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

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 rodshaped 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.