GSE98923
Timing and order of the molecular events marking the onset of berry ripening in grapevine
Grapevine (Vitis vinifera L.) is a model for the investigation of physiological and biochemical changes during the formation and ripening of non-climacteric fleshy fruits. However, the order and complexity of the molecular events during fruit development remain poorly understood. To identify the key molecular events controlling berry formation and ripening, we created a highly detailed transcriptomic and metabolomic map of berry development, based on samples collected every week from fruit-set to maturity in two grapevine genotypes for three consecutive years, resulting in 219 samples. Major transcriptomic changes were represented by coordinated waves of gene expression associated with early development, veraison (onset of ripening)/mid-ripening and late-ripening and were consistent across vintages. The two genotypes were clearly distinguished by metabolite profiles and transcriptional changes occurring primarily at the veraison/mid-ripening phase. Co-expression analysis identified a core network of transcripts as well as variations in the within-module connections representing varietal differences. By focusing on transcriptome rearrangements close to veraison, we identified two rapid and successive shared transitions involving genes whose expression profiles precisely locate the timing of the molecular reprogramming of berry development. Functional analyses of two transcription factors, markers of the first transition, suggested that they participate in a hierarchical cascade of gene activation at the onset of ripening. This study defined the initial transcriptional events that mark and trigger the onset of ripening and the molecular network that characterizes the whole process of berry development, providing a framework to model fruit development and maturation in grapevine. Overall design: Grape berries were collected at ten-day intervals in 2012, and weekly in 2013 and 2014 beginning at fruit set until harvest (24.5 °Brix) at the same time of day (8:00 am). Samples were collected in randomized block designs along three rows for each cultivar: 8- and 6-vine blocks for Pinot noir and Cabernet Sauvignon respectively. Each sample entailed the collection of 26 clusters from each vine block. 60 berries, selected from 6 isolated clusters randomly selected from the vine blocks, were ground under liquid nitrogen. Seeds were removed in the grinding process. Frozen powder was aliquoted in 100mg and 400 mg samples for metabolite and RNA extractions respectively. Transcriptomic and metabolomic approaches were used to monitor the expression of all grapevine genes and to elucidate grape berry metabolome during development.