Elucidation of the molecular responses to waterlogging in Jatropha roots by transcriptome profiling.
Identifieur interne : 002257 ( Main/Exploration ); précédent : 002256; suivant : 002258Elucidation of the molecular responses to waterlogging in Jatropha roots by transcriptome profiling.
Auteurs : Piyada Juntawong [Thaïlande] ; Anchalee Sirikhachornkit [Thaïlande] ; Rachaneeporn Pimjan [Thaïlande] ; Chutima Sonthirod [Thaïlande] ; Duangjai Sangsrakru [Thaïlande] ; Thippawan Yoocha [Thaïlande] ; Sithichoke Tangphatsornruang [Thaïlande] ; Peerasak Srinives [Thaïlande]Source :
- Frontiers in plant science [ 1664-462X ] ; 2014.
Abstract
Jatropha (Jatropha curcas) is a promising oil-seed crop for biodiesel production. However, the species is highly sensitive to waterlogging, which can result in stunted growth and yield loss. To date, the molecular mechanisms underlying the responses to waterlogging in Jatropha remain elusive. Here, the transcriptome adjustment of Jatropha roots to waterlogging was examined by high-throughput RNA-sequencing (RNA-seq). The results indicated that 24 h of waterlogging caused significant changes in mRNA abundance of 1968 genes. Comprehensive gene ontology and functional enrichment analysis of root transcriptome revealed that waterlogging promoted responses to hypoxia and anaerobic respiration. On the other hand, the stress inhibited carbohydrate synthesis, cell wall biogenesis, and growth. The results also highlighted the roles of ethylene, nitrate, and nitric oxide in waterlogging acclimation. In addition, transcriptome profiling identified 85 waterlogging-induced transcription factors including members of AP2/ERF, MYB, and WRKY families implying that reprogramming of gene expression is a vital mechanism for waterlogging acclimation. Comparative analysis of differentially regulated transcripts in response to waterlogging among Arabidopsis, gray poplar, Jatropha, and rice further revealed not only conserved but species-specific regulation. Our findings unraveled the molecular responses to waterlogging in Jatropha and provided new perspectives for developing a waterlogging tolerant cultivar in the future.
DOI: 10.3389/fpls.2014.00658
PubMed: 25520726
PubMed Central: PMC4251292
Affiliations:
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xml:lang="fr">Thaïlande</country><wicri:regionArea>Special Research Unit in Microalgal Molecular Genetics and Functional Genomics, Department of Genetics, Faculty of Science, Kasetsart University Bangkok</wicri:regionArea><wicri:noRegion>Kasetsart University Bangkok</wicri:noRegion></affiliation></author><author><name sortKey="Sirikhachornkit, Anchalee" sort="Sirikhachornkit, Anchalee" uniqKey="Sirikhachornkit A" first="Anchalee" last="Sirikhachornkit">Anchalee Sirikhachornkit</name><affiliation wicri:level="1"><nlm:affiliation>Special Research Unit in Microalgal Molecular Genetics and Functional Genomics, Department of Genetics, Faculty of Science, Kasetsart University Bangkok, Thailand.</nlm:affiliation><country xml:lang="fr">Thaïlande</country><wicri:regionArea>Special Research Unit in Microalgal Molecular Genetics and Functional Genomics, Department of Genetics, Faculty of Science, Kasetsart University Bangkok</wicri:regionArea><wicri:noRegion>Kasetsart University Bangkok</wicri:noRegion></affiliation></author><author><name sortKey="Pimjan, Rachaneeporn" sort="Pimjan, Rachaneeporn" uniqKey="Pimjan R" first="Rachaneeporn" last="Pimjan">Rachaneeporn Pimjan</name><affiliation wicri:level="1"><nlm:affiliation>Special Research Unit in Microalgal Molecular Genetics and Functional Genomics, Department of Genetics, Faculty of Science, Kasetsart University Bangkok, Thailand.</nlm:affiliation><country xml:lang="fr">Thaïlande</country><wicri:regionArea>Special Research Unit in Microalgal Molecular Genetics and Functional Genomics, Department of Genetics, Faculty of Science, Kasetsart University Bangkok</wicri:regionArea><wicri:noRegion>Kasetsart University Bangkok</wicri:noRegion></affiliation></author><author><name sortKey="Sonthirod, Chutima" sort="Sonthirod, Chutima" uniqKey="Sonthirod C" first="Chutima" last="Sonthirod">Chutima Sonthirod</name><affiliation wicri:level="1"><nlm:affiliation>National Center for Genetic Engineering and Biotechnology Pathumthani, Thailand.