Time-Series Comparative Transcriptome Analyses of Two Potato Cultivars with Different Verticillium Wilt Resistance

Comparative omics analysis offers one of the most direct and effective approaches to gain novel insights into crop traits, facilitating candidate gene identification and crop improvement. Verticillium dahliae causes one of the most globally devastating crop diseases, the Verticillium wilt (VW). However, comparative transcriptome resources regarding VW resistance remain scarce in a major host species potato. To address this knowledge gap, we provide a comprehensive comparative RNA-seq analysis of VW resistance between a VW-resistant and -susceptible potato cultivar (LS8 and SP, respectively). VW inoculation induced dramatic transcriptomic changes, resulting in 14,310 differentially expressed genes (DEGs) in LS8 and 21,739 DEGs in SP. With the time-series analysis, we disentangled the VW-associated transcriptomic responses from those reflected LS8-SP cultivar differences. Particularly, LS8 featured a rapid response of phytohormone salicylic acid and defense-related specialized metabolites at 1 day post inoculation (dpi), followed by large-scale metabolic reprogramming, including carbohydrate and choline metabolism and enhanced biosynthesis of secondary cell wall components (e.g., hemicellulose, xylan, cuticle, suberin, and wax). Furthermore, we identified highly expressed VW-responsive potato phenylalanine ammonia-lyase genes (StPALs) and revealed the higher PAL activities in LS8 associated with VW resistance. Overall, our results provide the first transcriptomic insights into VW resistance in potato and new candidate genes regarding VW resistance.