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

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

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.

MeSH terms

  • Brazil
  • Gene Expression Profiling*
  • Gene Expression*
  • Genes, Plant*
  • Plant Diseases / genetics*
  • Plant Diseases / virology*
  • Potyvirus*
  • RNA Virus Infections / genetics*
  • Real-Time Polymerase Chain Reaction*
  • Saccharum / genetics*
  • Saccharum / virology*

Supplementary concepts

  • Sugarcane mosaic virus