Evaluation of qPCR reference genes in two genotypes of Populus for use in photoperiod and low-temperature studies.
Identifieur interne : 002A99 ( Main/Exploration ); précédent : 002A98; suivant : 002B00Evaluation of qPCR reference genes in two genotypes of Populus for use in photoperiod and low-temperature studies.
Auteurs : Emily A. Pettengill [États-Unis] ; Cécile Parmentier-Line ; Gary D. ColemanSource :
- BMC research notes [ 1756-0500 ] ; 2012.
Descripteurs français
- KwdFr :
- Analyse de profil d'expression de gènes (normes), Basse température (MeSH), Feuilles de plante (génétique), Gènes de plante (MeSH), Gènes essentiels (MeSH), Génotype (MeSH), Logiciel (MeSH), Photopériode (MeSH), Populus (génétique), Pousses de plante (génétique), Réaction de polymérisation en chaine en temps réel (MeSH), Régulation de l'expression des gènes végétaux (MeSH), Saisons (MeSH), Écorce (génétique).
- MESH :
- génétique : Feuilles de plante, Populus, Pousses de plante, Écorce.
- normes : Analyse de profil d'expression de gènes.
- Basse température, Gènes de plante, Gènes essentiels, Génotype, Logiciel, Photopériode, Réaction de polymérisation en chaine en temps réel, Régulation de l'expression des gènes végétaux, Saisons.
English descriptors
- KwdEn :
- Cold Temperature (MeSH), Gene Expression Profiling (standards), Gene Expression Regulation, Plant (MeSH), Genes, Essential (MeSH), Genes, Plant (MeSH), Genotype (MeSH), Photoperiod (MeSH), Plant Bark (genetics), Plant Leaves (genetics), Plant Shoots (genetics), Populus (genetics), Real-Time Polymerase Chain Reaction (MeSH), Seasons (MeSH), Software (MeSH).
- MESH :
Abstract
BACKGROUND
Quantitative PCR (qPCR) is a widely used technique for gene expression analysis. A common normalization method for accurate qPCR data analysis involves stable reference genes to determine relative gene expression. Despite extensive research in the forest tree species Populus, there is not a resource for reference genes that meet the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) standards for qPCR techniques and analysis. Since Populus is a woody perennial species, studies of seasonal changes in gene expression are important towards advancing knowledge of this important developmental and physiological trait. The objective of this study was to evaluate reference gene expression stability in various tissues and growth conditions in two important Populus genotypes (P. trichocarpa "Nisqually 1" and P. tremula x P. alba 717 1-B4) following MIQE guidelines.
RESULTS
We evaluated gene expression stability in shoot tips, young leaves, mature leaves and bark tissues from P. trichocarpa and P. tremula. x P. alba grown under long-day (LD), short-day (SD) or SD plus low-temperatures conditions. Gene expression data were analyzed for stable reference genes among 18S rRNA, ACT2, CDC2, CYC063, TIP4-like, UBQ7, PT1 and ANT using two software packages, geNorm(PLUS) and BestKeeper. GeNorm(PLUS) ranked TIP4-like and PT1 among the most stable genes in most genotype/tissue combinations while BestKeeper ranked CDC2 and ACT2 among the most stable genes.
CONCLUSIONS
This is the first comprehensive evaluation of reference genes in two important Populus genotypes and the only study in Populus that meets MIQE standards. Both analysis programs identified stable reference genes in both genotypes and all tissues grown under different photoperiods. This set of reference genes was found to be suitable for either genotype considered here and may potentially be suitable for other Populus species and genotypes. These results provide a valuable resource for the Populus research community.
