Microarray-based uncovering reference genes for quantitative real time PCR in grapevine under abiotic stress

Bibliographic Details
Main Author: Coito, João L.
Publication Date: 2012
Other Authors: Rocheta, Margarida, Carvalho, Luísa, Amâncio, Sara
Format: Article
Language: eng
Source: Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
Download full: http://hdl.handle.net/10400.5/5029
Summary: Research Article
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spelling Microarray-based uncovering reference genes for quantitative real time PCR in grapevine under abiotic stressgrapevinemicroarrayreal time RT-PCRreference geneResearch ArticleBackground: Quantitative real time polymerase chain reaction is becoming the primary tool for detecting mRNA and transcription data analysis as it shows to have advantages over other more commonly used techniques. Nevertheless, it also presents a few shortcomings, with the most import being the need for data normalisation, usually with a reference gene. Therefore the choice of the reference gene(s) is of great importance for correct data analysis. Microarray data, when available, can be of great assistance when choosing reference genes. Grapevine was submitted to water stress and heat stress as well as a combination of both to test the stability of the possible reference genes. Results: Using the analysis of microarray data available for grapevine, six possible reference genes were selected for RT-qPCR validation: PADCP, ubiq, TIF, TIF-GTP, VH1-IK, aladin-related. Two additional genes that are commonly used as reference genes were included: act and L2. The stability of those genes was tested in leaves of grapevine in both field plants and in greenhouse plants under water or heat stress or a combination of both. Gene stability was analyzed with the softwares GeNorm, NormFinder and the ΔCq method resulting in several combinations of reference genes suitable for data normalisation. In order to assess the best combination, the reference genes were tested in putative stress marker genes (PCO, Galsynt, BKCoAS and HSP17) also chosen from the same microarray, in water stress, heat stress and the combination of both. Conclusions: Each method selected different gene combinations (PADCP + act, TIF + TIF-GTP and ubiq + act). However, as none of the combinations diverged significantly from the others used to normalize the expression of the putative stress marker genes, then any combination is suitable for data normalisation under the conditions tested. Here we prove the accuracy of choosing grapevine reference genes for RT-qPCR through a microarray analysisBioMed CentralRepositório da Universidade de LisboaCoito, João L.Rocheta, MargaridaCarvalho, LuísaAmâncio, Sara2013-01-21T14:25:10Z20122012-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10400.5/5029eng"BMC Research Notes". ISSN 1756-0500. 5:220 (2012)1756-0500info:eu-repo/semantics/openAccessreponame:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiainstacron:RCAAP2025-03-17T16:00:16Zoai:repositorio.ulisboa.pt:10400.5/5029Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireinfo@rcaap.ptopendoar:https://opendoar.ac.uk/repository/71602025-05-29T03:59:54.545547Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiafalse
dc.title.none.fl_str_mv Microarray-based uncovering reference genes for quantitative real time PCR in grapevine under abiotic stress
title Microarray-based uncovering reference genes for quantitative real time PCR in grapevine under abiotic stress
spellingShingle Microarray-based uncovering reference genes for quantitative real time PCR in grapevine under abiotic stress
Coito, João L.
grapevine
microarray
real time RT-PCR
reference gene
title_short Microarray-based uncovering reference genes for quantitative real time PCR in grapevine under abiotic stress
title_full Microarray-based uncovering reference genes for quantitative real time PCR in grapevine under abiotic stress
title_fullStr Microarray-based uncovering reference genes for quantitative real time PCR in grapevine under abiotic stress
title_full_unstemmed Microarray-based uncovering reference genes for quantitative real time PCR in grapevine under abiotic stress
title_sort Microarray-based uncovering reference genes for quantitative real time PCR in grapevine under abiotic stress
author Coito, João L.
author_facet Coito, João L.
Rocheta, Margarida
Carvalho, Luísa
Amâncio, Sara
author_role author
author2 Rocheta, Margarida
Carvalho, Luísa
Amâncio, Sara
author2_role author
author
author
dc.contributor.none.fl_str_mv Repositório da Universidade de Lisboa
dc.contributor.author.fl_str_mv Coito, João L.
Rocheta, Margarida
Carvalho, Luísa
Amâncio, Sara
dc.subject.por.fl_str_mv grapevine
microarray
real time RT-PCR
reference gene
topic grapevine
microarray
real time RT-PCR
reference gene
description Research Article
publishDate 2012
dc.date.none.fl_str_mv 2012
2012-01-01T00:00:00Z
2013-01-21T14:25:10Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10400.5/5029
url http://hdl.handle.net/10400.5/5029
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv "BMC Research Notes". ISSN 1756-0500. 5:220 (2012)
1756-0500
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
instacron:RCAAP
instname_str FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
instacron_str RCAAP
institution RCAAP
reponame_str Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
collection Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
repository.name.fl_str_mv Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
repository.mail.fl_str_mv info@rcaap.pt
_version_ 1833601904674865152

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