Integrative Physiological, Metabolomic, and Transcriptomic Analyses Provide New Insights into Potato Drought Stress Responses

Background Potato ( Solanum tuberosum L.) is an essential crop for food production and industrial use, yet its growth and development are substantially constrained by drought stress. Drought not only causes marked reductions in tuber yield but also compromises overall plant growth and health. Flavonoids, due to their antioxidant capacity, play a critical role in drought tolerance, and hormone signaling pathways also modulate drought responses. TFs further coordinate these processes by regulating genes in flavonoid biosynthesis and across hormone-signaling pathways. To elucidate the molecular basis of potato adaptation to drought, we conducted integrated metabolomic and transcriptomic analyses of two cultivars subjected to drought treatment. Results In this study, we identified 3,001 metabolites, including 88 classified as flavonoids. Under drought, both HL15 and J8 exhibited pronounced metabolite accumulation alongside significant up-regulation of genes in the flavonoid biosynthetic pathway, indicating a central role for flavonoid metabolism in the drought response of potato. Transcriptome profiling further showed that drought-responsive genes were predominantly enriched in pathways related to flavonoid biosynthesis and plant hormone signal transduction. Correlation analysis, combined with WGCNA, identified three transcription factors that may regulate flavonoid metabolism and hormone signaling under drought conditions. The expression of flavonoid biosynthetic genes, along with the accumulation of most flavonoid metabolites, contributed to enhanced drought tolerance. In addition, plant hormone signaling—particularly the abscisic acid (ABA) pathway—also shaped the drought response. We identified seven key candidate genes involved in regulating flavonoid biosynthesis under drought. Further investigation into flavonoid metabolism and ABA signaling identified three transcription factors as potential regulators of drought tolerance. Conclusions Collectively, these findings demonstrate a significant enrichment of flavonoid pathways and hormone signaling in drought-stressed potato seedlings, providing actionable insights and datasets to inform future studies on drought resistance.