Microarray-Based Uncovering of Reference Genes for Quantitative Real-Time PCR in Potato Tuber Infected with PVY

Abstract

Stored potato tubers are susceptible to pathogens, such as Potato virus Y, and studies of host/pathogen interactions on a gene transcription level can provide insight into the disease development. A method for studying individual gene expression is reverse trancription quantitative polymerase chain reaction (RT-qPCR) that relies on utilization of reference genes. To select appropriate reference genes with stable expression in our experimental setting, we screened the genome-wide microarray expression data for suitable candidate reference genes rather than to use generally recognised constitutively expressed housekeeping genes as reference genes. Four highly expressed genes with stable expression across several comparisons were selected based on microarray data. Stable expression of these candidate reference genes (Nicalin, Eukaryotic translation initiation factor 5A, Universal stress protein and Katanin p60 ATPase-containing subunit) was confirmed using RT-qPCR. Our candidate reference genes were more suitable than housekeeping genes often used as reference genes. Additionally, microarray expression data was evaluated for eight previously reported reference genes.