Grape Leafroll Virus: A Systems Approach to Understand its Interaction with the Plant and its Effect on Fruit Ripening

The post-transcriptional regulation of gene expression through miRNA and alternative splicing is an essential component of plant development and response to stress. The present study used RNA and small RNA sequencing technologies to assemble a holistic view of these regulatory agents during ripening in an economically important crop (wine grape) and in response to infection by Grape Leafroll associated Virus (GLRaV). mRNAs and small RNAs from healthy and GLRaV-infected pinot noir fruits were measured weekly from the ripening onset to fruit maturity. We observed approximately 1,700 differentially expressed genes upon comparing healthy and infected berries. Among these genes, a small subset was alternatively spliced (differential exon usage in healthy vs. virus-infected plants). Interestingly, between 1% and 3% of all small RNA reads in GLRaV-infected samples mapped exclusively to the viral genome, providing a trove of information to better understand the interaction between the plant and the virus. Finally, by constructing a network of viral infection-associated differentially expressed genes and incorporating information about changes in the small RNA landscape and the predicted targets of those small RNAs, we identified core nodes through which the presence of the virus potentially signals widespread changes in the berry transcriptome during ripening.