The single-berry metabolomic clock paradigm reveals new stages and metabolic switches during grapevine berry development.

Abstract

Asynchronicity causes metabolic chimerism in usual grapevine phenological stages, calling for a revisit of berry development at the individual fruit scale. To reveal the dynamics of metabolite composition in grapevine berries without phenological a priori, a dataset of 9,256 ions was obtained on 125 fruits at different stages by non-targeted ultra-performance liquid chromatography coupled to high-resolution mass spectrometry. This large metabolomic dataset was submitted to an analysis workflow combining classification and dimension reduction tools. This led to the clustering of metabolites into 12 specific kinetic patterns and a metabolome-based definition of the pericarp intrinsic clock outperforming expert timing procedures. Such increased temporal resolution enabled the identification of metabolite clusters that are annunciative of the onset of ripening, noticeably characterized by transient lipidic changes and the start of ABA accumulation. We also highlighted a cluster of stilbenes that accumulate during terminal fruit shriveling, after the arrest of phloem unloading. This non-targeted approach enables a more precise characterization of grapevine berry development through the concept of metabolomic clock. The discovery of new metabolic milestones of berry development paves the way toward a better assessment of the impact of environmental changes on the metabolism of non-climacteric fruit, in different genotypes.