Identification and Comparative Analysis of microRNA in Wheat (Triticum aestivum L.) Callus Derived from Mature and Immature Embryos during In vitro Culture
Identifieur interne : 002172 ( Ncbi/Merge ); précédent : 002171; suivant : 002173Identification and Comparative Analysis of microRNA in Wheat (Triticum aestivum L.) Callus Derived from Mature and Immature Embryos during In vitro Culture
Auteurs : Zongli Chu ; Junying Chen ; Haixia Xu ; Zhongdong Dong ; Feng Chen ; Dangqun CuiSource :
- Frontiers in Plant Science [ 1664-462X ] ; 2016.
Abstract
Feasible and efficient tissue culture plays an important role in plant genetic engineering. Wheat (
Url:
DOI: 10.3389/fpls.2016.01302
PubMed: 27625667
PubMed Central: 5003897
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Identification and Comparative Analysis of microRNA in Wheat (<italic>Triticum aestivum</italic> L.) Callus Derived from Mature and Immature Embryos during <italic>In vitro</italic> Culture</title><author><name sortKey="Chu, Zongli" sort="Chu, Zongli" uniqKey="Chu Z" first="Zongli" last="Chu">Zongli Chu</name></author><author><name sortKey="Chen, Junying" sort="Chen, Junying" uniqKey="Chen J" first="Junying" last="Chen">Junying Chen</name></author><author><name sortKey="Xu, Haixia" sort="Xu, Haixia" uniqKey="Xu H" first="Haixia" last="Xu">Haixia Xu</name></author><author><name sortKey="Dong, Zhongdong" sort="Dong, Zhongdong" uniqKey="Dong Z" first="Zhongdong" last="Dong">Zhongdong Dong</name></author><author><name sortKey="Chen, Feng" sort="Chen, Feng" uniqKey="Chen F" first="Feng" last="Chen">Feng Chen</name></author><author><name sortKey="Cui, Dangqun" sort="Cui, Dangqun" uniqKey="Cui D" first="Dangqun" last="Cui">Dangqun Cui</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27625667</idno><idno type="pmc">5003897</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5003897</idno><idno type="RBID">PMC:5003897</idno><idno type="doi">10.3389/fpls.2016.01302</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000F37</idno><idno type="wicri:Area/Pmc/Curation">000F36</idno><idno type="wicri:Area/Pmc/Checkpoint">000143</idno><idno type="wicri:Area/Ncbi/Merge">002172</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Identification and Comparative Analysis of microRNA in Wheat (<italic>Triticum aestivum</italic> L.) Callus Derived from Mature and Immature Embryos during <italic>In vitro</italic> Culture</title><author><name sortKey="Chu, Zongli" sort="Chu, Zongli" uniqKey="Chu Z" first="Zongli" last="Chu">Zongli Chu</name></author><author><name sortKey="Chen, Junying" sort="Chen, Junying" uniqKey="Chen J" first="Junying" last="Chen">Junying Chen</name></author><author><name sortKey="Xu, Haixia" sort="Xu, Haixia" uniqKey="Xu H" first="Haixia" last="Xu">Haixia Xu</name></author><author><name sortKey="Dong, Zhongdong" sort="Dong, Zhongdong" uniqKey="Dong Z" first="Zhongdong" last="Dong">Zhongdong Dong</name></author><author><name sortKey="Chen, Feng" sort="Chen, Feng" uniqKey="Chen F" first="Feng" last="Chen">Feng Chen</name></author><author><name sortKey="Cui, Dangqun" sort="Cui, Dangqun" uniqKey="Cui D" first="Dangqun" last="Cui">Dangqun Cui</name></author></analytic><series><title level="j">Frontiers in Plant Science</title><idno type="eISSN">1664-462X</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Feasible and efficient tissue culture plays an important role in plant genetic engineering. Wheat (<italic>Triticum aestivum</italic> L.) immature embryos (IMEs) are preferred for tissue culture to mature embryos (MEs) because IMEs easily generate embryogenic callus, producing large number of plants. The molecular mechanisms of regulation and the biological pathways involved in embryogenic callus formation in wheat remain unclear. Here, microRNAs (miRNAs) potentially involved in embryogenic callus formation and somatic embryogenesis were identified through deep sequencing of small RNAs (sRNAs) and analyzed with bioinformatics tools. Six sRNA libraries derived from calli of IMEs and MEs after 3, 6, or 15 d of culture (DC) were constructed and sequenced. A total of 85 known miRNAs were identified, of which 30, 33, and 18 were differentially