Transcription Profile of Potato (Solanum tuberosum L.) Growing In Vitro

Despite countless papers on plant tissue culture, few have assessed the transcriptional changes that occur in a developing explant from the moment it is cut and plated, and during early stages of development. In this study, the mRNA profile of in vitro potato (Solanum tuberosum L.) plantlets derived from internode stems was assessed via four comparisons during five time intervals (0 h, 24 h, 48 h, 1 week, and 4 weeks) using the Kyoto Encyclopedia of Genes and Genomes (KEGG) classification. After screening KEGG metabolic groups, 35 processes were shown to be either up- or down-regulated. The vast majority (28 processes) were related to growth or development. The expression intensity of 40,430 genes was assessed and 158, 107, 163, and 142 sequences were either significantly up- or down-regulated at 0 h vs 24 h, 24 h vs 48 h, 48 h vs 1 week, and 1 week vs 4 weeks, respectively. A total of 10 DEGs coding for transcription factors were significantly down-regulated, including five ethylene-responsive transcription factors, and two probable WRKY transcription factors. RT-qPCR was used to validate RNA-seq data: Spearman and Pearson correlation coefficients between SeqMonk LFC and RT-qPCR LFC were 0.748 and 0.879, respectively. To the best of our knowledge, this is the first transcriptomic assessment of the changes taking place in the mRNA profile of a developing potato stem explant.