title: Selection of reference genes for transcriptional analysis of edible tubers of potato (Solanum tuberosum L.).
abstract: Potato (Solanum tuberosum) yield has increased dramatically over the last 50 years and this has been achieved by a combination of improved agronomy and biotechnology efforts. Gene studies are taking place to improve new qualities and develop new cultivars. Reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) is a bench-marking analytical tool for gene expression analysis, but its accuracy is highly dependent on a reliable normalization strategy of an invariant reference genes. For this reason, the goal of this work was to select and validate reference genes for transcriptional analysis of edible tubers of potato. To do so, RT-qPCR primers were designed for ten genes with relatively stable expression in potato tubers as observed in RNA-Seq experiments. Primers were designed across exon boundaries to avoid genomic DNA contamination. Differences were observed in the ranking of candidate genes identified by geNorm, NormFinder and BestKeeper algorithms. The ranks determined by geNorm and NormFinder were very similar and for all samples the most stable candidates were C2, exocyst complex component sec3 (SEC3) and ATCUL3/ATCUL3A/CUL3/CUL3A (CUL3A). According to BestKeeper, the importin alpha and ubiquitin-associated/ts-n genes were the most stable. Three genes were selected as reference genes for potato edible tubers in RT-qPCR studies. The first one, called C2, was selected in common by NormFinder and geNorm, the second one is SEC3, selected by NormFinder, and the third one is CUL3A, selected by geNorm. Appropriate reference genes identified in this work will help to improve the accuracy of gene expression quantification analyses by taking into account differences that may be observed in RNA quality or reverse transcription efficiency across the samples.
authors.affiliation: Food Science Department, Food Science and Technology Institute, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.
authors.forename: Roberta Fogliatto
authors.initials: RF
authors.lastname: Mariot
authors.affiliation: Genetics Department, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.
authors.forename: Luisa Abruzzi
authors.initials: LA
authors.lastname: de Oliveira
authors.affiliation: RIKILT, Wageningen UniversityR, Wageningen, The Netherlands.
authors.forename: Marleen M
authors.initials: MM
authors.lastname: Voorhuijzen
authors.affiliation: RIKILT, Wageningen UniversityR, Wageningen, The Netherlands.
authors.forename: Martijn
authors.initials: M
authors.lastname: Staats
authors.affiliation: Plant Breeding, Wageningen UR, Wageningen, The Netherlands.
authors.forename: Ronald C B
authors.initials: RC
authors.lastname: Hutten
authors.affiliation: RIKILT, Wageningen UniversityR, Wageningen, The Netherlands.
authors.forename: Jeroen P
authors.initials: JP
authors.lastname: Van Dijk
authors.affiliation: RIKILT, Wageningen UniversityR, Wageningen, The Netherlands.
authors.forename: Esther
authors.initials: E
authors.lastname: Kok
authors.affiliation: Food Science Department, Food Science and Technology Institute, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.
authors.forename: Jeverson
authors.initials: J
authors.lastname: Frazzon
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000592:standards*; D017343:Genes, Plant / Q000235:genetics*; D014644:Genetic Variation; D035281:Plant Tubers / Q000235:genetics*; D012015:Reference Standards; D017423:Sequence Analysis, RNA; D011198:Solanum tuberosum / Q000235:genetics*; D014158:Transcription, Genetic
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