expressed (<italic>P</italic> < 0.05) between the IME and ME libraries at 3, 6, and 15 DC, respectively. Additionally, 171 novel and 41 candidate miRNAs were also identified, of the novel miRNA, 69, 67, and 37 were differentially expressed (<italic>P</italic> < 0.05) between the two types of libraries at 3, 6, and 15 DC, respectively. The expression patterns of eight known and eight novel miRNAs were validated using quantitative real-time polymerase chain reaction. Gene ontology annotation of differentially expressed miRNA targets provided information regarding the underlying molecular functions, biological processes, and cellular components involved in embryogenic callus development. Functional miRNAs, such as miR156, miR164, miR1432, miR398, and miR397, differentially expressed in IMEs and MEs might be related to embryogenic callus formation and somatic embryogenesis. This study suggests that miRNA plays an important role in embryogenic callus formation and somatic embryogenesis in wheat, and our data provide a useful resource for further research.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Anil, V S" uniqKey="Anil V">V. S. Anil</name></author><author><name sortKey="Rao, K S" uniqKey="Rao K">K. S. Rao</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Allen, R S" uniqKey="Allen R">R. S. Allen</name></author><author><name sortKey="Li, J" uniqKey="Li J">J. Li</name></author><author><name sortKey="Stahle, M I" uniqKey="Stahle M">M. I. Stahle</name></author><author><name sortKey="Dubroue, A" uniqKey="Dubroue A">A. Dubroué</name></author><author><name sortKey="Gubler, F" uniqKey="Gubler F">F. Gubler</name></author><author><name sortKey="Millar, A A" uniqKey="Millar A">A. A. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Front Plant Sci</journal-id><journal-id journal-id-type="iso-abbrev">Front Plant Sci</journal-id><journal-id journal-id-type="publisher-id">Front. Plant Sci.</journal-id><journal-title-group><journal-title>Frontiers in Plant Science</journal-title></journal-title-group><issn pub-type="epub">1664-462X</issn><publisher><publisher-name>Frontiers Media S.A.</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">27625667</article-id><article-id pub-id-type="pmc">5003897</article-id><article-id pub-id-type="doi">10.3389/fpls.2016.01302</article-id><article-categories><subj-group subj-group-type="heading"><subject>Plant Science</subject><subj-group><subject>Original Research</subject></subj-group></subj-group></article-categories><title-group><article-title>Identification and Comparative Analysis of microRNA in Wheat (<italic>Triticum aestivum</italic> L.) Callus Derived from Mature and Immature Embryos during <italic>In vitro</italic> Culture</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Chu</surname><given-names>Zongli</given-names></name><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/345949/overview"></uri></contrib><contrib contrib-type="author"><name><surname>Chen</surname><given-names>Junying</given-names></name></contrib><contrib contrib-type="author"><name><surname>Xu</surname><given-names>Haixia</given-names></name></contrib><contrib contrib-type="author"><name><surname>Dong</surname><given-names>Zhongdong</given-names></name></contrib><contrib contrib-type="author"><name><surname>Chen</surname><given-names>Feng</given-names></name><xref ref-type="author-notes" rid="fn001"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>Cui</surname><given-names>Dangqun</given-names></name><xref ref-type="author-notes" rid="fn002"><sup>*</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/273992/overview"></uri></contrib></contrib-group><aff><institution>National Key Laboratory of Wheat and Maize Science, Collaborative Innovation Center of Henan Grain Crops, Agronomy College, Henan Agricultural University</institution><country>Zhengzhou, China</country></aff><author-notes><fn fn-type="edited-by"><p>Edited by: Claudio Bonghi, University of Padua, Italy</p></fn><fn fn-type="edited-by"><p>Reviewed by: Shengwu Hu, Northwest A&F University, China; Jihua Tang, Henan Agricultural University, China</p></fn><corresp id="fn001">*Correspondence: Feng Chen <email