Reference gene selection for the shell gland of laying hens in response to time-points of eggshell formation and nicarbazin
Identifieur interne : 000373 ( Pmc/Checkpoint ); précédent : 000372; suivant : 000374Reference gene selection for the shell gland of laying hens in response to time-points of eggshell formation and nicarbazin
Auteurs : Sami Samiullah ; Juliet Roberts ; Shu-Biao WuSource :
- PLoS ONE [ 1932-6203 ] ; 2017.
Abstract
Ten reference genes were investigated for normalization of gene expression data in the shell gland of laying hens. Analyses performed with geNorm revealed that hypoxanthine phosphoribosyltransferase 1 (
Url:
DOI: 10.1371/journal.pone.0180432
PubMed: 28671969
PubMed Central: 5495395
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Reference gene selection for the shell gland of laying hens in response to time-points of eggshell formation and nicarbazin</title><author><name sortKey="Samiullah, Sami" sort="Samiullah, Sami" uniqKey="Samiullah S" first="Sami" last="Samiullah">Sami Samiullah</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Roberts, Juliet" sort="Roberts, Juliet" uniqKey="Roberts J" first="Juliet" last="Roberts">Juliet Roberts</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Wu, Shu Biao" sort="Wu, Shu Biao" uniqKey="Wu S" first="Shu-Biao" last="Wu">Shu-Biao Wu</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">28671969</idno><idno type="pmc">5495395</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5495395</idno><idno type="RBID">PMC:5495395</idno><idno type="doi">10.1371/journal.pone.0180432</idno><date when="2017">2017</date><idno type="wicri:Area/Pmc/Corpus">000993</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000993</idno><idno type="wicri:Area/Pmc/Curation">000993</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000993</idno><idno type="wicri:Area/Pmc/Checkpoint">000373</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000373</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Reference gene selection for the shell gland of laying hens in response to time-points of eggshell formation and nicarbazin</title><author><name sortKey="Samiullah, Sami" sort="Samiullah, Sami" uniqKey="Samiullah S" first="Sami" last="Samiullah">Sami Samiullah</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Roberts, Juliet" sort="Roberts, Juliet" uniqKey="Roberts J" first="Juliet" last="Roberts">Juliet Roberts</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Wu, Shu Biao" sort="Wu, Shu Biao" uniqKey="Wu S" first="Shu-Biao" last="Wu">Shu-Biao Wu</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2017">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Ten reference genes were investigated for normalization of gene expression data in the shell gland of laying hens. Analyses performed with geNorm revealed that hypoxanthine phosphoribosyltransferase 1 (<italic>HPRT1</italic>) and hydroxymethylbilane synthase (<italic>HMBS</italic>) were the two most stable reference genes in response to post-oviposition time alone (POT) or with nicarbazin treatment (POT+N) of laying hens. NormFinder analyses showed that the two most stable reference genes in response to POT and POT+N were 18S ribosomal RNA (<italic>18S rRNA</italic>), ribosomal protein L4 (<italic>RPL4</italic>) and <italic>HMBS</italic>, <italic>RPL4</italic>, respectively. BestKeeper analyses showed that <italic>18S rRNA</italic>, <italic>RPL4</italic> and <italic>HPRT1</italic>, <italic>HMBS</italic> were the two most stable reference genes for POT, and POT+N, respectively. Of the ten reference genes, all except <italic>B2M</italic> showed geNorm M <0.5, suggesting that they were stably expressed in the shell gland tissue. Consensus from these three programs suggested <italic>HPRT1</italic> and <italic>HMBS</italic> could be used as the two most stable reference genes in the present study. Expression analyses of four candidate target genes with the two most and the two least stable genes showed that a combination of stable reference genes leads to more discriminable quantification of expression levels of target genes, while the least stable genes failed to do so. Therefore, <italic>HMBS</italic> and <italic>HPRT1</italic> are recommended as the two most stable reference genes for the normalization of gene expression data at different stages of eggshell formation in brown-egg laying hens. Available statistical programs for reference gene ranking should include more robust analysis capability to analyse the gene expression data generated from factorial design experiments.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Nys, Y" uniqKey="Nys Y">Y Nys</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Melek, O" uniqKey="Melek O">O Melek</name></author><author><name sortKey="Morris, T" uniqKey="Morris T">T Morris</name></author><author><name sortKey="Jennings, R" uniqKey="Jennings R">R Jennings</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Johnson, Al" uniqKey="Johnson A">AL Johnson</name></author><author><name sortKey="Cc, S" uniqKey="Cc S">S CC</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Arias, Jl" uniqKey="Arias J">JL Arias</name></author><author><name sortKey="Fink, Dj" uniqKey="Fink D">DJ 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Z J" uniqKey="Wu Z">Z-J Wu</name></author><author><name sortKey="Tian, C" uniqKey="Tian C">C Tian</name></author><author><name sortKey="Jiang, Q" uniqKey="Jiang Q">Q Jiang</name></author><author><name sortKey="Li, X