Abstract
Background
Red blotch disease, caused by Grapevine red blotch virus (GRBV, genus Grablovirus, family Geminiviridae), negatively impacts vine health, fruit yield, and quality, leading to substantial economic losses to growers. While recent studies have enhanced our understanding of the epidemiology of GRBV and its effects, little is known about the molecular basis of the host-virus interactions. Since small RNAs (sRNAs) are known to play a central role in host-virus interactions, this study was undertaken to investigate sRNA dynamics in leaves and berries at two phenological stages (asymptomatic pre- and symptomatic post-veraison) of GRBV-infected grapevines (Vitis vinifera cv. Merlot).
Results
Among the 140 microRNAs (miRNAs) detected, 41 isoforms belonging to 18 miRNA families exhibited significant differential expression in response to GRBV infection. Furthermore, 50 miRNAs showed differential expression in samples from pre- and post-veraison stages. A total of 58 conserved and 41 novel targets for known V. vinifera miRNAs were validated using degradome sequencing data from leaf samples of pre- and post-veraison stages. Viroid-derived small-interfering RNAs (vdsiRNAs) specific to Grapevine yellow-speckle viroid-1 and Hop stunt viroid were also identified in all samples, while virus-derived siRNAs (vsiRNAs) specific to GRBV were present only in GRBV-positive samples. The vsiRNAs predominantly ranged from 19 to 24 nucleotides (nt), with the 21nt size being the most abundant. Mapping vsiRNAs across the GRBV genome revealed an uneven distribution, with vsiRNA-generating hotspots predominantly located in the V3 ORF. Of the 83 most abundant vsiRNAs, targets within the grapevine transcriptome were identified for eight of them. Significantly higher levels of HSVd RNAs were observed in GRBV-positive samples compared to GRBV-negative samples, suggesting a potential synergistic interaction between the two pathogens.
Conclusions
The predominance of 21-nt long vsiRNAs, as well as the predominance of those mapping to the V3 ORF compared to other ORFs, provide insight into both the biogenesis and methods of action of GRBV vsiRNAs. Target validations of vsiRNAs and differentially expressed miRNAs are indicative of pathways and mechanisms which may lead to the expression of Grapevine red blotch disease symptoms. This research serves as a foundation for future studies on the molecular interactions in this plant-geminivirus pathosystem.