the Entire Growth Period

Metabolite Changes in Soybean (Glycine max) Leaves during the Entire Growth Period

Proteomics and Co-expression Network Analysis Reveal the Importance of Hub Proteins and Metabolic Pathways in Nicotine Synthesis and Accumulation in Tobacco (Nicotiana tabacum L.)

Cross‐kingdom transcriptomic trends in the evolution of hybrid gene expression

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