Comparative transcriptome analysis implied a ZEP paralog was a key gene involved in carotenoid accumulation in yellow-fleshed sweetpotato

Suematsu, Koichi; Tanaka, Masaru; Kurata, Rie; Yu, Kai

doi:10.1038/s41598-020-77293-7

Cited by 20 publications

(19 citation statements)

References 57 publications

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“…Our results showed that the three PSY genes have differentially expressed patterns during the panicle development stage, suggesting that they have differential functions in regulating carotenoid metabolism ux [49]. Additionally, many studies have demonstrated that ZEP is an important node for ne-tuning carotenoid metabolism in Arabidopsis [50,51]. The SNP variants of ZEP in sorghum and Arabidopsis were signi cantly correlated with the zeaxanthin content and lutein/zeaxanthin ratio [52,53].…”

Section: Characteristics Of Carotenoid Content Variations In Plantsmentioning

confidence: 60%

Comparative Metabolomic And Transcriptomic Analysis Reveals A Coexpression Network of The Carotenoid Metabolism Pathway In The Panicle of Setaria Italica

Han

Huo

et al. 2021

Preprint

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[Background]The grains of foxtail millet are enriched in carotenoids, which endow this plant with a yellow color and extremely high nutritional value. However, the underlying molecular regulation mechanism and gene coexpression network remain unclear.[Methods] The carotenoid species and content were detected by HPLC for two foxtail millet varieties at three panicle development stages. Based on a homologous sequence BLAST analysis, these genes related to carotenoid metabolism were identified from the foxtail millet genome database. The conserved protein domains, chromosome locations, gene structures and phylogenetic trees were analyzed using bioinformatics tools. RNA-seq was performed for these samples to identify differentially expressed genes (DEGs). A Pearson correlation analysis was performed between the expression of genes related to carotenoid metabolism and the content of carotenoid metabolites. Furthermore, the expression levels of the key DEGs were verified by qRT-PCR. The gene coexpression network was constructed by a weighted gene coexpression network analysis (WGCNA).[Result] The major carotenoid metabolites in the panicles of DHD and JG21 were lutein and β-carotene. These carotenoid metabolite contents sharply decreased during the panicle development stage. The lutein and β-carotene contents were highest at the S1 stage of DHD, with values of 11.474 μg/100 mg and 12.524 μg/100 mg, respectively. Fifty-four genes related to carotenoid metabolism were identified in the foxtail millet genome. Cis-acting element analysis showed that these gene promoters mainly contain ‘light-responsive’ and ‘ABA-responsive’ elements. In the carotenoid metabolic pathways, SiHDS, SiHMGS3, SiPDS and SiNCED1 were more highly expressed in the panicle of foxtail millet. The expression of SiCMT, SiAACT3, SiPSY1, SiZEP1/2, and SiCCD8c/8d was significantly correlated with the lutein content. The expression of SiCMT, SiHDR, SiIDI2, SiAACT3, SiPSY1, and SiZEP1/2 was significantly correlated with the content of β-carotene. WGCNA showed that the coral module was highly correlated with lutein and β-carotene, and 13 structural genes from the carotenoid biosynthetic pathway were identified. Network visualization revealed 25 intramodular hub genes that putatively control carotenoid metabolism.[Conclusion] Based on the integrative analysis of the transcriptomics and carotenoid metabonomics, we found that DEGs related to carotenoid metabolism had a stronger correlation with the key carotenoid metabolite content. The correlation analysis and WGCNA identified and predicted the gene regulation network related to carotenoid metabolism. These results lay the foundation for exploring the key target genes regulating carotenoid metabolism flux in the panicle of foxtail millet. We hope that these target genes could be used to genetically modify millet to enhance the carotenoid content in the future.

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Section: Characteristics Of Carotenoid Content Variations In Plantsmentioning

confidence: 60%

Comparative Metabolomic And Transcriptomic Analysis Reveals A Coexpression Network of The Carotenoid Metabolism Pathway In The Panicle of Setaria Italica

Han

Huo

et al. 2021

Preprint

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“…Studies have shown that CRTISO (prolycopene isomerase) is one of the enzymes that catalyze the synthesis of lycopene from phytoene, and has a critical role in carotenoid biosynthesis pathway in the dark and in nonphotosynthetic tissues (Isaacson et al, 2002). Suematsu et al (Suematsu et al, 2020) identified ZEP paralog (g1103.t1) as a key gene involves in carotenoid accumulation by regulating epoxidation of b-carotene and b-cryptoxanthin in yellowfleshed sweetpotato. Cytochrome P450 (CYP97) family is the key enzyme that catalyzes carotene to produce xanthophylls (Li and Wei 2020).…”

Section: The Key Genes Involved In Carotenoid Metabolic Pathwaymentioning

confidence: 99%

“…In the δ-carotene branch, lutein is finally produced by lycopene ϵ-cyclase ( LCYE ), lycopene β-cyclase ( LCYB ), and carotenoid ϵ-hydroxylase (CYP97C1) and β-carotene hydroxylase ( CHYB ). In the γ-carotene branch, the carotenoids synthesized with the help of lycopene β-cyclase ( LCYB ), β-carotene hydroxylase ( CHYB ), zeaxanthin epoxidase ( ZEP ), violaxanthin de-epoxidase ( VDE ) ( Liu et al., 2020 ; Suematsu et al., 2020 ; Xu et al., 2021 ; KEGG, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

