Reference genes in plant–pathogen interaction: a bibliometric analysis

Plant–pathogen interactions are complex biological processes characterized by dynamic changes in genes expression. In molecular plant pathology research, RT-qPCR has proven to be a valuable tool for investigating plant–pathogen interactions by examining gene expression changes in both plants and pathogens during infection. The choice of reliable reference genes is crucial, as this directly affects the robustness of normalization and the accuracy of analyzing the expression of genes of interest. A systematic literature search was conducted across relevant academic databases, resulting in the selection of 47 articles (38 on fungi and oomycetes, 7 on bacteria and 2 covering both bacteria, fungi and oomycetes) that evaluated the stability of 190 candidate reference genes. The most used reference genes in plant—fungal and oomycete pathosystems were GAPDH, ACT, TUB and EF, whereas UBQ, TUB, EF and ACT were most used in plant—bacterial pathosystems. Reference genes revealed considerable variability in their stability across different crops, pathogens and experimental conditions. Notably, several classical reference genes, traditionally assumed to maintain stable expression, exhibited considerable variability, supporting concerns regarding their reliability as universal references. Therefore, this review provides important insights for researchers seeking to identify suitable reference genes for their validation studies in plant–pathogen interaction.