MRNA transcription profile of potato (Solanum tuberosum L.) in response to explant cutting

Abstract

The explant is an important parameter in plant tissue culture. Most plant tissue culture studies in the literature have focused almost exclusively on the use of explants as a tool for organogenesis or (micro)propagation, and there is limited information that documents the changes that occur in explants in response to cutting during explant preparation just prior to or during culture. To better understand the molecular changes occurring during the wounding process that accompanies the preparation of an explant, this study examined the mRNA transcription profile of 4-week-old potato (Solanum tuberosum L. cv. Desirée) single-node stem segments. To achieve this, RNA-seq analysis was performed to identify significantly differentially expressed genes (DEGs) that existed between uncut in vitro plantlets and cut explants. DEGs corresponding to specific enzyme profiles were broadly connected to cellular processes in the extracellular region, nucleus, and plasma membrane, and were associated with biosynthesis, carbohydrate metabolism and catabolism, cellular protein modification, growth and development, and response to stress. The RNA-seq data of eight highly up- or down-regulated DEGs was validated by RT-qPCR, showing high positive Spearman and Pearson correlation coefficients (0.73 and 0.95, respectively) between SeqMonk LFC and RT-qPCR LFC. These results provide a novel perspective of the changes taking place within explants when they are cut and serve as a valuable basis for the study of explant-related stress in plant tissue culture in other species. In addition, our findings may contribute to an understanding of the success or failure of the tissue culture protocol and subsequent establishment of in vitro cultures by better appreciating the stress-related molecular changes taking place.