Transcriptome Analysis of Potato (Solanum tuberosum L.) Seedlings with Varying Resistance Levels Reveals Diverse Molecular Pathways in Early Blight Resistance

Early blight, caused by the pathogen <i>Alternaria solani</i>, is a major fungal disease impacting potato production globally, with reported yield losses of up to 40% in susceptible varieties. As one of the most common diseases affecting potatoes, its incidence has been steadily increasing year after year. This study aimed to elucidate the molecular mechanisms underlying resistance to early blight by comparing gene expression profiles in resistant (B1) and susceptible (D30) potato seedlings. Transcriptome sequencing was conducted at three time points post-infection (3, 7, and 10 dpi) to identify differentially expressed genes (DEGs). Weighted Gene Co-expression Network Analysis (WGCNA) and pathway enrichment analyses were performed to explore resistance-associated pathways and hub genes. Over 11,537 DEGs were identified, with the highest number observed at 10 dpi. Genes such as <i>LOC102603761</i> and <i>LOC102573998</i> were significantly differentially expressed across multiple comparisons. In the resistant B1 variety, upregulated genes were enriched in plant-pathogen interaction, MAPK signaling, hormonal signaling, and secondary metabolite biosynthesis pathways, particularly flavonoid biosynthesis, which likely contributes to biochemical defense against <i>A. solani</i>. WGCNA identified 24 distinct modules, with hub transcription factors (e.g., <i>WRKY33</i>, <i>MYB</i>, and <i>NAC</i>) as key regulators of resistance. These findings highlight critical molecular pathways and candidate genes involved in early blight resistance, providing a foundation for further functional studies and breeding strategies to enhance potato resilience.