</nlm:affiliation><country xml:lang="fr">Thaïlande</country><wicri:regionArea>National Center for Genetic Engineering and Biotechnology Pathumthani</wicri:regionArea></affiliation></author><author><name sortKey="Sangsrakru, Duangjai" sort="Sangsrakru, Duangjai" uniqKey="Sangsrakru D" first="Duangjai" last="Sangsrakru">Duangjai Sangsrakru</name><affiliation wicri:level="1"><nlm:affiliation>National Center for Genetic Engineering and Biotechnology Pathumthani, Thailand.</nlm:affiliation><country xml:lang="fr">Thaïlande</country><wicri:regionArea>National Center for Genetic Engineering and Biotechnology Pathumthani</wicri:regionArea></affiliation></author><author><name sortKey="Yoocha, Thippawan" sort="Yoocha, Thippawan" uniqKey="Yoocha T" first="Thippawan" last="Yoocha">Thippawan Yoocha</name><affiliation wicri:level="1"><nlm:affiliation>National Center for Genetic Engineering and Biotechnology Pathumthani, Thailand.</nlm:affiliation><country xml:lang="fr">Thaïlande</country><wicri:regionArea>National Center for Genetic Engineering and Biotechnology Pathumthani</wicri:regionArea></affiliation></author><author><name sortKey="Tangphatsornruang, Sithichoke" sort="Tangphatsornruang, Sithichoke" uniqKey="Tangphatsornruang S" first="Sithichoke" last="Tangphatsornruang">Sithichoke Tangphatsornruang</name><affiliation wicri:level="1"><nlm:affiliation>National Center for Genetic Engineering and Biotechnology Pathumthani, Thailand.</nlm:affiliation><country xml:lang="fr">Thaïlande</country><wicri:regionArea>National Center for Genetic Engineering and Biotechnology Pathumthani</wicri:regionArea></affiliation></author><author><name sortKey="Srinives, Peerasak" sort="Srinives, Peerasak" uniqKey="Srinives P" first="Peerasak" last="Srinives">Peerasak Srinives</name><affiliation wicri:level="1"><nlm:affiliation>Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University Nakhon Pathom, Thailand.</nlm:affiliation><country xml:lang="fr">Thaïlande</country><wicri:regionArea>Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University Nakhon Pathom</wicri:regionArea><wicri:noRegion>Kasetsart University Nakhon Pathom</wicri:noRegion></affiliation></author></analytic><series><title level="j">Frontiers in plant science</title><idno type="ISSN">1664-462X</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Jatropha (Jatropha curcas) is a promising oil-seed crop for biodiesel production. However, the species is highly sensitive to waterlogging, which can result in stunted growth and yield loss. To date, the molecular mechanisms underlying the responses to waterlogging in Jatropha remain elusive. Here, the transcriptome adjustment of Jatropha roots to waterlogging was examined by high-throughput RNA-sequencing (RNA-seq). The results indicated that 24 h of waterlogging caused significant changes in mRNA abundance of 1968 genes. Comprehensive gene ontology and functional enrichment analysis of root transcriptome revealed that waterlogging promoted responses to hypoxia and anaerobic respiration. On the other hand, the stress inhibited carbohydrate synthesis, cell wall biogenesis, and growth. The results also highlighted the roles of ethylene, nitrate, and nitric oxide in waterlogging acclimation. In addition, transcriptome profiling identified 85 waterlogging-induced transcription factors including members of AP2/ERF, MYB, and WRKY families implying that reprogramming of gene expression is a vital mechanism for waterlogging acclimation. Comparative analysis of differentially regulated transcripts in response to waterlogging among Arabidopsis, gray poplar, Jatropha, and rice further revealed not only conserved but species-specific regulation. Our findings unraveled the molecular responses to waterlogging in Jatropha and provided new perspectives for developing a waterlogging tolerant cultivar in the future. </div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">25520726</PMID><DateCompleted><Year>2014</Year><Month>12</Month><Day>18</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-462X</ISSN><JournalIssue CitedMedium="Print"><Volume>5</Volume><PubDate><Year>2014</Year></PubDate></JournalIssue><Title>Frontiers in plant science</Title><ISOAbbreviation>Front Plant Sci</ISOAbbreviation></Journal><ArticleTitle>Elucidation of the molecular responses to waterlogging in Jatropha roots by transcriptome profiling.