Selection of reliable reference genes for quantitative real-time PCR gene expression analysis in Jute (Corchorus capsularis) under stress treatments
Identifieur interne : 000085 ( Pmc/Curation ); précédent : 000084; suivant : 000086Selection of reliable reference genes for quantitative real-time PCR gene expression analysis in Jute (Corchorus capsularis) under stress treatments
Auteurs : Xiaoping Niu [République populaire de Chine] ; Jianmin Qi [République populaire de Chine] ; Gaoyang Zhang [République populaire de Chine] ; Jiantang Xu [République populaire de Chine] ; Aifen Tao [République populaire de Chine] ; Pingping Fang [République populaire de Chine] ; Jianguang Su [République populaire de Chine]Source :
- Frontiers in Plant Science [ 1664-462X ] ; 2015.
Abstract
To accurately measure gene expression using quantitative reverse transcription PCR (qRT-PCR), reliable reference gene(s) are required for data normalization.
Url:
DOI: 10.3389/fpls.2015.00848
PubMed: 26528312
PubMed Central: 4604321
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Selection of reliable reference genes for quantitative real-time PCR gene expression analysis in Jute (<italic>Corchorus capsularis</italic>) under stress treatments</title><author><name sortKey="Niu, Xiaoping" sort="Niu, Xiaoping" uniqKey="Niu X" first="Xiaoping" last="Niu">Xiaoping Niu</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University</institution><country>Fuzhou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Qi, Jianmin" sort="Qi, Jianmin" uniqKey="Qi J" first="Jianmin" last="Qi">Jianmin Qi</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University</institution><country>Fuzhou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Zhang, Gaoyang" sort="Zhang, Gaoyang" uniqKey="Zhang G" first="Gaoyang" last="Zhang">Gaoyang Zhang</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University</institution><country>Fuzhou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>College of Life Sciences, Shangrao Normal University</institution><country>Shangrao, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Xu, Jiantang" sort="Xu, Jiantang" uniqKey="Xu J" first="Jiantang" last="Xu">Jiantang Xu</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University</institution><country>Fuzhou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Tao, Aifen" sort="Tao, Aifen" uniqKey="Tao A" first="Aifen" last="Tao">Aifen Tao</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University</institution><country>Fuzhou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Fang, Pingping" sort="Fang, Pingping" uniqKey="Fang P" first="Pingping" last="Fang">Pingping Fang</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University</institution><country>Fuzhou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Su, Jianguang" sort="Su, Jianguang" uniqKey="Su J" first="Jianguang" last="Su">Jianguang Su</name><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences</institution><country>Changsha, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26528312</idno><idno type="pmc">4604321</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4604321</idno><idno type="RBID">PMC:4604321</idno><idno type="doi">10.3389/fpls.2015.00848</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000085</idno><idno type="wicri:Area/Pmc/Curation">000085</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Selection of reliable reference genes for quantitative real-time PCR gene expression analysis in Jute (<italic>Corchorus capsularis</italic>) under stress treatments</title><author><name sortKey="Niu, Xiaoping" sort="Niu, Xiaoping" uniqKey="Niu X" first="Xiaoping" last="Niu">Xiaoping Niu</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University</institution><country>Fuzhou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Qi, Jianmin" sort="Qi, Jianmin" uniqKey="Qi J" first="Jianmin" last="Qi">Jianmin Qi</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University</institution><country>Fuzhou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Zhang, Gaoyang" sort="Zhang, Gaoyang" uniqKey="Zhang G" first="Gaoyang" last="Zhang">Gaoyang Zhang</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University</institution><country>Fuzhou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>College of Life Sciences, Shangrao Normal University</institution><country>Shangrao, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Xu, Jiantang" sort="Xu, Jiantang" uniqKey="Xu J" first="Jiantang" last="Xu">Jiantang Xu</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University</institution><country>Fuzhou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Tao, Aifen" sort="Tao, Aifen" uniqKey="Tao