Reference genes for gene expression studies targeting sugarcane infected with Sugarcane mosaic virus (SCMV)

OBJECTIVE: The selection of reference genes in sugarcane under Sugarcane mosaic virus (SCMV) infection has not been reported and is indispensable to get reliable reverse transcription quantitative PCR (RT-qPCR) results for validation of transcriptome analysis. In this regard, seven potential referen...

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Autores principales: da Silva, Marcel Fernando, Gonçalves, Marcos Cesar, dos Santos Brito, Michael, Nóbile, Paula Macedo, de Andrade, Larissa Mara, Medeiros, Cibele Nataliane, Creste, Silvana, Pinto, Luciana Rossini
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Research Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6423880/
https://www.ncbi.nlm.nih.gov/pubmed/30885257
http://dx.doi.org/10.1186/s13104-019-4168-5
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author da Silva, Marcel Fernando
Gonçalves, Marcos Cesar
dos Santos Brito, Michael
Nóbile, Paula Macedo
de Andrade, Larissa Mara
Medeiros, Cibele Nataliane
Creste, Silvana
Pinto, Luciana Rossini
author_facet da Silva, Marcel Fernando
Gonçalves, Marcos Cesar
dos Santos Brito, Michael
Nóbile, Paula Macedo
de Andrade, Larissa Mara
Medeiros, Cibele Nataliane
Creste, Silvana
Pinto, Luciana Rossini
author_sort da Silva, Marcel Fernando
collection PubMed
description OBJECTIVE: The selection of reference genes in sugarcane under Sugarcane mosaic virus (SCMV) infection has not been reported and is indispensable to get reliable reverse transcription quantitative PCR (RT-qPCR) results for validation of transcriptome analysis. In this regard, seven potential reference genes were tested by RT-qPCR and ranked according to their stability using BestKeeper, NormFinder and GeNorm algorithms, and RefFinder WEB-based software in an experiment performed with samples from two sugarcane cultivars contrasting for SCMV resistance, when mechanically inoculated with a severe SCMV strain and using mock inoculated plant controls. RESULTS: The genes Uridylate kinase (UK) and Ubiquitin-conjugating enzyme 18 (UBC18) were the most stable according to GeNorm algorithm and the Pearson correlation coefficients with the BestKeeper index. On the other hand, ribosomal protein L35-4 (RPL1), Actin (ACT) and Ubiquitin1 (UBQ1) were the least stable genes for all algorithms tested. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13104-019-4168-5) contains supplementary material, which is available to authorized users.
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spelling pubmed-64238802019-03-28 Reference genes for gene expression studies targeting sugarcane infected with Sugarcane mosaic virus (SCMV) da Silva, Marcel Fernando Gonçalves, Marcos Cesar dos Santos Brito, Michael Nóbile, Paula Macedo de Andrade, Larissa Mara Medeiros, Cibele Nataliane Creste, Silvana Pinto, Luciana Rossini BMC Res Notes Research Note OBJECTIVE: The selection of reference genes in sugarcane under Sugarcane mosaic virus (SCMV) infection has not been reported and is indispensable to get reliable reverse transcription quantitative PCR (RT-qPCR) results for validation of transcriptome analysis. In this regard, seven potential reference genes were tested by RT-qPCR and ranked according to their stability using BestKeeper, NormFinder and GeNorm algorithms, and RefFinder WEB-based software in an experiment performed with samples from two sugarcane cultivars contrasting for SCMV resistance, when mechanically inoculated with a severe SCMV strain and using mock inoculated plant controls. RESULTS: The genes Uridylate kinase (UK) and Ubiquitin-conjugating enzyme 18 (UBC18) were the most stable according to GeNorm algorithm and the Pearson correlation coefficients with the BestKeeper index. On the other hand, ribosomal protein L35-4 (RPL1), Actin (ACT) and Ubiquitin1 (UBQ1) were the least stable genes for all algorithms tested. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13104-019-4168-5) contains supplementary material, which is available to authorized users. BioMed Central 2019-03-18 /pmc/articles/PMC6423880/ /pubmed/30885257 http://dx.doi.org/10.1186/s13104-019-4168-5 Text en © The Author(s) 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Note
da Silva, Marcel Fernando
Gonçalves, Marcos Cesar
dos Santos Brito, Michael
Nóbile, Paula Macedo
de Andrade, Larissa Mara
Medeiros, Cibele Nataliane
Creste, Silvana
Pinto, Luciana Rossini
Reference genes for gene expression studies targeting sugarcane infected with Sugarcane mosaic virus (SCMV)
title Reference genes for gene expression studies targeting sugarcane infected with Sugarcane mosaic virus (SCMV)
title_full Reference genes for gene expression studies targeting sugarcane infected with Sugarcane mosaic virus (SCMV)
title_fullStr Reference genes for gene expression studies targeting sugarcane infected with Sugarcane mosaic virus (SCMV)
title_full_unstemmed Reference genes for gene expression studies targeting sugarcane infected with Sugarcane mosaic virus (SCMV)
title_short Reference genes for gene expression studies targeting sugarcane infected with Sugarcane mosaic virus (SCMV)
title_sort reference genes for gene expression studies targeting sugarcane infected with sugarcane mosaic virus (scmv)
topic Research Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6423880/
https://www.ncbi.nlm.nih.gov/pubmed/30885257
http://dx.doi.org/10.1186/s13104-019-4168-5
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