Network Analysis of the Late Stages of Grape Berry Ripening

Senescent-like processes such as chloroplast disorganization and cell death occur in grape berries in the late stages of ripening. Berry skins are an important source of flavor, color and other berry quality traits. Network analyses, both standard (a posteriori) and weighted gene coexpression network analysis (WGCNA, a priori), were used to elucidate common network modules and hub genes associated with traits in the berry skins of the late stages of berry ripening. RNA-seq analysis of the skins of 7 grapevine cultivars (Cabernet Franc, Cabernet Sauvignon, Merlot, Pinot Noir, Chardonnay, Sauvignon Blanc and Semillon) identified approximately 8,000 differentially expressed genes across 4 different berry sugar levels (20 to 26 °Brix) for all 7 cultivars. Standard network analysis revealed genes involved in light regulation (photosynthesis and the circadian clock), translation, sugar metabolism, phenylpropanoid metabolism, epigenetic regulation, and post-embryonic development. Genes involved in physiological processes like photosynthesis and translation were declining with increasing sugar levels in the berries. Other processes increased such as phenylpropanoid metabolism, sugar metabolism and epigenetic regulation. WGCNA identified 64 gene modules that were organized into 12 gene module networks and 6 higher order gene networks. Some of these gene networks were highly correlated with sugar levels. Some of these networks were highly enriched in the chloroplast and nucleus. Hub genes were identified in these networks. Many members of the core circadian clock were hub genes and associated with several of these gene networks. An integrated model was constructed linking light sensing, alternative splicing, chromosome remodeling and the circadian clock with berry sugar accumulation and development. A common set of genes and gene networks from 7 different cultivars were elucidated for the skins of the late stages of grapevine berry ripening. A complex transcriptional network was elucidated involving berry senescent processes, the circadian clock, RNA splicing, proteolysis and epigenetic regulation. New hypotheses were formulated involving sugar accumulation, the circadian clock, epigenetic regulation, seed and fruit development, which may lead to a better understanding of berry development and fruit quality.