xlink:type="simple">chf0088@163.com</email></corresp><corresp id="fn002">Dangqun Cui <email xlink:type="simple">cdq62@sohu.com</email></corresp><fn fn-type="other" id="fn003"><p>This article was submitted to Crop Science and Horticulture, a section of the journal Frontiers in Plant Science</p></fn></author-notes><pub-date pub-type="epub"><day>30</day><month>8</month><year>2016</year></pub-date><pub-date pub-type="collection"><year>2016</year></pub-date><volume>7</volume><elocation-id>1302</elocation-id><history><date date-type="received"><day>03</day><month>5</month><year>2016</year></date><date date-type="accepted"><day>15</day><month>8</month><year>2016</year></date></history><permissions><copyright-statement>Copyright © 2016 Chu, Chen, Xu, Dong, Chen and Cui.</copyright-statement><copyright-year>2016</copyright-year><copyright-holder>Chu, Chen, Xu, Dong, Chen and Cui</copyright-holder><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</license-p></license></permissions><abstract><p>Feasible and efficient tissue culture plays an important role in plant genetic engineering. Wheat (<italic>Triticum aestivum</italic> L.) immature embryos (IMEs) are preferred for tissue culture to mature embryos (MEs) because IMEs easily generate embryogenic callus, producing large number of plants. The molecular mechanisms of regulation and the biological pathways involved in embryogenic callus formation in wheat remain unclear. Here, microRNAs (miRNAs) potentially involved in embryogenic callus formation and somatic embryogenesis were identified through deep sequencing of small RNAs (sRNAs) and analyzed with bioinformatics tools. Six sRNA libraries derived from calli of IMEs and MEs after 3, 6, or 15 d of culture (DC) were constructed and sequenced. A total of 85 known miRNAs were identified, of which 30, 33, and 18 were differentially expressed (<italic>P</italic> < 0.05) between the IME and ME libraries at 3, 6, and 15 DC, respectively. Additionally, 171 novel and 41 candidate miRNAs were also identified, of the novel miRNA, 69, 67, and 37 were differentially expressed (<italic>P</italic> < 0.05) between the two types of libraries at 3, 6, and 15 DC, respectively. The expression patterns of eight known and eight novel miRNAs were validated using quantitative real-time polymerase chain reaction. Gene ontology annotation of differentially expressed miRNA targets provided information regarding the underlying molecular functions, biological processes, and cellular components involved in embryogenic callus development. Functional miRNAs, such as miR156, miR164, miR1432, miR398, and miR397, differentially expressed in IMEs and MEs might be related to embryogenic callus formation and somatic embryogenesis. This study suggests that miRNA plays an important role in embryogenic callus formation and somatic embryogenesis in wheat, and our data provide a useful resource for further research.</p></abstract><kwd-group><kwd>wheat (<italic>Triticum aestivum</italic> L.)</kwd><kwd>embryogenic callus</kwd><kwd>immature embryo</kwd><kwd>mature embryo</kwd><kwd>microRNA</kwd></kwd-group><counts><fig-count count="9"></fig-count><table-count count="8"></table-count><equation-count count="0"></equation-count><ref-count count="81"></ref-count><page-count count="20"></page-count><word-count count="12503"></word-count></counts></article-meta></front></pmc><affiliations><list></list><tree><noCountry><name sortKey="Chen, Feng" sort="Chen, Feng" uniqKey="Chen F" first="Feng" last="Chen">Feng Chen</name><name sortKey="Chen, Junying" sort="Chen, Junying" uniqKey="Chen J" first="Junying" last="Chen">Junying Chen</name><name sortKey="Chu, Zongli" sort="Chu, Zongli" uniqKey="Chu Z" first="Zongli" last="Chu">Zongli Chu</name><name sortKey="Cui, Dangqun" sort="Cui, Dangqun" uniqKey="Cui D" first="Dangqun" last="Cui">Dangqun Cui</name><name sortKey="Dong, Zhongdong" sort="Dong, Zhongdong" uniqKey="Dong Z" first="Zhongdong" last="Dong">Zhongdong Dong</name><name sortKey="Xu, Haixia" sort="Xu, Haixia" uniqKey="Xu H" first="Haixia" last="Xu">Haixia Xu</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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