Transcriptomic analysis of differentially expressed genes in an orange-pericarp mutant and wild type in pummelo (Citrus grandis)
Identifieur interne : 000391 ( Main/Exploration ); précédent : 000390; suivant : 000392Transcriptomic analysis of differentially expressed genes in an orange-pericarp mutant and wild type in pummelo (Citrus grandis)
Auteurs : Fei Guo [République populaire de Chine] ; Huiwen Yu [République populaire de Chine] ; Qiang Xu [République populaire de Chine] ; Xiuxin Deng [République populaire de Chine]Source :
- BMC Plant Biology [ 1471-2229 ] ; 2015.
Abstract
The external colour of fruit is a crucial quality feature, and the external coloration of most citrus fruits is due to the accumulation of carotenoids. The molecular regulation of carotenoid biosynthesis and accumulation in pericarp is limited due to the lack of mutant. In this work, an
High Performance Liquid Chromatography (HPLC) analysis revealed that the pericarp from MT fruits had a 10.5-fold increase of β-carotene content over that of the Wild Type (WT). Quantitative real-time PCR (qRT-PCR) analysis showed that the expression of all downstream carotenogenic genes was lower in MT than in WT, suggesting that down-regulation is critical for the β-carotene increase in the MT pericarp. RNA-seq analysis of the transcriptome revealed extensive changes in the MT gene expression level, with 168 genes down-regulated and 135 genes up-regulated. Gene ontology (GO) and KEGG pathway analyses indicated seven reliable metabolic pathways are altered in the mutant, including carbon metabolism, starch and sucrose metabolism and biosynthesis of amino acids. The transcription factors and genes corresponding to effected metabolic pathways may involved in the carotenoid regulation was confirmed by the qRT-PCR analysis in the MT pericarp.
This study has provided a global picture of the gene expression changes in a novel mutant with distinct color in the fruit pericarp of pummelo. Interpretation of differentially expressed genes (DEGs) revealed new insight into the molecular regulation of β-carotene accumulation in the MT pericarp.
The online version of this article (doi:10.1186/s12870-015-0435-3) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12870-015-0435-3
PubMed: 25849782
PubMed Central: 4352283
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Transcriptomic analysis of differentially expressed genes in an <italic>orange-pericarp</italic> mutant and wild type in pummelo (<italic>Citrus grandis</italic>)</title><author><name sortKey="Guo, Fei" sort="Guo, Fei" uniqKey="Guo F" first="Fei" last="Guo">Fei Guo</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan</wicri:regionArea><wicri:noRegion>Wuhan</wicri:noRegion></affiliation></author><author><name sortKey="Yu, Huiwen" sort="Yu, Huiwen" uniqKey="Yu H" first="Huiwen" last="Yu">Huiwen Yu</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan</wicri:regionArea><wicri:noRegion>Wuhan</wicri:noRegion></affiliation></author><author><name sortKey="Xu, Qiang" sort="Xu, Qiang" uniqKey="Xu Q" first="Qiang" last="Xu">Qiang Xu</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan</wicri:regionArea><wicri:noRegion>Wuhan</wicri:noRegion></affiliation></author><author><name sortKey="Deng, Xiuxin" sort="Deng, Xiuxin" uniqKey="Deng X" first="Xiuxin" last="Deng">Xiuxin Deng</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan</wicri:regionArea><wicri:noRegion>Wuhan</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25849782</idno><idno type="pmc">4352283</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4352283</idno><idno type="RBID">PMC:4352283</idno><idno type="doi">10.1186/s12870-015-0435-3</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000625</idno><idno type="wicri:Area/Pmc/Curation">000624</idno><idno type="wicri:Area/Pmc/Checkpoint">000305</idno><idno type="wicri:Area/Ncbi/Merge">001A73</idno><idno type="wicri:Area/Ncbi/Curation">001A73</idno><idno type="wicri:Area/Ncbi/Checkpoint">001A73</idno><idno type="wicri:Area/Main/Merge">000391</idno><idno type="wicri:Area/Main/Curation">000391</idno><idno type="wicri:Area/Main/Exploration">000391</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Transcriptomic analysis of differentially expressed genes in an <italic>orange-pericarp</italic> mutant and wild type in pummelo (<italic>Citrus grandis</italic>)</title><author><name