H" uniqKey="Li X">X-H Li</name></author><author><name sortKey="Zhuang, J" uniqKey="Zhuang J">J Zhuang</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, CA USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">28671969</article-id><article-id pub-id-type="pmc">5495395</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0180432</article-id><article-id pub-id-type="publisher-id">PONE-D-16-45782</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Genetics</subject><subj-group><subject>Gene Expression</subject></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and life sciences</subject><subj-group><subject>Biochemistry</subject><subj-group><subject>Nucleic acids</subject><subj-group><subject>RNA</subject><subj-group><subject>Non-coding RNA</subject><subj-group><subject>Ribosomal RNA</subject></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and life sciences</subject><subj-group><subject>Biochemistry</subject><subj-group><subject>Ribosomes</subject><subj-group><subject>Ribosomal RNA</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and life sciences</subject><subj-group><subject>Cell biology</subject><subj-group><subject>Cellular structures and organelles</subject><subj-group><subject>Ribosomes</subject><subj-group><subject>Ribosomal RNA</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Computer and Information Sciences</subject><subj-group><subject>Computer Software</subject></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Organisms</subject><subj-group><subject>Animals</subject><subj-group><subject>Vertebrates</subject><subj-group><subject>Amniotes</subject><subj-group><subject>Birds</subject><subj-group><subject>Fowl</subject><subj-group><subject>Gamefowl</subject><subj-group><subject>Chickens</subject></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Organisms</subject><subj-group><subject>Animals</subject><subj-group><subject>Vertebrates</subject><subj-group><subject>Amniotes</subject><subj-group><subject>Birds</subject><subj-group><subject>Poultry</subject><subj-group><subject>Chickens</subject></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Genetics</subject><subj-group><subject>Animal Genetics</subject><subj-group><subject>Bird Genetics</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Molecular Biology</subject><subj-group><subject>Molecular Biology Techniques</subject><subj-group><subject>Artificial Gene Amplification and Extension</subject><subj-group><subject>Polymerase Chain Reaction</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Research and Analysis Methods</subject><subj-group><subject>Molecular Biology Techniques</subject><subj-group><subject>Artificial Gene Amplification and Extension</subject><subj-group><subject>Polymerase Chain Reaction</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Cell Biology</subject><subj-group><subject>Cellular Structures and Organelles</subject><subj-group><subject>Cell Membranes</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Genetics</subject><subj-group><subject>Gene Amplification</subject></subj-group></subj-group></subj-group></article-categories><title-group><article-title>Reference gene selection for the shell gland of laying hens in response to time-points of eggshell formation and nicarbazin</article-title><alt-title alt-title-type="running-head">Reference gene selection for the shell gland of laying hens</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Samiullah</surname><given-names>Sami</given-names></name><xref ref-type="aff" rid="aff001"></xref></contrib><contrib contrib-type="author"><name><surname>Roberts</surname><given-names>Juliet</given-names></name><xref ref-type="aff" rid="aff001"></xref></contrib><contrib contrib-type="author"><contrib-id authenticated="true" contrib-id-type="orcid">http://orcid.org/0000-0002-1790-6015</contrib-id><name><surname>Wu</surname><given-names>Shu-Biao</given-names></name><xref ref-type="aff" rid="aff001"></xref><xref ref-type="corresp" rid="cor001">*</xref></contrib></contrib-group><aff id="aff001"><addr-line>Animal Science, School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Woloschak</surname><given-names>Gayle E.</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>Northwestern University Feinberg School of Medicine, UNITED STATES</addr-line></aff><author-notes><fn fn-type="COI-statement" id="coi001"><p><bold>Competing Interests: </bold>This study was funded by Australian Egg Corporation Limited (AECL). AECL has made no attempt to influence the reporting of the results of the present study and no aspect of the findings of the present study has any direct bearing on AECL commercial activities. This does not alter our adherence to PLOS ONE policies on sharing data and materials. AECL is one of 15 Rural Research and Development Corporations (RDCs) which receives funding from the Australian Government as well as from industry levies (see <ext-link ext-link-type="uri" xlink:href="http://www.ruralrdc.com.au/rural-research-development-corporations/">http://www.ruralrdc.com.au/rural-research-development-corporations/</ext-link>). The AECL R&D Program is administered independently from the commercial aspects of the AECL as required as a condition of Australian Government funding (see <ext-link ext-link-type="uri" xlink:href="http://www.ruralrdc.com.au/abouttherrdcs/#governance">http://www.ruralrdc.com.au/abouttherrdcs/#governance</ext-link>). SBW is currently serving on the editorial board of PLOS ONE. There are no patents, products in development or marketed products to declare. This does not alter our adherence to all the PLOS ONE policies on sharing data and materials.