Dynamics of small RNAs in a red-fruited wine grape cultivar infected with Grapevine red blotch virus

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-véraison) of GRBV-infected grapevines (Vitis vinifera cv. Merlot).

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-véraison 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-véraison stages. Additionally, 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, grapevine target transcripts were identified for eight of them.

Identification of differentially expressed miRNAs and vsiRNAs, as well as their targets, offered important insights into various pathways and mechanisms that were affected in grapevine infected with GRBV and in modulating different host responses in leaves and berries. This research serves as a foundation for a better understanding of the molecular interactions in this plant-geminivirus pathosystem.