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

Grapevine varieties showing putative resistance to pathogens are a promising alternative to reduce the impact of disease management. Despite research efforts in understanding pathogen susceptibility/resistance to pathogens, the mechanisms that regulate these processes remain unclear. To identify the molecular and metabolic mechanisms associated with putative different susceptibility to pathogens and/or constitutive resistance, comparative transcriptomics and metabolomics were carried out in cultured cells of V. vinifera ‘Malvasia’ and V. rupestris ‘Du Lot’. 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, γ-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 insights for sustainable viticulture through improved breeding programs.