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Reference gene selection for qPCR analysis in tomato-bipartite begomovirus interaction and validation in additional tomato-virus pathosystems

PLoS ONE (2015) 10(8)
DOI: 10.1371/journal.pone.0136820
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Abstract

Quantitative Polymerase Chain Reaction (qPCR) is currently the most sensitive technique used for absolute and relative quantification of a target gene transcript, requiring the use of appropriated reference genes for data normalization. To accurately estimate the relative expression of target tomato (Solanum lycopersicum L.) genes responsive to several virus species in reverse transcription qPCR analysis, the identification of reliable reference genes is mandatory. In the present study, ten reference genes were analyzed across a set of eight samples: two tomato contrasting genotypes ('Santa Clara', susceptible, and its near-isogenic line 'LAM 157', resistant); subjected to two treatments (inoculation with Tomato chlorotic mottle virus (ToCMoV) and its mock-inoculated control) and in two distinct times after inoculation (early and late). Reference genes stability was estimated by three statistical programs (geNorm, NormFinderand BestKeeper). To validate the results over broader experimental conditions, a set of ten samples, corresponding to additional three tomato-virus pathosystems that included tospovirus, crinivirus and tymovirus + tobamovirus, was analyzed together with the tomato-ToCMoV pathosystem dataset, using the same algorithms. Taking into account the combined analyses of the ranking order outputs from the three algorithms, TIP41 and EF1 were identified as the most stable genes for tomato-ToCMoV pathosystem, and TIP41 and EXP for the four pathosystems together, and selected to be used as reference in the forthcoming expression qPCR analysis of target genes in experimental conditions involving the aforementioned tomato-virus pathosystems. Copyright:

Figures

  • Table 1. Description of the reference and target genes used for qPCR analysis.
  • Fig 1. Cycle of quantification (Cq) values distribution of candidate reference genes. Box-whisker plot showing Cq values distribution of each reference gene considering all samples together (entire dataset). The quartiles with medians are represented by boxes green (upper) and red (lower). Whiskers represent the maximum and minimum values.
  • Table 2. Evaluation of expression stability of reference genes by geNorm, NormFinder, and BestKeeper, considering the entire dataset of ‘Santa Clara’- and ‘LAM 157’-ToCMoV samples.
  • Fig 2. Pairwise variation (V) of candidate reference genes as predicted by geNorm. Pairwise variation (Vn/Vn+1) for determination of the optimal number of reference genes predicted by geNorm and calculated between the normalization factors NFn and NFn+1, with a recommended cutoff threshold of 0.150. The pairwise variation was analyzed considering either all samples together (entire dataset) or in six separate subsets: ‘Santa Clara’ and ‘LAM 157’ (genotype subsets); control and inoculated (treatment subsets) and early and late (time after inoculation subsets).
  • Table 3. Gene stability ranking order by geNorm, NormFinder and BestKeeper; and their respective arithmetic mean ranking values, considering the entire dataset of ‘Santa Clara’-ToCMoV and ‘LAM 157’-ToCMoV samples.
  • Table 4. Gene stability ranking order obtained by geNorm, NormFinder and BestKeeper, considering six subsets of ‘Santa Clara’ and ‘LAM 157’ samples inoculated with ToCMoV.
  • Table 5. Gene stability ranking order by geNorm, NormFinder and BestKeeper, considering 18 samples of ‘Santa Clara’; ‘LAM 157’; ‘Moneymaker’ and ‘LAM 144’ inoculated with ToCV; GRSV; ToBMV+ TMV or ToCMoV.
  • Fig 3. Expression quantification of target genes in ‘LAM 157’-ToCMoV interaction using different combinations of normalizers. The normalization of relative expression data was made with two combinations of reference genes: the two most stable genes (TIP41 and EF1) and the two least stable genes (ACT and TUB) genes. The relative expression of two target genes [Necrotic spotted lesions 1 (NECRO) and HR-like lesion inducer (HR-Li)] was evaluated in ToCMoV inoculated plants of ‘LAM 157’ (resistant genotype) at early (3 and 6 DAI) and late (9, 12 and 15 DAI) times after virus inoculation relative to their respective mock-inoculated controls. Error bars represent the standard deviation of three technical replicates.

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CITATION STYLE

APA

Lacerda, A. L. M., Fonseca, L. N., Blawid, R., Boiteux, L. S., Ribeiro, S. G., & Brasileiro, A. C. M. (2015). Reference gene selection for qPCR analysis in tomato-bipartite begomovirus interaction and validation in additional tomato-virus pathosystems. PLoS ONE, 10(8). https://doi.org/10.1371/journal.pone.0136820

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