Abiotic and Biotic Stress Responses in Solanum tuberosum Group Phureja DM1‐3 516 R44 as Measured through Whole Transcriptome Sequencing

Abstract

This study conducted an in‐depth analysis of the potato (Solanum tuberosum L.) transcriptome in response to abiotic (salinity, drought, and heat) and biotic (Phytophthora infestans, DL‐β‐amino‐n‐butyric acid, and acibenzolar‐s‐methyl) stresses and plant hormone treatment (abscisic acid, 6‐benzylaminopurine, gibberellic acid, and indole‐3‐acetic acid) using ribonucleic acid sequencing (RNA‐seq) of the doubled monoploid S. tuberosum Group Phureja DM1‐3 516 R44 clone. Extensive changes in gene expression were observed with 37% of the expressed genes being differentially expressed in at least one comparison of stress to control tissue. Stress‐inducible genes known to function in stress tolerance or to be involved in the regulation of gene expression were among the highest differentially expressed. Members of the MYB, APETALA2 (AP2)/ethylene‐responsive element binding factor (ERF), and NAM, ATAF1/2, and CUC2 (NAC) transcription factor families were the most represented regulatory genes. A weighted gene co‐expression network analysis yielded 37 co‐expression modules containing 9198 genes. Fifty percent of the genes within these co‐expression modules were specific to a stress condition indicating condition‐specific responses. Cross‐species comparison between potato and Arabidopsis thaliana (L.) Heynh. uncovered differentially expressed orthologs and defined evolutionary conserved genes. Collectively, the transcriptional profiling of RNA‐seq data presented here provide a valuable reference for potato stress responses to environmental factors that is supported by statistically significant differences in expression changes, highly interconnected genes in co‐expression networks, and evidence of evolutionary conservation.