Influence of Developmental Stage and Shading on Apple ( Malus domestica ) Flesh Polyphenols via Ecophysiological and Epigenetic Mechanisms

Polyphenols are important components of cultivated apple (Malus domestica). Their contents in the flesh undergo deep changes during fruit development and ripening. The controls of these changes are not fully understood and involve many molecular players. In this work, we investigated the link between polyphenol profiles (targeted analysis through UPLC-DAD-ESI-TQ), gene expression patterns, and variations in flesh methylome during development and ripening while applying shading at specific developmental stages. Polyphenol changes occurred early during the cell division period (-74% from unripe to ripe). Gene expression analysis showed an enrichment of the flavonoid pathway during development and ripening, which was associated with increased cytosine methylation in the promoter regions of polyphenol biosynthetic genes. Fruit shading treatments modified flesh composition only if applied early during the cell division period. This effect was not entirely maintained at maturity. The multiomics analysis in dynamics allows us to discuss the underlying mechanisms controlling fruit metabolism.