“…The main carotenoid in orange-fleshed sweetpotato is β-carotene (80–92%), whereas other carotenoids constitute less than 2% of the total in three different cultivars ( Ishiguro et al., 2010 ). Some genes encoding enzymes in the carotenoid metabolic pathway, including PSY , PDS , ZDS , CRTISO , LCYB , LCYE , CHYB , ZEP, 9-cis-epoxycarotenoid dioxygenase ( NCED ), and carotenoid cleavage dioxygenases ( CCD ), have previously been cloned and characterized in sweetpotato ( Kim et al., 2013 ; Kang et al., 2017 ; Kang et al., 2018 ; Suematsu et al., 2020 ). It is reported that silencing of CHYB , LCYB , or LCYE using RNAi increases carotenoid accumulation and resistance to abiotic stress such as heat, drought, and salt in transgenic sweetpotato plants and calli ( Kim et al., 2012 ; Kim et al., 2013 ; Kim et al., 2014 ; Kang et al., 2017 ; Kang et al., 2018 ; Ke et al., 2019 ).…”

Section: Introductionmentioning

confidence: 99%

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Integrated analysis of carotenoid metabolites and transcriptome identifies key genes controlling carotenoid compositions and content in sweetpotato tuberous roots (Ipomoea batatas L.)

et al. 2022

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Sweetpotato (Ipomoea batatas L.) with different depths of yellow color contains different compositions of carotenoids, which are beneficial for human health. In this study, we performed an integrated analysis of metabolomic and transcriptomic to identify key genes playing a major role in carotenoid coloration in sweetpotato tuberous roots. Herein, 14 carotenoids were identified in five sweetpotatoes. Orange-red and orange cultivars were dominated by β-carotene (385.33 μg/g and 85.07 μg/g), yellow cultivar had a high β-cryptoxanthin (11.23 μg/g), light-yellow cultivar was rich in zeaxanthin (5.12 μg/g), whereas lutein (3.34 μg/g) was the main carotenoid in white cultivar. Furthermore, 27 differentially expressed genes involved in carotenoid metabolism were identified based on comparative transcriptome. Weighted gene co-expression network analysis identified 15 transcription factors highly associated with carotenoid content in sweetpotatoes. These results provide valuable information for revealing the regulatory mechanism of carotenoid metabolism in different-colored sweetpotato tuberous roots.

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“…However, there are no reports regarding the molecular mechanisms underlying weevil resistance in sweetpotato using transcriptome-based analysis. Recently, with the decreasing costs and increasing throughput of NGS technology, several groups have reported large-scale transcriptome studies in sweetpotato, revealing the key genes and a comprehensive knowledge of the mechanisms underlying important agricultural traits [ 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 ]. In addition, the whole genome sequence and functionally annotated genes of the closely related diploid species Ipomoea trifida have been previously released [ 21 , 22 , 23 ].…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Analysis Reveals Key Genes Involved in Weevil Resistance in the Hexaploid Sweetpotato

Nokihara

Okada

Ohata

et al. 2021

Plants

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Because weevils are the most damaging pests of sweetpotato, the development of cultivars resistant to weevil species is considered the most important aspect in sweetpotato breeding. However, the genes and the underlying molecular mechanisms related to weevil resistance are yet to be elucidated. In this study, we performed an RNA sequencing-based transcriptome analysis using the resistant Kyushu No. 166 (K166) and susceptible Tamayutaka cultivars. The weevil resistance test showed a significant difference between the two cultivars at 30 days after the inoculation, specifically in the weevil growth stage and the suppressed weevil pupation that was only observed in K166. Differential expression and gene ontology analyses revealed that the genes upregulated after inoculation in K166 were related to phosphorylation, metabolic, and cellular processes. Because the weevil resistance was considered to be related to the suppression of larval pupation, we investigated the juvenile hormone (JH)-related genes involved in the inhibition of insect metamorphosis. We found that the expression of some terpenoid-related genes, which are classified as plant-derived JHs, was significantly increased in K166. This is the first study involving a comprehensive gene expression analysis that provides new insights about the genes and mechanisms associated with weevil resistance in sweetpotato.

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Comparative transcriptome analysis implied a ZEP paralog was a key gene involved in carotenoid accumulation in yellow-fleshed sweetpotato

Cited by 20 publications

References 57 publications

Comparative Metabolomic And Transcriptomic Analysis Reveals A Coexpression Network of The Carotenoid Metabolism Pathway In The Panicle of Setaria Italica

Comparative Metabolomic And Transcriptomic Analysis Reveals A Coexpression Network of The Carotenoid Metabolism Pathway In The Panicle of Setaria Italica

Integrated analysis of carotenoid metabolites and transcriptome identifies key genes controlling carotenoid compositions and content in sweetpotato tuberous roots (Ipomoea batatas L.)

Transcriptome Analysis Reveals Key Genes Involved in Weevil Resistance in the Hexaploid Sweetpotato

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