Metabolomics and Lipidomics: insights into resistant grapevine plant defense system against Downy and Powdery mildew

In recent years, increased sensitivity to environmental problems, as well as consumer interest in the nutritional and health aspects of wine production have prompted scientists to deepen their research into the relationships between the vine and its pathogens in order to develop operational strategies to better protect the agricultural environment and improve product quality. Although Vitis vinifera is not resistant to the most common fungal pathogens, different levels of resistance were found in the cultivated varieties. This thesis investigated mono-locus resistant genotypes carrying one locus associated with Plasmopara viticola resistance (Rpv), respectively with Erysiphe necator (Run/Ren) as well as pyramided resistant genotypes carrying more than one resistant gene against two major parasitic diseases of the vine: downy mildew, P. viticola, and powdery mildew, E. necator. The choice of vines was done considering their degree of resistance and susceptibility to the pathogens. The study looked into five resistant mono-locus varieties: BC4, ‘Bianca’, F12P160, ‘Kishmish vatkhana’, ‘Solaris’; five resistant pyramided varieties: F12P127, F13P71, F12P60, F26P92, and NY42; and two susceptible varieties: ‘Pinot Noir’ and ‘Teroldego’. In order to confirm any connections with the various degrees of resistance, the OIV of the infected leaf tissues was also determined. We have performed metabolomic and lipidomic analyses on completely detached leaves, which gave us a molecular snapshot of the complex and quickly evolving metabolic perturbations taking place inside the leaves as a reaction to the pathogen’s infection. The targeted metabolomics approach was used for the analysis of the main classes of plant metabolites (primary compounds, lipids, phenols, and volatile organic compounds), while the semi-targeted lipidomics approach was used for the analysis of lipids only. These cutting-edge "omics" technologies enabled us to investigate alterations in the most important categories of plant metabolites involved in plant defense. Understanding the interactions between plants and diseases aids in the understanding of plant defense systems as well as the characterization of the plant-pathogen relationship and its metabolic disruption. It may also aid in the discovery of pathogen resistance-related biomarkers, which can provide a thorough interpretation of the antagonistic interactions between V. vinifera and the two pathogen infections, as well as useful information for breeders. The metabolomics response of resistant vines to P. viticola during the first 96 hours after pathogen inoculation revealed 22 potential biomarkers of resistance. Metabolite modulation was greatest in mono-locus genotypes at 48 and 96 hpi, compared to pyramided genotypes, where changes began as early as 12 hpi. The metabolomics changes that occurred inside the E. necator-resistant vines provided us with a picture of plant metabolome disturbance, which contributed to the expansion of current understanding about the perturbations that occur in the defense plant system following biotic stress. Several molecules were altered in the pyramided and mono-locus genotypes as compared to the susceptible variety. Among these compounds, ten were highly accumulated after the infection with E. necator. Thus, they have been proposed by our study as potential biomarkers of the resistant varieties. A deeper investigation and a better comprehension of the role of lipids in the plant defense response were necessary in light of the little information currently known about the participation of lipids in the pathosystem of resistant grapevine genotypes—E. necator. Our research found that lipidome changes were most obvious at 24 and 48 hours after inoculation. The extra-plastidial lipids (PC, PE), the signaling lipids (PA and PI), the plastid lipids (PG, MGDG, and DGDG), and in lesser amounts: LPC, LPG, LPI, and LPE were among the lipids that were most frequently discovered in the leaves of the grapevine that had been infected with E. necator. Furthermore, the down-accumulation of the lipid classes distinguished the resistant genotypes, while the up-accumulation of the lipid classes distinguished the susceptible genotype