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. 2019 Mar 18;12(1):149.
doi: 10.1186/s13104-019-4168-5.

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

Marcel Fernando da Silva  1 , Marcos Cesar Gonçalves  2 , Michael Dos Santos Brito  3 , Paula Macedo Nóbile  1 , Larissa Mara de Andrade  1 , Cibele Nataliane Medeiros  1 , Silvana Creste  1 , Luciana Rossini Pinto  4
Affiliations

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

Marcel Fernando da Silva et al. BMC Res Notes. .

Abstract

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.

Keywords: BestKeeper; GeNorm; NormFinder; Normalization; RefFinder; Saccharum spp.; Sugarcane mosaic disease.

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Conflict of interest statement

The authors declare that they have no competing interest.

Figures

Fig. 1
Fig. 1
Pairwise variation analysis between the normalization factors NFn and NFn+1 of candidate reference genes calculated by GeNorm in order to determine the optimal number of control genes for normalization
See this image and copyright information in PMC

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