Investigating Grapevine Red Blotch Virus Infection in Vitis vinifera L. cv. Cabernet Sauvignon Grapes: A Multi-Omics Approach

Abstract

Grapevine red blotch virus (GRBV) is a recently identified virus. Previous research indicates primarily a substantial impact on berry ripening in all varieties studied. The current study analyzed grapes' primary and secondary metabolism across grapevine genotypes and seasons to reveal both conserved and variable impacts to GRBV infection. Vitis vinifera cv. Cabernet Sauvignon (CS) grapevines grafted on two different rootstocks (110R and 420A) were analyzed in 2016 and 2017. Metabolite profiling revealed a considerable impact on amino acid and malate acid levels, volatile aroma compounds derived from the lipoxygenase pathway, and anthocyanins synthesized in the phenylpropanoid pathway. Conserved transcriptional responses to GRBV showed induction of auxin-mediated pathways and photosynthesis with inhibition of transcription and translation processes mainly at harvest. There was an induction of plant-pathogen interactions at pre-veraison, for all genotypes and seasons, except for CS 110R in 2017. Lastly, differential co-expression analysis revealed a transcriptional shift from metabolic synthesis and energy metabolism to transcription and translation processes associated with a virus-induced gene silencing transcript. This plant-derived defense response transcript was only significantly upregulated at veraison for all genotypes and seasons, suggesting a phenological association with disease expression and plant immune responses.

Keywords: grape metabolism; grape ripening; grapevine red blotch virus; plant-pathogen interactions; virus-induced gene silencing.

Figure 1

Log fold changes of primary metabolite concentrations through ripening in Cabernet Sauvignon grapes grafted onto 110R and 420A rootstocks in 2016 and 2017. Negative values (blue) indicate a decrease in concentration and positive values (red) indicate an increase in concentration in RB(+) grapes compared to RB(−) grapes. Color gradient indicates the size of log fold change. Values in bold indicate a significant difference (p < 0.05, FDR correction). CS = Cabernet Sauvignon, PV = pre-veraison, V = veraison, PoV = post-veraison, and H = harvest.

Figure 2

Log fold changes of secondary metabolite concentrations through ripening in Cabernet Sauvignon grapes grafted onto 110R and 420A rootstocks in 2016 and 2017. Negative values (blue) indicate a decrease in concentration and positive values (red) indicate an increase in concentration in RB(+) grapes compared to RB(−) grapes. Color gradient indicates the size of log fold change. Bolded values indicate a significant difference (p < 0.05, FDR correction). CS = Cabernet Sauvignon, PV = pre-veraison, V = veraison, PoV = post-veraison, and H = harvest.

Figure 3

Number of significantly (p < 0.01) differentially expressed genes at each ripeness level across genotype and season. Different coloring indicates different gene ontology classifications based on biological processes. Negative values indicate significantly down regulated genes and positive values indicate significantly upregulated genes. CS = Cabernet Sauvignon, PV = pre-veraison, V = veraison, PoV = post-veraison, H = harvest.

Figure 4

Venn Diagram of upregulated differentially expressed genes (A) and downregulated differentially expressed genes (B) for each rootstock and season. The genes at each ripeness level were pooled for each rootstock and season combination to find the conserved up and downregulated genes due to GRBV infection. CS = Cabernet Sauvignon.

Figure 5

Log fold change of conserved genes affected by GRBV infection based on results from the Venn Diagram in Figure 4. Transcripts are grouped together in clusters based on dendrogram output. Negative values (blue) indicates a decrease in gene expression in diseased grapes and positive values (red) indicate an increase in gene expression in diseased grapes compared to healthy grapes. Color gradient indicates the size of log fold change. 110R = Cabernet Sauvignon on rootstock 110R and 420A = Cabernet Sauvignon on rootstock 420A.

Figure 5

Log fold change of conserved genes affected by GRBV infection based on results from the Venn Diagram in Figure 4. Transcripts are grouped together in clusters based on dendrogram output. Negative values (blue) indicates a decrease in gene expression in diseased grapes and positive values (red) indicate an increase in gene expression in diseased grapes compared to healthy grapes. Color gradient indicates the size of log fold change. 110R = Cabernet Sauvignon on rootstock 110R and 420A = Cabernet Sauvignon on rootstock 420A.

Figure 6

Two networks produced through differential co-expression analysis, one showing a gain in co-expression (A) and one showing a loss in co-expression (B). The centralized gene is VIT_04s0023g00920, which encodes for a dicer-like protein The transcripts on the exterior are associated with (a) transcription and translation processes or (b) with metabolite synthesis and energy metabolism.

Figure 7

Comparison of viral gene expression in each season (A) and cumulative growing degree days in each season (B). 110R = Cabernet Sauvignon on 110R rootstock and 420A = Cabernet Sauvignon on 420A rootstock. Viral counts consist of the two mRNAs (sense strand and antisense strands) thought to translate the five proteins encoded by the GRBV genome.