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Selection of housekeeping genes for qRT-PCR analysis in potato tubers under cold stress

Abstract

Quantitative real-time polymerase chain reaction (qRT-PCR) is currently the most sensitive method used for quantitative gene expression studies. However, minimal variation in the amount of material and presence of inhibitors affecting enzyme efficiency can lead to significant quantification errors. Accurate data normalization is vital using reference genes as internal controls. Many so-called housekeeping genes or reference genes with assumed stable expression can exhibit either up- or downregulation depending on the developmental stage or other environmental conditions. We have evaluated six reference genes (actin, APRT, 18S rRNA, ef1α, β-tubulin and ribosomal protein L2) for qRT-PCR profiling experiments in potato tuber tissues of five varieties during cold storage at different temperatures and treatment periods. Genes were ranked according to their expression stability by BestKeeper, geNorm and NormFinder software tools in the same order. This means that any of them can be used for this purpose. The results indicated that ef1α and APRT were the most stably expressed genes in the potato tuber tissues under different cold storage regimes. We therefore recommend use of this pair of genes as internal controls for gene expression studies under the described conditions.

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Acknowledgments

The authors especially thank Dr. Cristina Lacasta for technical assistance. Part of this work was financed within the project INIA RTA2011-00018-C03-02.

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Correspondence to Jose Ignacio Ruiz de Galarreta.

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Lopez-Pardo, R., Ruiz de Galarreta, J.I. & Ritter, E. Selection of housekeeping genes for qRT-PCR analysis in potato tubers under cold stress. Mol Breeding 31, 39–45 (2013). https://doi.org/10.1007/s11032-012-9766-z

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  • DOI: https://doi.org/10.1007/s11032-012-9766-z

Keywords

  • qRT-PCR
  • Housekeeping
  • Solanum tuberosum L.
  • Cold
  • Potato tuber