Stability analysis of reference genes for RT-qPCR assays involving compatible and incompatible Ralstonia solanacearum-tomato ‘Hawaii 7996’ interactions

Abstract Reverse transcription-quantitative PCR (RT-qPCR) is an analytical tool for gene expression quantification. Reference genes are not yet available for gene expression analysis during interactions of Ralstonia solanacearum with ‘Hawaii 7996’ (the most stable source of resistance in tomato). He...

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Autores principales:	Greecy M. R. Albuquerque, Fernando C. A. Fonseca, Leonardo S. Boiteux, Rafaela C. F. Borges, Robert N. G. Miller, Carlos A. Lopes, Elineide B. Souza, Maria Esther N. Fonseca
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/1dad8363b18545ee8ae8649a16115c56
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spelling	oai:doaj.org-article:1dad8363b18545ee8ae8649a16115c562021-12-02T18:48:09ZStability analysis of reference genes for RT-qPCR assays involving compatible and incompatible Ralstonia solanacearum-tomato ‘Hawaii 7996’ interactions10.1038/s41598-021-97854-82045-2322https://doaj.org/article/1dad8363b18545ee8ae8649a16115c562021-09-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-97854-8https://doaj.org/toc/2045-2322Abstract Reverse transcription-quantitative PCR (RT-qPCR) is an analytical tool for gene expression quantification. Reference genes are not yet available for gene expression analysis during interactions of Ralstonia solanacearum with ‘Hawaii 7996’ (the most stable source of resistance in tomato). Here, we carried out a multi-algorithm stability analysis of eight candidate reference genes during interactions of ‘Hawaii 7996’ with one incompatible/avirulent and two compatible/virulent (= resistance-breaking) bacterial isolates. Samples were taken at 24- and 96-h post-inoculation (HPI). Analyses were performed using the ∆∆Ct method and expression stability was estimated using BestKeeper, NormFinder, and geNorm algorithms. TIP41 and EF1α (with geNorm), TIP41 and ACT (with NormFinder), and UBI3 and TIP41 (with BestKeeper), were the best combinations for mRNA normalization in incompatible interactions at 24 HPI and 96 HPI. The most stable genes in global compatible and incompatible interactions at 24 HPI and 96 HPI were PDS and TIP41 (with geNorm), TIP41 and ACT (with NormFinder), and UBI3 and PDS/EXP (with BestKeeper). Global analyses on the basis of the three algorithms across 20 R. solanacearum-tomato experimental conditions identified UBI3, TIP41 and ACT as the best choices as reference tomato genes in this important pathosystem.Greecy M. R. AlbuquerqueFernando C. A. FonsecaLeonardo S. BoiteuxRafaela C. F. BorgesRobert N. G. MillerCarlos A. LopesElineide B. SouzaMaria Esther N. FonsecaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Greecy M. R. Albuquerque Fernando C. A. Fonseca Leonardo S. Boiteux Rafaela C. F. Borges Robert N. G. Miller Carlos A. Lopes Elineide B. Souza Maria Esther N. Fonseca Stability analysis of reference genes for RT-qPCR assays involving compatible and incompatible Ralstonia solanacearum-tomato ‘Hawaii 7996’ interactions
description	Abstract Reverse transcription-quantitative PCR (RT-qPCR) is an analytical tool for gene expression quantification. Reference genes are not yet available for gene expression analysis during interactions of Ralstonia solanacearum with ‘Hawaii 7996’ (the most stable source of resistance in tomato). Here, we carried out a multi-algorithm stability analysis of eight candidate reference genes during interactions of ‘Hawaii 7996’ with one incompatible/avirulent and two compatible/virulent (= resistance-breaking) bacterial isolates. Samples were taken at 24- and 96-h post-inoculation (HPI). Analyses were performed using the ∆∆Ct method and expression stability was estimated using BestKeeper, NormFinder, and geNorm algorithms. TIP41 and EF1α (with geNorm), TIP41 and ACT (with NormFinder), and UBI3 and TIP41 (with BestKeeper), were the best combinations for mRNA normalization in incompatible interactions at 24 HPI and 96 HPI. The most stable genes in global compatible and incompatible interactions at 24 HPI and 96 HPI were PDS and TIP41 (with geNorm), TIP41 and ACT (with NormFinder), and UBI3 and PDS/EXP (with BestKeeper). Global analyses on the basis of the three algorithms across 20 R. solanacearum-tomato experimental conditions identified UBI3, TIP41 and ACT as the best choices as reference tomato genes in this important pathosystem.
format	article
author	Greecy M. R. Albuquerque Fernando C. A. Fonseca Leonardo S. Boiteux Rafaela C. F. Borges Robert N. G. Miller Carlos A. Lopes Elineide B. Souza Maria Esther N. Fonseca
author_facet	Greecy M. R. Albuquerque Fernando C. A. Fonseca Leonardo S. Boiteux Rafaela C. F. Borges Robert N. G. Miller Carlos A. Lopes Elineide B. Souza Maria Esther N. Fonseca
author_sort	Greecy M. R. Albuquerque
title	Stability analysis of reference genes for RT-qPCR assays involving compatible and incompatible Ralstonia solanacearum-tomato ‘Hawaii 7996’ interactions
title_short	Stability analysis of reference genes for RT-qPCR assays involving compatible and incompatible Ralstonia solanacearum-tomato ‘Hawaii 7996’ interactions
title_full	Stability analysis of reference genes for RT-qPCR assays involving compatible and incompatible Ralstonia solanacearum-tomato ‘Hawaii 7996’ interactions
title_fullStr	Stability analysis of reference genes for RT-qPCR assays involving compatible and incompatible Ralstonia solanacearum-tomato ‘Hawaii 7996’ interactions
title_full_unstemmed	Stability analysis of reference genes for RT-qPCR assays involving compatible and incompatible Ralstonia solanacearum-tomato ‘Hawaii 7996’ interactions
title_sort	stability analysis of reference genes for rt-qpcr assays involving compatible and incompatible ralstonia solanacearum-tomato ‘hawaii 7996’ interactions
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/1dad8363b18545ee8ae8649a16115c56
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Stability analysis of reference genes for RT-qPCR assays involving compatible and incompatible Ralstonia solanacearum-tomato ‘Hawaii 7996’ interactions

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