Cargando…
Reference genes for normalization of qPCR assays in sugarcane plants under water deficit
BACKGROUND: Sugarcane (Saccharum spp.) is the main raw material for sugar and ethanol production. Among the abiotic stress, drought is the main one that negatively impact sugarcane yield. Although gene expression analysis through quantitative PCR (qPCR) has increased our knowledge about biological p...
Autores principales: | , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2017
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5392966/ https://www.ncbi.nlm.nih.gov/pubmed/28428808 http://dx.doi.org/10.1186/s13007-017-0178-2 |
_version_ | 1783229502531305472 |
---|---|
author | de Andrade, Larissa Mara dos Santos Brito, Michael Fávero Peixoto Junior, Rafael Marchiori, Paulo Eduardo Ribeiro Nóbile, Paula Macedo Martins, Alexandre Palma Boer Ribeiro, Rafael Vasconcelos Creste, Silvana |
author_facet | de Andrade, Larissa Mara dos Santos Brito, Michael Fávero Peixoto Junior, Rafael Marchiori, Paulo Eduardo Ribeiro Nóbile, Paula Macedo Martins, Alexandre Palma Boer Ribeiro, Rafael Vasconcelos Creste, Silvana |
author_sort | de Andrade, Larissa Mara |
collection | PubMed |
description | BACKGROUND: Sugarcane (Saccharum spp.) is the main raw material for sugar and ethanol production. Among the abiotic stress, drought is the main one that negatively impact sugarcane yield. Although gene expression analysis through quantitative PCR (qPCR) has increased our knowledge about biological processes related to drought, gene network that mediates sugarcane responses to water deficit remains elusive. In such scenario, validation of reference gene is a major requirement for successful analyzes involving qPCR. RESULTS: In this study, candidate genes were tested for their suitable as reference genes for qPCR analyses in two sugarcane cultivars with varying drought tolerance. Eight candidate reference genes were evaluated in leaves sampled in plants subjected to water deficit in both field and greenhouse conditions. In addition, five genes were evaluated in shoot roots of plants subjected to water deficit by adding PEG8000 to the nutrient solution. NormFinder and RefFinder algorithms were used to identify the most stable gene(s) among genotypes and under different experimental conditions. Both algorithms revealed that in leaf samples, UBQ1 and GAPDH genes were more suitable as reference genes, whereas GAPDH was the best reference one in shoot roots. CONCLUSION: Reference genes suitable for sugarcane under water deficit were identified, which would lead to a more accurate and reliable analysis of qPCR. Thus, results obtained in this study may guide future research on gene expression in sugarcane under varying water conditions. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13007-017-0178-2) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5392966 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-53929662017-04-20 Reference genes for normalization of qPCR assays in sugarcane plants under water deficit de Andrade, Larissa Mara dos Santos Brito, Michael Fávero Peixoto Junior, Rafael Marchiori, Paulo Eduardo Ribeiro Nóbile, Paula Macedo Martins, Alexandre Palma Boer Ribeiro, Rafael Vasconcelos Creste, Silvana Plant Methods Methodology BACKGROUND: Sugarcane (Saccharum spp.) is the main raw material for sugar and ethanol production. Among the abiotic stress, drought is the main one that negatively impact sugarcane yield. Although gene expression analysis through quantitative PCR (qPCR) has increased our knowledge about biological processes related to drought, gene network that mediates sugarcane responses to water deficit remains elusive. In such scenario, validation of reference gene is a major requirement for successful analyzes involving qPCR. RESULTS: In this study, candidate genes were tested for their suitable as reference genes for qPCR analyses in two sugarcane cultivars with varying drought tolerance. Eight candidate reference genes were evaluated in leaves sampled in plants subjected to water deficit in both field and greenhouse conditions. In addition, five genes were evaluated in shoot roots of plants subjected to water deficit by adding PEG8000 to the nutrient solution. NormFinder and RefFinder algorithms were used to identify the most stable gene(s) among genotypes and under different experimental conditions. Both algorithms revealed that in leaf samples, UBQ1 and GAPDH genes were more suitable as reference genes, whereas GAPDH was the best reference one in shoot roots. CONCLUSION: Reference genes suitable for sugarcane under water deficit were identified, which would lead to a more accurate and reliable analysis of qPCR. Thus, results obtained in this study may guide future research on gene expression in sugarcane under varying water conditions. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13007-017-0178-2) contains supplementary material, which is available to authorized users. BioMed Central 2017-04-17 /pmc/articles/PMC5392966/ /pubmed/28428808 http://dx.doi.org/10.1186/s13007-017-0178-2 Text en © The Author(s) 2017 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 | Methodology de Andrade, Larissa Mara dos Santos Brito, Michael Fávero Peixoto Junior, Rafael Marchiori, Paulo Eduardo Ribeiro Nóbile, Paula Macedo Martins, Alexandre Palma Boer Ribeiro, Rafael Vasconcelos Creste, Silvana Reference genes for normalization of qPCR assays in sugarcane plants under water deficit |
title | Reference genes for normalization of qPCR assays in sugarcane plants under water deficit |
title_full | Reference genes for normalization of qPCR assays in sugarcane plants under water deficit |
title_fullStr | Reference genes for normalization of qPCR assays in sugarcane plants under water deficit |
title_full_unstemmed | Reference genes for normalization of qPCR assays in sugarcane plants under water deficit |
title_short | Reference genes for normalization of qPCR assays in sugarcane plants under water deficit |
title_sort | reference genes for normalization of qpcr assays in sugarcane plants under water deficit |
topic | Methodology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5392966/ https://www.ncbi.nlm.nih.gov/pubmed/28428808 http://dx.doi.org/10.1186/s13007-017-0178-2 |
work_keys_str_mv | AT deandradelarissamara referencegenesfornormalizationofqpcrassaysinsugarcaneplantsunderwaterdeficit AT dossantosbritomichael referencegenesfornormalizationofqpcrassaysinsugarcaneplantsunderwaterdeficit AT faveropeixotojuniorrafael referencegenesfornormalizationofqpcrassaysinsugarcaneplantsunderwaterdeficit AT marchioripauloeduardoribeiro referencegenesfornormalizationofqpcrassaysinsugarcaneplantsunderwaterdeficit AT nobilepaulamacedo referencegenesfornormalizationofqpcrassaysinsugarcaneplantsunderwaterdeficit AT martinsalexandrepalmaboer referencegenesfornormalizationofqpcrassaysinsugarcaneplantsunderwaterdeficit AT ribeirorafaelvasconcelos referencegenesfornormalizationofqpcrassaysinsugarcaneplantsunderwaterdeficit AT crestesilvana referencegenesfornormalizationofqpcrassaysinsugarcaneplantsunderwaterdeficit |