</ArticleTitle><Pagination><MedlinePgn>658</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fpls.2014.00658</ELocationID><Abstract><AbstractText>Jatropha (Jatropha curcas) is a promising oil-seed crop for biodiesel production. However, the species is highly sensitive to waterlogging, which can result in stunted growth and yield loss. To date, the molecular mechanisms underlying the responses to waterlogging in Jatropha remain elusive. Here, the transcriptome adjustment of Jatropha roots to waterlogging was examined by high-throughput RNA-sequencing (RNA-seq). The results indicated that 24 h of waterlogging caused significant changes in mRNA abundance of 1968 genes. Comprehensive gene ontology and functional enrichment analysis of root transcriptome revealed that waterlogging promoted responses to hypoxia and anaerobic respiration. On the other hand, the stress inhibited carbohydrate synthesis, cell wall biogenesis, and growth. The results also highlighted the roles of ethylene, nitrate, and nitric oxide in waterlogging acclimation. In addition, transcriptome profiling identified 85 waterlogging-induced transcription factors including members of AP2/ERF, MYB, and WRKY families implying that reprogramming of gene expression is a vital mechanism for waterlogging acclimation. Comparative analysis of differentially regulated transcripts in response to waterlogging among Arabidopsis, gray poplar, Jatropha, and rice further revealed not only conserved but species-specific regulation. Our findings unraveled the molecular responses to waterlogging in Jatropha and provided new perspectives for developing a waterlogging tolerant cultivar in the future. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Juntawong</LastName><ForeName>Piyada</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Special Research Unit in Microalgal Molecular Genetics and Functional Genomics, Department of Genetics, Faculty of Science, Kasetsart University Bangkok, Thailand.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sirikhachornkit</LastName><ForeName>Anchalee</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Special Research Unit in Microalgal Molecular Genetics and Functional Genomics, Department of Genetics, Faculty of Science, Kasetsart University Bangkok, Thailand.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pimjan</LastName><ForeName>Rachaneeporn</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Special Research Unit in Microalgal Molecular Genetics and Functional Genomics, Department of Genetics, Faculty of Science, Kasetsart University Bangkok, Thailand.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sonthirod</LastName><ForeName>Chutima</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>National Center for Genetic Engineering and Biotechnology Pathumthani, Thailand.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sangsrakru</LastName><ForeName>Duangjai</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>National Center for Genetic Engineering and Biotechnology Pathumthani, Thailand.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yoocha</LastName><ForeName>Thippawan</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>National Center for Genetic Engineering and Biotechnology Pathumthani, Thailand.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tangphatsornruang</LastName><ForeName>Sithichoke</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>National Center for Genetic Engineering and Biotechnology Pathumthani, Thailand.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Srinives</LastName><ForeName>Peerasak</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University Nakhon Pathom, Thailand.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>12</Month><Day>02</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Plant Sci</MedlineTA><NlmUniqueID>101568200</NlmUniqueID><ISSNLinking>1664-462X</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">ERFs</Keyword><Keyword MajorTopicYN="N">Jatropha curcas</Keyword><Keyword MajorTopicYN="N">RNA-seq</Keyword><Keyword MajorTopicYN="N">genomics</Keyword><Keyword MajorTopicYN="N">low oxygen</Keyword><Keyword MajorTopicYN="N">transcriptional control</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2014</Year><Month>05</Month><Day>20</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2014</Year><Month>11</Month><Day>04</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>12</Month><Day>19</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>12</Month><Day>19</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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