MicroRNA expression dynamics reshape the cultivar-specific response of pepper (Capsicum annuum L.) to potato spindle tuber viroid (PSTVd) infection

Abstract Potato spindle tuber viroid (PSTVd) is one of the smallest pathogenic RNAs infecting plants. It harbors a circular single-stranded RNA genome, which, owing to its considerable self-complementarity, can adopt a specific rod-shaped secondary structure. PSTVd pathogenicity is a complex phenomenon mediated by the sequence- and structure-specific characteristics of the viroid strain, host species-specific genomic traits, and interactions between PSTVd and its host in a dynamic environment. Viroid-responsive miRNAs and their potential role as regulatory determinants in the pathogenicity of PSTVd have been studied in two Bulgarian pepper (Capsicum annuum L.) cultivars: Djulunska shipka (DS) and Kurtovska kapia (KK). In these cultivars, conserved miRNAs such as can-miR397, can-miR398, can-miR408, and can-miR482 display cultivar-specific expression upon PSTVd infection at 28 days post-inoculation (dpi), as shown by sRNA-seq and validated by RT-qPCR. Unlike in KK, the level of can-miR397a-5p was significantly reduced in PSTVd-infected DS, and the expression of its corresponding target gene, Laccase-like 4, was proportionately upregulated at 43 dpi, suggesting that this miRNA/mRNA circuit is implicated in the susceptibility of DS to PSTVd. These results advance our understanding of the cultivar-specific regulation of miRNAs associated with PSTVd response in pepper, and extend the functional role of miRNAs in regulatory networks that operate in the PSTVd–pepper pathosystem.