Dynamic transcriptomic responses reveal candidate defense genes against Spongospora subterranea f. sp. subterranea and Potato mop-top virus infection

Powdery scab, caused by Spongospora subterranea f.sp. subterranea ( Sss ), is persistent soilborne disease of potato. Sss is also a vector for Potato mop-top virus (PMTV), posing another significant threat to tuber quality and marketability. Although currently available cultivars exhibit partial resistance to both Sss and PMTV, the genetic mechanisms of resistance remain poorly understood. In this study, we investigated the molecular basis of resistance to Sss and PMTV using a transcriptomics approach. Early infection time-course RNA-seq data were analyzed from three potato cultivars exhibiting differential susceptibility. Integrative analysis of differential gene expression (DGE) and gene co-expression networks (GCN) identified 80 high-confidence candidate genes associated with defense responses, comprising 52 genes associated with Sss infection and 28 with PMTV infection. These included putative immune receptor genes such as nucleotide-binding leucine-rich repeat (NLR) proteins and leucine-rich repeat receptor-like kinases (LRR-RLKs), which function as resistance (R) genes and pattern recognition receptors (PRRs), respectively. Additional candidates included phytohormone-related genes and those encoding lipoxygenase (LOX), glutathione-S-transferase (GST), and Bet v I family protein (PR10). These findings advance our understanding of host defense mechanisms against Sss and PMTV and provide molecular targets for resistance breeding and genetic improvement of commercially important potato cultivars.