Transcriptomic and genomic structural variation analyses on grape cultivars reveal new insights into the genotype-dependent responses to water stress

Abstract

Grapevine ( Vitis vinifera L.) is importantly cultivated worldwide for table grape and wine production. Its cultivation requires irrigation supply, especially in arid and semiarid areas. Water deficiency can affect berry and wine quality mostly depending on the extent of plant perceived stress, which is a cultivar-specific trait. We tested the physiological and molecular responses to water deficiency of two table grape cultivars, Italia and Autumn royal, and we highlighted their different adaptation. Microarray analyses revealed that Autumn royal reacts involving only 29 genes, related to plant stress response and ABA/hormone signal transduction, to modulate the response to water deficit. Instead, cultivar Italia orchestrates a very broad response (we found 1037 differentially expressed genes) that modifies the cell wall organization, carbohydrate metabolism, response to reactive oxygen species, hormones and osmotic stress. For the first time, we integrated transcriptomic data with cultivar-specific genomics and found that ABA-perception and –signalling are key factors mediating the varietal-specific behaviour of the early response to drought. We were thus able to isolate candidate genes for the genotype-dependent response to drought. These insights will allow the identification of reliable plant stress indicators and the definition of sustainable cultivar-specific protocols for water management.

Grapevine adaptation to drought: New candidate genes for the genotype-dependent response

“…During this period, we first investigated the influence of rootstock and irrigation treatments on the vine water status and further we tested the physiological and molecular responses to water deficiency of two different table grape cultivars, Italia and Autumn Royal under WD conditions. This paper summarizes some of the results reported in Perniola et al 2016 [10] and Catacchio et al 2019 [11].…”

“…Vine water status and leaf gas exchange were calculated during the steady period of the water potential diurnal curve (generally between 12.30 and 13.30 h), following the protocols described in [10,11].…”

“…In order to have a comprehensive view on the DEGs belonging to specific pathways of interest, an integrated approach based on multiple annotation methods was used. For detailed protocols see Catacchio et al [11].…”

“…We further analysed the function of those polymorphic genes and we selected putative candidate genes as detailed in [11]. Notably, we found that the higher CN differences affected some well-known stress-related gene families, such as ankyrin repeat proteins belonging to the RING finger family, recently described as specifically related to drought response in Arabidopsis thaliana [15,16].…”

“…DEGs under WD in Italia and Autumn Royal. As modified byCatacchio et al (2019). A) Venn diagrams show down-and up-regulated genes between different water conditions.…”