Reference gene validation for quantitative RT-PCR during biotic and abiotic stresses in Vitis vinifera.

Grapevine is one of the most cultivated fruit crop worldwide with Vitis vinifera being the species with the highest economical importance. Being highly susceptible to fungal pathogens and increasingly affected by environmental factors, it has become an important agricultural research area, where gen...

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Autores principales:	Alexandre Filipe Borges, Catarina Fonseca, Ricardo Boavida Ferreira, Ana Maria Lourenço, Sara Monteiro
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/19558c5f70764520a9aa10abb261373f
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spelling	oai:doaj.org-article:19558c5f70764520a9aa10abb261373f2021-11-25T05:55:25ZReference gene validation for quantitative RT-PCR during biotic and abiotic stresses in Vitis vinifera.1932-620310.1371/journal.pone.0111399https://doaj.org/article/19558c5f70764520a9aa10abb261373f2014-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0111399https://doaj.org/toc/1932-6203Grapevine is one of the most cultivated fruit crop worldwide with Vitis vinifera being the species with the highest economical importance. Being highly susceptible to fungal pathogens and increasingly affected by environmental factors, it has become an important agricultural research area, where gene expression analysis plays a fundamental role. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is currently amongst the most powerful techniques to perform gene expression studies. Nevertheless, accurate gene expression quantification strongly relies on appropriate reference gene selection for sample normalization. Concerning V. vinifera, limited information still exists as for which genes are the most suitable to be used as reference under particular experimental conditions. In this work, seven candidate genes were investigated for their stability in grapevine samples referring to four distinct stresses (Erysiphe necator, wounding and UV-C irradiation in leaves and Phaeomoniella chlamydospora colonization in wood). The expression stability was evaluated using geNorm, NormFinder and BestKeeper. In all cases, full agreement was not observed for the three methods. To provide comprehensive rankings integrating the three different programs, for each treatment, a consensus ranking was created using a non-weighted unsupervised rank aggregation method. According to the last, the three most suitable reference genes to be used in grapevine leaves, regardless of the stress, are UBC, VAG and PEP. For the P. chlamydospora treatment, EF1, CYP and UBC were the best scoring genes. Acquaintance of the most suitable reference genes to be used in grapevine samples can contribute for accurate gene expression quantification in forthcoming studies.Alexandre Filipe BorgesCatarina FonsecaRicardo Boavida FerreiraAna Maria LourençoSara MonteiroPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 10, p e111399 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Alexandre Filipe Borges Catarina Fonseca Ricardo Boavida Ferreira Ana Maria Lourenço Sara Monteiro Reference gene validation for quantitative RT-PCR during biotic and abiotic stresses in Vitis vinifera.
description	Grapevine is one of the most cultivated fruit crop worldwide with Vitis vinifera being the species with the highest economical importance. Being highly susceptible to fungal pathogens and increasingly affected by environmental factors, it has become an important agricultural research area, where gene expression analysis plays a fundamental role. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is currently amongst the most powerful techniques to perform gene expression studies. Nevertheless, accurate gene expression quantification strongly relies on appropriate reference gene selection for sample normalization. Concerning V. vinifera, limited information still exists as for which genes are the most suitable to be used as reference under particular experimental conditions. In this work, seven candidate genes were investigated for their stability in grapevine samples referring to four distinct stresses (Erysiphe necator, wounding and UV-C irradiation in leaves and Phaeomoniella chlamydospora colonization in wood). The expression stability was evaluated using geNorm, NormFinder and BestKeeper. In all cases, full agreement was not observed for the three methods. To provide comprehensive rankings integrating the three different programs, for each treatment, a consensus ranking was created using a non-weighted unsupervised rank aggregation method. According to the last, the three most suitable reference genes to be used in grapevine leaves, regardless of the stress, are UBC, VAG and PEP. For the P. chlamydospora treatment, EF1, CYP and UBC were the best scoring genes. Acquaintance of the most suitable reference genes to be used in grapevine samples can contribute for accurate gene expression quantification in forthcoming studies.
format	article
author	Alexandre Filipe Borges Catarina Fonseca Ricardo Boavida Ferreira Ana Maria Lourenço Sara Monteiro
author_facet	Alexandre Filipe Borges Catarina Fonseca Ricardo Boavida Ferreira Ana Maria Lourenço Sara Monteiro
author_sort	Alexandre Filipe Borges
title	Reference gene validation for quantitative RT-PCR during biotic and abiotic stresses in Vitis vinifera.
title_short	Reference gene validation for quantitative RT-PCR during biotic and abiotic stresses in Vitis vinifera.
title_full	Reference gene validation for quantitative RT-PCR during biotic and abiotic stresses in Vitis vinifera.
title_fullStr	Reference gene validation for quantitative RT-PCR during biotic and abiotic stresses in Vitis vinifera.
title_full_unstemmed	Reference gene validation for quantitative RT-PCR during biotic and abiotic stresses in Vitis vinifera.
title_sort	reference gene validation for quantitative rt-pcr during biotic and abiotic stresses in vitis vinifera.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/19558c5f70764520a9aa10abb261373f
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Reference gene validation for quantitative RT-PCR during biotic and abiotic stresses in Vitis vinifera.

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