A" first="Aifen" last="Tao">Aifen Tao</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University</institution><country>Fuzhou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Fang, Pingping" sort="Fang, Pingping" uniqKey="Fang P" first="Pingping" last="Fang">Pingping Fang</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University</institution><country>Fuzhou, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Su, Jianguang" sort="Su, Jianguang" uniqKey="Su J" first="Jianguang" last="Su">Jianguang Su</name><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences</institution><country>Changsha, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author></analytic><series><title level="j">Frontiers in Plant Science</title><idno type="eISSN">1664-462X</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>To accurately measure gene expression using quantitative reverse transcription PCR (qRT-PCR), reliable reference gene(s) are required for data normalization. <italic>Corchorus capsularis</italic>, an annual herbaceous fiber crop with predominant biodegradability and renewability, has not been investigated for the stability of reference genes with qRT-PCR. In this study, 11 candidate reference genes were selected and their expression levels were assessed using qRT-PCR. To account for the influence of experimental approach and tissue type, 22 different jute samples were selected from abiotic and biotic stress conditions as well as three different tissue types. The stability of the candidate reference genes was evaluated using geNorm, NormFinder, and BestKeeper programs, and the comprehensive rankings of gene stability were generated by aggregate analysis. For the biotic stress and NaCl stress subsets, <italic>ACT7</italic> and <italic>RAN</italic> were suitable as stable reference genes for gene expression normalization. For the PEG stress subset, <italic>UBC</italic>, and <italic>DnaJ</italic> were sufficient for accurate normalization. For the tissues subset, four reference genes <italic>TUB</italic>β, <italic>UBI, EF1</italic>α, and <italic>RAN</italic> were sufficient for accurate normalization. The selected genes were further validated by comparing expression profiles of <italic>WRKY15</italic> in various samples, and two stable reference genes were recommended for accurate normalization of qRT-PCR data. Our results provide researchers with appropriate reference genes for qRT-PCR in <italic>C</italic>. <italic>capsularis</italic>, and will facilitate gene expression study under these conditions.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Alam, M M" uniqKey="Alam M">M. M. Alam</name></author><author><name sortKey="Sharmin, S" uniqKey="Sharmin S">S. Sharmin</name></author><author><name sortKey="Nabi, Z" uniqKey="Nabi Z">Z. Nabi</name></author><author><name sortKey="Mondal, S I" uniqKey="Mondal S">S. I. Mondal</name></author><author><name sortKey="Islam, M S" uniqKey="Islam M">M. S. Islam</name></author><author><name sortKey="Bin Nayeem, S" uniqKey="Bin Nayeem S">S. 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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">26528312</article-id><article-id pub-id-type="pmc">4604321</article-id><article-id pub-id-type="doi">10.3389/fpls.2015.00848</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>Selection of reliable reference genes for quantitative real-time PCR gene expression analysis in Jute (<italic>Corchorus capsularis</italic>) under stress treatments</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Niu</surname><given-names>Xiaoping</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/263356/overview"></uri></contrib><contrib contrib-type="author"><name><surname>Qi</surname><given-names>Jianmin</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="author-notes" rid="fn001"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Gaoyang</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Xu</surname><given-names>Jiantang</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Tao</surname><given-names>Aifen</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Fang</surname><given-names>Pingping</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Su</surname><given-names>Jianguang</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref><xref ref-type="author-notes" rid="fn002"><sup>*</sup></xref></contrib></contrib-group><aff id="aff1"><sup>1</sup><institution>Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University</institution><country>Fuzhou, China</country></aff><aff id="aff2"><sup>2</sup><institution>College