Abstract
BackgroundGene transcripts that show invariant abundance during development are ideal as reference genes (RGs) for accurate gene expression analyses, such as RNA blot analysis and reverse transcription–quantitative real time PCR (RT-qPCR) analyses. In a genome-wide analysis, we selected three “Commonly used” housekeeping genes (HKGs), fifteen “Traditional” HKGs, and nine novel genes as candidate RGs based on 80 publicly available transcriptome libraries that include data for receptacle development in eight strawberry cultivars.ResultsThe results of the multifaceted assessment consistently revealed that expression of the novel RGs showed greater stability compared with that of the “Commonly used” and “Traditional” HKGs in transcriptome and RT-qPCR analyses. Notably, the majority of stably expressed genes were associated with the ubiquitin proteasome system. Among these, two 26 s proteasome subunits, RPT6A and RPN5A, showed superior expression stability and abundance, and are recommended as the optimal RGs combination for normalization of gene expression during strawberry receptacle development.ConclusionThese findings provide additional useful and reliable RGs as resources for the accurate study of gene expression during receptacle development in strawberry cultivars.
Highlights
Gene transcripts that show invariant abundance during development are ideal as reference genes (RGs) for accurate gene expression analyses, such as RNA blot analysis and reverse transcription–quantitative real time PCR (RT-qPCR) analyses
26–18S rRNA, CHP1, ENP1 and UBQ11 were not analyzed because they were not annotated as a gene in the strawberry genome, or no sequence information is provided in the previous reports
To identify eligible RGs from the aforementioned Traditional kousekeeping gene (HKG) families for strawberry receptacle development, we used a similar approach as described by Dekkers et al [26]
Summary
Gene transcripts that show invariant abundance during development are ideal as reference genes (RGs) for accurate gene expression analyses, such as RNA blot analysis and reverse transcription–quantitative real time PCR (RT-qPCR) analyses. In a genome-wide analysis, we selected three “Commonly used” housekeeping genes (HKGs), fifteen “Traditional” HKGs, and nine novel genes as candidate RGs based on 80 publicly available transcriptome libraries that include data for receptacle development in eight strawberry cultivars. Reverse transcription–quantitative real time PCR (RT-qPCR) is a favored approach used for quantification of gene expression on account of its specificity, accuracy, and reproducibility. Accurate normalization is fundamental for reliable analysis of RT-qPCR data. This technology requires stably expressed reference genes (RGs) for expression normalization of target genes. Failure to use an appropriate RG may lead to biased gene expression profiles and low reproducibility
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