Field Systems Biology of Grapevine Diseases

Vitis vinifera cultivars are susceptible to a wide range of pathogens that infect vegetative, woody and fruit tissues. Understanding how grapevines and pathogens interact in the vineyard is crucial to improve crop traits under naturally fluctuating environments. In the last three years we have developed genome and transcriptome information for some of the most important grapevine fungal pathogens, including the causal agents of powdery mildew and trunk cankers. Besides the annotation of potential virulence factors, these genomes have provided the references necessary to determine fungal species composition and virulence factor expression patterns in diseased vineyard samples using metagenomics and metatranscriptomics approaches. We have also applied systems biology approaches to characterize changes in grapevine development and responses to biotic stress under field conditions. We have integrated transcriptomics, metabolomics, and enzyme activity assays to characterize the impact of noble rot on the development and metabolism of white-skinned grape berries. We identified grape molecular pathways that were triggered by Botrytis cinerea during noble rot, some of which correspond to plant stress responses, while others are related to ripening processes. Developmental and metabolic changes induced by noble rot also occur during normal development of red-skinned berries, including the activation of secondary metabolic pathways that are absent or have limited flux in white-skinned grape cultivars. We further validated the induction of these pathways using noble-rotted berries from two additional years. We also confirmed that the impact of noble rot on grape metabolism is still detectable in botrytized wines produced from the same vineyard.