Gene Set Enrichment Analysis Highlights ATP Hydrolysis and Membrane-Associated Pathways in Drought-Tolerant Potato Cultivars

Abstract

This study investigated the molecular responses of drought-tolerant and drought-sensitive potato cultivars using Gene Set Enrichment Analysis (GSEA) on RNA-seq data. The main objective was to identify activated or suppressed biological pathways and functional gene groups under drought stress, providing insights into drought tolerance mechanisms. Principal Component Analysis (PCA) and heatmap analysis revealed distinct gene expression profiles between the drought-tolerant cultivar FB and the drought-sensitive cultivar Cardinal. GSEA identified statistically significant enrichment of the ATP hydrolysis activity (GO:0016887) term in the FB cultivar, suggesting enhanced energy metabolism under drought conditions. While other GO terms—such as those related to the plasma membrane (GO:0005886), transmembrane transport (GO:0055085), and intracellular membrane-bounded organelles (GO:0043231)—did not reach statistical significance, their positive normalized enrichment scores (NES) indicated a trend toward higher expression in FB. The observed upregulation of ATP hydrolysis activity suggests the critical role of energy-dependent processes, such as protein repair and ion transport, in drought tolerance. Additionally, the results showed the importance of maintaining plasma membrane integrity, regulating transmembrane transport for water conservation, and the involvement of intracellular organelles in adapting to drought stress.