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 ( L.) transcriptome in response to abiotic (salinity, drought, and heat) and biotic (, 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 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 (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.