DOI: 10.1186/1756-0500-5-366
PubMed: 22824181
PubMed Central: PMC3479007
Affiliations:
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Pettengill</name><affiliation wicri:level="4"><nlm:affiliation>Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742-4452, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742-4452</wicri:regionArea><placeName><region type="state">Maryland</region><settlement type="city">College Park (Maryland)</settlement></placeName><orgName type="university">Université du Maryland</orgName></affiliation></author><author><name sortKey="Parmentier Line, Cecile" sort="Parmentier Line, Cecile" uniqKey="Parmentier Line C" first="Cécile" last="Parmentier-Line">Cécile Parmentier-Line</name></author><author><name sortKey="Coleman, Gary D" sort="Coleman, Gary D" uniqKey="Coleman G" first="Gary D" last="Coleman">Gary D. Coleman</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2012">2012</date><idno type="RBID">pubmed:22824181</idno><idno type="pmid">22824181</idno><idno type="doi">10.1186/1756-0500-5-366</idno><idno type="pmc">PMC3479007</idno><idno type="wicri:Area/Main/Corpus">002958</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">002958</idno><idno type="wicri:Area/Main/Curation">002958</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">002958</idno><idno type="wicri:Area/Main/Exploration">002958</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Evaluation of qPCR reference genes in two genotypes of Populus for use in photoperiod and low-temperature studies.</title><author><name sortKey="Pettengill, Emily A" sort="Pettengill, Emily A" uniqKey="Pettengill E" first="Emily A" last="Pettengill">Emily A. Pettengill</name><affiliation wicri:level="4"><nlm:affiliation>Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742-4452, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742-4452</wicri:regionArea><placeName><region type="state">Maryland</region><settlement type="city">College Park (Maryland)</settlement></placeName><orgName type="university">Université du Maryland</orgName></affiliation></author><author><name sortKey="Parmentier Line, Cecile" sort="Parmentier Line, Cecile" uniqKey="Parmentier Line C" first="Cécile" last="Parmentier-Line">Cécile Parmentier-Line</name></author><author><name sortKey="Coleman, Gary D" sort="Coleman, Gary D" uniqKey="Coleman G" first="Gary D" last="Coleman">Gary D. Coleman</name></author></analytic><series><title level="j">BMC research notes</title><idno type="eISSN">1756-0500</idno><imprint><date when="2012" type="published">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Cold Temperature (MeSH)</term><term>Gene Expression Profiling (standards)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Genes, Essential (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Genotype (MeSH)</term><term>Photoperiod (MeSH)</term><term>Plant Bark (genetics)</term><term>Plant Leaves (genetics)</term><term>Plant Shoots (genetics)</term><term>Populus (genetics)</term><term>Real-Time Polymerase Chain Reaction (MeSH)</term><term>Seasons (MeSH)</term><term>Software (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de profil d'expression de gènes (normes)</term><term>Basse température (MeSH)</term><term>Feuilles de plante (génétique)</term><term>Gènes de plante (MeSH)</term><term>Gènes essentiels (MeSH)</term><term>Génotype (MeSH)</term><term>Logiciel (MeSH)</term><term>Photopériode (MeSH)</term><term>Populus (génétique)</term><term>Pousses de plante (génétique)</term><term>Réaction de polymérisation en chaine en temps réel (MeSH)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Saisons (MeSH)</term><term>Écorce (génétique)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Plant Bark</term><term>Plant Leaves</term><term>Plant Shoots</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Feuilles de plante</term><term>Populus</term><term>Pousses de plante</term><term>Écorce</term></keywords><keywords scheme="MESH" qualifier="normes" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term></keywords><keywords scheme="MESH" qualifier="standards" xml:lang="en"><term>Gene Expression Profiling</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Cold Temperature</term><term>Gene Expression Regulation, Plant</term><term>Genes, Essential</term><term>Genes, Plant</term><term>Genotype</term><term>Photoperiod</term><term>Real-Time Polymerase Chain Reaction</term><term>Seasons</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Basse température</term><term>Gènes de plante</term><term>Gènes essentiels</term><term>Génotype</term><term>Logiciel</term><term>Photopériode</term><term>Réaction de polymérisation en chaine en temps réel</term><term>Régulation de l'expression des gènes végétaux</term><term>Saisons</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Quantitative PCR (qPCR) is a widely used technique for gene expression analysis. A common normalization method for accurate qPCR data analysis involves stable reference genes to determine relative gene expression. Despite extensive research in the forest tree species Populus, there is not a resource for reference genes that meet the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) standards for qPCR techniques and analysis. Since Populus is a woody perennial species, studies of seasonal changes in gene expression are important towards advancing knowledge of this important developmental and physiological trait. The objective of this study was to evaluate reference gene expression stability in various tissues and growth conditions in two important Populus genotypes (P. trichocarpa "Nisqually 1" and P. tremula x P. alba 717 1-B4) following MIQE guidelines.