Single berry sampling reveals novel insights into transcriptomic changes induced by leafroll virus infections in grapevine (V. vinifera)

Abstract

Background Grapevine leafroll associated viruses (GLRaV), the causing agents of grapevine leafroll disease (GLD) are amongst the most devastating graft and vector transmitted pathogens in viticulture and responsible for important economic losses in the wine industry. Reported fruit alterations caused by GLD consist in a delay of ripening, a reduction in anthocyanins, aroma compounds and sugar concentration. The molecular interactions underlying the quality deteriorating effects are not well understood so far. The few conducted molecular studies on infected berries did associate the lack of anthocyanin and sugar content with a repression of key genes of the respective pathways. However, sampling protocols in such studies never accounted for berry heterogeneity and potential virus induced phenological shifts. Thus, such commonly used sampling strategies could have introduced unquantifiable biases in gene expression studies which would impede the discovery of novel molecular information. The aim of the present study was to investigate the effects of GLRaV-1 and GLRaV-1&3 infections on berry physiology of Pinot Noir vines. Berries of different treatments were individually sampled and analyzed for sugar and organic acids. According to this biochemical analysis 2 homogenous stages were reconstituted to circumvent berry heterogeneity and compensate for virus induced phenological shifts. RNA of 18 reconstituted samples (2 stages and 3 treatments) was extracted, sequenced and analyzed for differentially expressed genes (DEGs). Results A total of 2136 transcripts were modulated by GLRaV-1 and GLRaV-1&3 infections. Interestingly the transcriptome of the early ripening berry was much more affected as the later ripening stage. Several pathways related to abiotic and biotic stress, defense mechanism as well as plant immunity showed a virus-induced upregulation in dependence to ripening stage and infection severity. Surprisingly, the previously reported repression of anthocyanin biosynthesis and sugar metabolism could not be confirmed by gene expression. This illustrates that the main damaging effect on GLRaV infection is rather related to a phenological shift than to a direct impact on metabolism. Conclusions The here reported results give new insight in the mechanism of leafroll infection and emphasize the importance of the sampling protocol of molecular studies investigating berry metabolism.

Modifications of Grapevine Berry Composition Induced by Main Viral and Fungal Pathogens in a Climate Change Scenario

“…In a very comprehensive study on Carbernet Franc over 2 years on different rootstocks, Vondras et al (2021) observed a rootstock specific transcriptomic response of berries from GLRaV-infected vines. Latter authors observed the modulation of genes related to pathogen detection, for example NBS-LRR genes that confer resistance to powdery and downy mildew (DM) in grapevine (Riaz et al, 2011;Zini et al, 2019), as well as abscisic acid (ABA) signaling, phenylpropanoid biosynthesis, and cytoskeleton remodeling similar to previous studies of Vega et al (2011) and Ghaffari et al (2020). Interestingly the increase of ABA abundance in GLRD-infected berries (Vondras et al, 2021) was different than that observed for red blotch virus-infected berries, in which ABA abundance and NCED expression decrease in infected berries after véraison (Blanco-Ulate et al, 2017).…”

“…Vega et al (2011) also observed a viral repression of sugar transporters, which translated to lower sugar concentration in grapes. Interestingly, a study using a different berry sampling approach, which accounts for potential phenological shifts and intracluster berry heterogeneity, has demonstrated that the downregulation of genes belonging to primary and secondary metabolite pathways was mainly due to the berry phenological delay induced by GLRD infection and not to a direct effect of the viral infection (Rienth et al, 2019b;Ghaffari et al, 2020). In a very comprehensive study on Carbernet Franc over 2 years on different rootstocks, Vondras et al (2021) observed a rootstock specific transcriptomic response of berries from GLRaV-infected vines.…”

“…However, molecular data regarding the interactions between pathogens and the berry are scarce. Nevertheless, the rapid development and improvement of omic tools continuously increase our insights into plant-berry pathogen interactions (Blanco-Ulate et al, 2015Rienth et al, 2019b;Ghaffari et al, 2020;Toffolatti et al, 2020;Pimentel et al, 2021). The first part of this review aims to summarize the most important and recent studies dealing with the effects of gray mold, PM, and DM on berry quality and metabolism.…”