Combined analysis of mRNA and miRNA transcriptomes reveals the regulatory mechanism of PVY resistance in tobacco

Potyvirus (viruses in the genus Potyvirus, family Potyviridae, PVY) is one of the most important pathogens in tobacco (Nicotiana tabacum L.) and other main crops, which cause devastating epidemic and significant production losses of crops worldwide. K326 is an important tobacco cultivar worldwide, but it is seriously plagued by PVY. In this study, an ethyl methanesulfonate (EMS) mutant M867 from K326 was developed, which was highly resistant to PVY. To explore the molecular mechanism of M867 resistance to PVY, RNA-seq and small RNA-seq were applied to analyze the differences between K326 and M867 responds to PVY infection. There are a total of 34 differentially expressed miRNAs and 5083 mRNAs were identified between K326 and M867 following PVY infection. GO and KEGG enrichment analysis showed PVY response process was significantly related with photosynthesis, carbon metabolism, and antioxidant activity. Thereafter, the results of hormone determination showed that the IAA level of K326 was almost zero after PVY infection, but M867 maintained a high IAA content. Simultaneously, the contents of JA and SA in M867 showed a substantial increase. M867 auxin-related genes (e.g., AUX1, IAA4, and ARF9) were significantly down-regulated after PVY infection compared to K326, but genes related to various hormones, such as CTK, GA, ABA, JA, and SA, showed significant up-regulation. Redox-related peroxidase, superoxide dismutase, and catalase were significantly up-regulated by PVY infection. Besides, six pairs of significant mRNA-miRNA interactions were found, and these genes may be closely related to PVY-host interactions. Furthermore, our findings revealed that the differences between M867 and K326 in hormones, redox reactions, and energy metabolism changed the molecular pathway of the PVY-host interaction, which led to PVY resistance in M867. These results provide valuable resources for elucidating the molecular mechanism of the tobacco-PVY interaction.