sortKey="Guo, Fei" sort="Guo, Fei" uniqKey="Guo F" first="Fei" last="Guo">Fei Guo</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan</wicri:regionArea><wicri:noRegion>Wuhan</wicri:noRegion></affiliation></author><author><name sortKey="Yu, Huiwen" sort="Yu, Huiwen" uniqKey="Yu H" first="Huiwen" last="Yu">Huiwen Yu</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan</wicri:regionArea><wicri:noRegion>Wuhan</wicri:noRegion></affiliation></author><author><name sortKey="Xu, Qiang" sort="Xu, Qiang" uniqKey="Xu Q" first="Qiang" last="Xu">Qiang Xu</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan</wicri:regionArea><wicri:noRegion>Wuhan</wicri:noRegion></affiliation></author><author><name sortKey="Deng, Xiuxin" sort="Deng, Xiuxin" uniqKey="Deng X" first="Xiuxin" last="Deng">Xiuxin Deng</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan</wicri:regionArea><wicri:noRegion>Wuhan</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Plant Biology</title><idno type="eISSN">1471-2229</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>The external colour of fruit is a crucial quality feature, and the external coloration of most citrus fruits is due to the accumulation of carotenoids. The molecular regulation of carotenoid biosynthesis and accumulation in pericarp is limited due to the lack of mutant. In this work, an <italic>orange-pericarp</italic> mutant (MT) which showed altered pigmentation in the pericarp was used to identify genes potentially related to the regulation of carotenoid accumulation in the pericarp.</p></sec><sec><title>Results</title><p>High Performance Liquid Chromatography (HPLC) analysis revealed that the pericarp from MT fruits had a 10.5-fold increase of β-carotene content over that of the Wild Type (WT). Quantitative real-time PCR (qRT-PCR) analysis showed that the expression of all downstream carotenogenic genes was lower in MT than in WT, suggesting that down-regulation is critical for the β-carotene increase in the MT pericarp. RNA-seq analysis of the transcriptome revealed extensive changes in the MT gene expression level, with 168 genes down-regulated and 135 genes up-regulated. Gene ontology (GO) and KEGG pathway analyses indicated seven reliable metabolic pathways are altered in the mutant, including carbon metabolism, starch and sucrose metabolism and biosynthesis of amino acids. The transcription factors and genes corresponding to effected metabolic pathways may involved in the carotenoid regulation was confirmed by the qRT-PCR analysis in the MT pericarp.</p></sec><sec><title>Conclusions</title><p>This study has provided a global picture of the gene expression changes in a novel mutant with distinct color in the fruit pericarp of pummelo. Interpretation of differentially expressed genes (DEGs) revealed new insight into the molecular regulation of β-carotene accumulation in the MT pericarp.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12870-015-0435-3) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Talon, M" uniqKey="Talon M">M Talon</name></author><author><name sortKey="Gmitter, Fg" uniqKey="Gmitter F">FG Gmitter</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Alquezar, B" uniqKey="Alquezar B">B Alquézar</name></author><author><name sortKey="Rodrigo, M" uniqKey="Rodrigo M">M Rodrigo</name></author><author><name sortKey="Zacarias, L" uniqKey="Zacarias L">L Zacarías</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Demmig Adams, B" uniqKey="Demmig 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Schmittgen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yun, Z" uniqKey="Yun Z">Z Yun</name></author><author><name sortKey="Gao, Hj" uniqKey="Gao H">HJ Gao</name></author><author><name sortKey="Liu, P" uniqKey="Liu P">P Liu</name></author><author><name sortKey="Liu, Sz" uniqKey="Liu S">SZ Liu</name></author><author><name sortKey="Luo, T" uniqKey="Luo T">T Luo</name></author><author><name sortKey="Jin, S" uniqKey="Jin S">S Jin</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Guo, Fei" sort="Guo, Fei" uniqKey="Guo F" first="Fei" last="Guo">Fei Guo</name></noRegion><name sortKey="Deng, Xiuxin" sort="Deng, Xiuxin" uniqKey="Deng X" first="Xiuxin" last="Deng">Xiuxin Deng</name><name sortKey="Xu, Qiang" sort="Xu, Qiang" uniqKey="Xu Q" first="Qiang" last="Xu">Qiang 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