</p></fn><fn fn-type="con"><p><list list-type="simple"><list-item><p><bold>Conceptualization:</bold> SS JR SBW.</p></list-item><list-item><p><bold>Data curation:</bold> SS SBW.</p></list-item><list-item><p><bold>Formal analysis:</bold> SS SBW.</p></list-item><list-item><p><bold>Funding acquisition:</bold> JR.</p></list-item><list-item><p><bold>Investigation:</bold> SS JR SBW.</p></list-item><list-item><p><bold>Methodology:</bold> SS JR SBW.</p></list-item><list-item><p><bold>Project administration:</bold> JR SBW.</p></list-item><list-item><p><bold>Resources:</bold> JR SBW.</p></list-item><list-item><p><bold>Supervision:</bold> SBW JR.</p></list-item><list-item><p><bold>Visualization:</bold> SS.</p></list-item><list-item><p><bold>Writing – original draft:</bold> SS SBW.</p></list-item><list-item><p><bold>Writing – review & editing:</bold> SBW JR.</p></list-item></list></p></fn><corresp id="cor001">* E-mail: <email>shubiao.wu@une.edu.au</email></corresp></author-notes><pub-date pub-type="epub"><day>3</day><month>7</month><year>2017</year></pub-date><pub-date pub-type="collection"><year>2017</year></pub-date><volume>12</volume><issue>7</issue><elocation-id>e0180432</elocation-id><history><date date-type="received"><day>17</day><month>11</month><year>2016</year></date><date date-type="accepted"><day>15</day><month>6</month><year>2017</year></date></history><permissions><copyright-statement>© 2017 Samiullah et al</copyright-statement><copyright-year>2017</copyright-year><copyright-holder>Samiullah et al</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 <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p></license></permissions><self-uri content-type="pdf" xlink:href="pone.0180432.pdf"></self-uri><abstract><p>Ten reference genes were investigated for normalization of gene expression data in the shell gland of laying hens. Analyses performed with geNorm revealed that hypoxanthine phosphoribosyltransferase 1 (<italic>HPRT1</italic>) and hydroxymethylbilane synthase (<italic>HMBS</italic>) were the two most stable reference genes in response to post-oviposition time alone (POT) or with nicarbazin treatment (POT+N) of laying hens. NormFinder analyses showed that the two most stable reference genes in response to POT and POT+N were 18S ribosomal RNA (<italic>18S rRNA</italic>), ribosomal protein L4 (<italic>RPL4</italic>) and <italic>HMBS</italic>, <italic>RPL4</italic>, respectively. BestKeeper analyses showed that <italic>18S rRNA</italic>, <italic>RPL4</italic> and <italic>HPRT1</italic>, <italic>HMBS</italic> were the two most stable reference genes for POT, and POT+N, respectively. Of the ten reference genes, all except <italic>B2M</italic> showed geNorm M <0.5, suggesting that they were stably expressed in the shell gland tissue. Consensus from these three programs suggested <italic>HPRT1</italic> and <italic>HMBS</italic> could be used as the two most stable reference genes in the present study. Expression analyses of four candidate target genes with the two most and the two least stable genes showed that a combination of stable reference genes leads to more discriminable quantification of expression levels of target genes, while the least stable genes failed to do so. Therefore, <italic>HMBS</italic> and <italic>HPRT1</italic> are recommended as the two most stable reference genes for the normalization of gene expression data at different stages of eggshell formation in brown-egg laying hens. Available statistical programs for reference gene ranking should include more robust analysis capability to analyse the gene expression data generated from factorial design experiments.</p></abstract><funding-group><award-group id="award001"><funding-source><institution-wrap><institution-id institution-id-type="funder-id">http://dx.doi.org/10.13039/501100000976</institution-id><institution>Australian Egg Corporation Limited</institution></institution-wrap></funding-source><award-id>AECL1UN121</award-id><principal-award-recipient><name><surname>Roberts</surname><given-names>Juliet</given-names></name></principal-award-recipient></award-group><funding-statement>This study was financially supported by Australian Egg Corporation Limited (AECL) under grant number AECL 1UN121. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement></funding-group><counts><fig-count count="5"></fig-count><table-count count="8"></table-count><page-count count="20"></page-count></counts><custom-meta-group><custom-meta id="data-availability"><meta-name>Data Availability</meta-name><meta-value>All relevant data are within the paper. We do not have any supporting information in this paper.</meta-value></custom-meta></custom-meta-group></article-meta><notes><title>Data Availability</title><p>All relevant data are within the paper. We do not have any supporting information in this paper.</p></notes></front></pmc><affiliations><list></list><tree><noCountry><name sortKey="Roberts, Juliet" sort="Roberts, Juliet" uniqKey="Roberts J" first="Juliet" last="Roberts">Juliet Roberts</name><name sortKey="Samiullah, Sami" sort="Samiullah, Sami" uniqKey="Samiullah S" first="Sami" last="Samiullah">Sami Samiullah</name><name sortKey="Wu, Shu Biao" sort="Wu, Shu Biao" uniqKey="Wu S" first="Shu-Biao" last="Wu">Shu-Biao Wu</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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