Integrative physiological, metabolomic, and transcriptomic analyses provide new insights into potato drought stress response

Potatoes (Solanum tuberosum L.) are an essential crop for food production and industrial use; however, their 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. Owing to their antioxidant capacity, flavonoids play a critical role in drought tolerance, and hormone signaling pathways also modulate plant drought responses. Transcription factors further coordinate these processes by regulating genes involved in flavonoid biosynthesis and hormone signaling pathways. Therefore, the purpose of this study was to elucidate the molecular basis of drought adaptation in potatoes. To this end, we subjected the drought-resistant potato cultivar J8 and drought-sensitive potato cultivar HL15 to drought treatment and conducted integrated metabolomic and transcriptomic analyses. We identified 3001 metabolites, including 88 flavonoids. Under drought conditions, both HL15 and J8 exhibited pronounced metabolite accumulation, along with significant up-regulation of genes in the flavonoid biosynthetic pathway, indicating the central role of flavonoid metabolism in the drought responses of potatoes. Transcriptome profiling revealed that the drought-responsive genes were predominantly enriched in pathways related to flavonoid biosynthesis and plant hormone signal transduction. Correlation analysis, combined with weighted gene co-expression network analysis, 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 flavonoid metabolites, contributed to enhanced drought tolerance. In addition, plant hormone signaling, particularly the abscisic acid (ABA) signaling pathway shaped the drought response. We identified seven candidate genes involved in the regulation of flavonoid biosynthesis under drought conditions. Further investigation of flavonoid metabolism and ABA signaling identified three transcription factors as potential regulators of drought tolerance. Collectively, these findings demonstrate substantial enrichment of flavonoid pathways and hormone signaling in potato seedlings under drought stress, providing actionable insights and data to inform future studies on drought resistance.