RNA-seq Profiling Reveals the Transcriptional Response Against Potato Spindle Tuber Viroid in Different Potato Cultivars and Developmental Stages

Potato ( Solanum tuberosum L.) is an important food crop but its production is affected by potato spindle tuber viroid (PSTVd). In this study, five potato cultivars, including Jizhangshu 12, Kexin 1, Jizhangshu 8, Shepody, and Minfenghong, were inoculated with PSTVd, and RNA-seq was carried out to analyse gene expression profiles during PSTVd infection. We also conducted a time-course investigation of three different stages of Jizhangshu 8 infected with PSTVd and control individuals. The results showed that the different cultivars have different genes and pathways to response against PSTVd infection, and most of the upregulated genes were related to biosynthesis and developmental processes, including the development of the stomatal complex, tissues, and the epidermis. The RPP13 gene was upregulated during PSTVd infection in all five cultivars and may play important roles in the PSTVd response process. This study provides insight into the tolerant mechanism against PSTVd and facilitates the mining of PSTVd-tolerant genes in potatoes for innovating germplasm resources. In addition, this study presents valuable genomic data from different potato cultivars and development stages for further studies.