Comparative transcriptomics and metabolomics in Vitis vinifera cv. Malvasia and Vitis rupestris cv. Du Lot cultured cells provide insights in possible innate resistance against pathogens

Vitis vinifera is one of the most extensively cultivated crops with worldwide economic importance, being the only grapevine species used for the production of wine.The V. vinifera varieties are susceptible to various pathogens responsible for severe crop losses. For these reasons, the cultivation of pathogen-resistant grapevine is one of the most straightforward strategies to reduce the impact of plant infection. Despite research efforts in understanding pathogen susceptibility/resistance in grapevine, the mechanisms that regulate these processes remain unclear. In an attempt to identify the molecular and metabolic mechanisms associated with putative different susceptibility to pathogens, a transcriptome and metabolome profile were carried out in cultured cells of V. vinifera cv. Malvasia and V. rupetris cv. du Lot.Comparative transcriptomic analysis revealed a higher enrichment of genes involved in biosynthesis of cell wall proteins, PR protein, ROS activation, phenylpropanoid pathway, TIR-NBS-LRR proteins and WRKY transcription factors in V. rupestris compared to V. vinifera. 1H-NMR based metabolomic analysis highlighted that leucine, isoleucine, valine, threonine, alanine, gamma-aminobutyric acid (GABA), glutamine, phenylalanine and pyruvate significantly increased in V. rupestris compared to V. vinifera. Conversely, glucose, sucrose, and fumarate significantly decreased in V. rupestris compared to V. vinifera. Our findings reveal distinct pre-constitutive defense systems in two species consisting in an up-regulation of genes and primary metabolites involved in plant defense responses. These responses could be constitutively activated in V. rupestris opening new perspectives for sustainable viticulture through improved breeding programs. The number of up-regulated loci as well as the fold change values were greater in V. rupestris than V. vinifera.