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>We evaluated gene expression stability in shoot tips, young leaves, mature leaves and bark tissues from P. trichocarpa and P. tremula. x P. alba grown under long-day (LD), short-day (SD) or SD plus low-temperatures conditions. Gene expression data were analyzed for stable reference genes among 18S rRNA, ACT2, CDC2, CYC063, TIP4-like, UBQ7, PT1 and ANT using two software packages, geNorm(PLUS) and BestKeeper. GeNorm(PLUS) ranked TIP4-like and PT1 among the most stable genes in most genotype/tissue combinations while BestKeeper ranked CDC2 and ACT2 among the most stable genes.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>This is the first comprehensive evaluation of reference genes in two important Populus genotypes and the only study in Populus that meets MIQE standards. Both analysis programs identified stable reference genes in both genotypes and all tissues grown under different photoperiods. This set of reference genes was found to be suitable for either genotype considered here and may potentially be suitable for other Populus species and genotypes. These results provide a valuable resource for the Populus research community.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">22824181</PMID><DateCompleted><Year>2013</Year><Month>02</Month><Day>12</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1756-0500</ISSN><JournalIssue CitedMedium="Internet"><Volume>5</Volume><PubDate><Year>2012</Year><Month>Jul</Month><Day>23</Day></PubDate></JournalIssue><Title>BMC research notes</Title><ISOAbbreviation>BMC Res Notes</ISOAbbreviation></Journal><ArticleTitle>Evaluation of qPCR reference genes in two genotypes of Populus for use in photoperiod and low-temperature studies.</ArticleTitle><Pagination><MedlinePgn>366</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1756-0500-5-366</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Quantitative PCR (qPCR) is a widely used technique for gene expression analysis. A common normalization method for accurate qPCR data analysis involves stable reference genes to determine relative gene expression. Despite extensive research in the forest tree species Populus, there is not a resource for reference genes that meet the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) standards for qPCR techniques and analysis. Since Populus is a woody perennial species, studies of seasonal changes in gene expression are important towards advancing knowledge of this important developmental and physiological trait. The objective of this study was to evaluate reference gene expression stability in various tissues and growth conditions in two important Populus genotypes (P. trichocarpa "Nisqually 1" and P. tremula x P. alba 717 1-B4) following MIQE guidelines.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We evaluated gene expression stability in shoot tips, young leaves, mature leaves and bark tissues from P. trichocarpa and P. tremula. x P. alba grown under long-day (LD), short-day (SD) or SD plus low-temperatures conditions. Gene expression data were analyzed for stable reference genes among 18S rRNA, ACT2, CDC2, CYC063, TIP4-like, UBQ7, PT1 and ANT using two software packages, geNorm(PLUS) and BestKeeper. GeNorm(PLUS) ranked TIP4-like and PT1 among the most stable genes in most genotype/tissue combinations while BestKeeper ranked CDC2 and ACT2 among the most stable genes.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">This is the first comprehensive evaluation of reference genes in two important Populus genotypes and the only study in Populus that meets MIQE standards. Both analysis programs identified stable reference genes in both genotypes and all tissues grown under different photoperiods. This set of reference genes was found to be suitable for either genotype considered here and may potentially be suitable for other Populus species and genotypes. These results provide a valuable resource for the Populus research community.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Pettengill</LastName><ForeName>Emily A</ForeName><Initials>EA</Initials><AffiliationInfo><Affiliation>Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742-4452, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Parmentier-Line</LastName><ForeName>Cécile</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Coleman</LastName><ForeName>Gary D</ForeName><Initials>GD</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate 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IdType="pubmed">15317655</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Maryland</li></region><settlement><li>College Park (Maryland)</li></settlement><orgName><li>Université du Maryland</li></orgName></list><tree><noCountry><name sortKey="Coleman, Gary D" sort="Coleman, Gary D" uniqKey="Coleman G" first="Gary D" last="Coleman">Gary D. Coleman</name><name sortKey="Parmentier Line, Cecile" sort="Parmentier Line, Cecile" uniqKey="Parmentier Line C" first="Cécile" last="Parmentier-Line">Cécile Parmentier-Line</name></noCountry><country name="États-Unis"><region name="Maryland"><name sortKey="Pettengill, Emily A" sort="Pettengill, Emily A" uniqKey="Pettengill E" first="Emily A" last="Pettengill">Emily A. Pettengill</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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