of Life Sciences, Shangrao Normal University</institution><country>Shangrao, China</country></aff><aff id="aff3"><sup>3</sup><institution>Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences</institution><country>Changsha, China</country></aff><author-notes><fn fn-type="edited-by"><p>Edited by: Ashraf El-Kereamy, University of California Cooperative Extension, Kern county, USA</p></fn><fn fn-type="edited-by"><p>Reviewed by: Qingshun Quinn Li, Western University of Health Sciences, USA; M. Teresa Sanchez-Ballesta, Institute of Food Science, Technology and Nutrition - Spanish National Research Council, Spain</p></fn><corresp id="fn001">*Correspondence: Jianmin Qi <email xlink:type="simple">qijm863@163.com</email>;</corresp><corresp id="fn002">Jianguang Su <email xlink:type="simple">jgsu@vip.163.com</email></corresp><fn fn-type="other" id="fn003"><p>This article was submitted to Technical Advances in Plant Science, a section of the journal Frontiers in Plant Science</p></fn></author-notes><pub-date pub-type="epub"><day>14</day><month>10</month><year>2015</year></pub-date><pub-date pub-type="collection"><year>2015</year></pub-date><volume>6</volume><elocation-id>848</elocation-id><history><date date-type="received"><day>07</day><month>8</month><year>2015</year></date><date date-type="accepted"><day>28</day><month>9</month><year>2015</year></date></history><permissions><copyright-statement>Copyright © 2015 Niu, Qi, Zhang, Xu, Tao, Fang and Su.</copyright-statement><copyright-year>2015</copyright-year><copyright-holder>Niu, Qi, Zhang, Xu, Tao, Fang and Su</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>To accurately measure gene expression using quantitative reverse transcription PCR (qRT-PCR), reliable reference gene(s) are required for data normalization. <italic>Corchorus capsularis</italic>, an annual herbaceous fiber crop with predominant biodegradability and renewability, has not been investigated for the stability of reference genes with qRT-PCR. In this study, 11 candidate reference genes were selected and their expression levels were assessed using qRT-PCR. To account for the influence of experimental approach and tissue type, 22 different jute samples were selected from abiotic and biotic stress conditions as well as three different tissue types. The stability of the candidate reference genes was evaluated using geNorm, NormFinder, and BestKeeper programs, and the comprehensive rankings of gene stability were generated by aggregate analysis. For the biotic stress and NaCl stress subsets, <italic>ACT7</italic> and <italic>RAN</italic> were suitable as stable reference genes for gene expression normalization. For the PEG stress subset, <italic>UBC</italic>, and <italic>DnaJ</italic> were sufficient for accurate normalization. For the tissues subset, four reference genes <italic>TUB</italic>β, <italic>UBI, EF1</italic>α, and <italic>RAN</italic> were sufficient for accurate normalization. The selected genes were further validated by comparing expression profiles of <italic>WRKY15</italic> in various samples, and two stable reference genes were recommended for accurate normalization of qRT-PCR data. Our results provide researchers with appropriate reference genes for qRT-PCR in <italic>C</italic>. <italic>capsularis</italic>, and will facilitate gene expression study under these conditions.</p></abstract><kwd-group><kwd>jute (<italic>Corchorus capsularis</italic>)</kwd><kwd>qRT-PCR</kwd><kwd>reference genes</kwd><kwd>gene expression</kwd><kwd>abiotic and biotic stress</kwd></kwd-group><funding-group><award-group><funding-source id="cn001">the 948 project of the Agricultural Department of China</funding-source><award-id rid="cn001">2013–Z70</award-id></award-group><award-group><funding-source id="cn002">the National Bast Fiber Germplasm Resources Project of China</funding-source><award-id rid="cn002">K47NI201A</award-id></award-group><award-group><funding-source id="cn003">the National Bast Fiber Research System of China</funding-source><award-id rid="cn003">CARS–19–E06</award-id></award-group><award-group><funding-source id="cn004">National Natural Science Foundation of China<named-content content-type="fundref-id">10.13039/501100001809</named-content></funding-source><award-id rid="cn004">31471549</award-id></award-group></funding-group><counts><fig-count count="4"></fig-count><table-count count="5"></table-count><equation-count count="0"></equation-count><ref-count count="58"></ref-count><page-count count="12"></page-count><word-count count="9106"></word-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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