Exploring the metabolic and genetic landscape of potato plants in response to late blight using metabolomic and transcriptomic profiling

Abstract

In this study, a comprehensive metabolomics and transcriptomics analysis was conducted to identify the changes in gene expression, transcription factors (TFs) and metabolites in potato plants upon infection with Phytophthora infestans across infection groups of different time points including CK (healthy leaves without any infection), LK (susceptible early infected leaves), MK (middle stage infected leaves) and FK (late-infected leaves). A total of 1368 metabolites were identified and these metabolites, particularly flavonoids like diglucosyl myricitrin and phenolic acids like 1, 3-O-dicaffeoylquinic acid, were significantly regulated, suggesting their roles in plant defense. Metabolites including isoguanine, flavonoids, alkaloids, phenolic acids and lipids reflect a consistent pattern of metabolic alterations across the different comparison groups which suggests a fundamental shift in key metabolic pathways, including nucleotide metabolism, flavonoid biosynthesis, alkaloid regulation and lipid metabolism. The transcriptome analysis identified numerous novel genes and differential gene expression (DEGs) analysis further uncovered genes involved in stress responses, metabolism and hormone regulation, with significant shifts in expression patterns across infection groups. Significant up regulation was observed in genes related to stress responses, metabolic processes, and defense mechanisms, whereas genes involved in signaling pathways and protein kinases were predominantly down regulated. Various transcription factors such as NAP1 (NAC) and WRKY75, linked to defense, environmental stress adaptation and hormone signaling pathways showed significant differential expression. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis emphasized metabolic, secondary metabolite biosynthesis and environmental information processing pathways, underscoring the complex regulatory networks involved in plant adaptation to P. infestans induced stress. Comparative analysis with related species, Solanum lycopersicum and Solanum pennellii, revealed conserved genes across the solanaceae family, suggesting functional divergence. This further underscores the evolutionary conservation of key stress-response and metabolic genes within the family. Our findings underscored the critical role of both metabolic and genetic responses in enhancing resistance to late blight, offering valuable insights for targeted breeding and bio control strategies.