Ripening Transcriptomic Program in Red and White Grapevine Varieties Correlates with Berry Skin Anthocyanin Accumulation

Abstract

Grapevine () berry development involves a succession of physiological and biochemical changes reflecting the transcriptional modulation of thousands of genes. Although recent studies have investigated the dynamic transcriptome during berry development, most have focused on a single grapevine variety, so there is a lack of comparative data representing different cultivars. Here, we report, to our knowledge, the first genome-wide transcriptional analysis of 120 RNA samples corresponding to 10 Italian grapevine varieties collected at four growth stages. The 10 varieties, representing five red-skinned and five white-skinned berries, were all cultivated in the same experimental vineyard to reduce environmental variability. The comparison of transcriptional changes during berry formation and ripening allowed us to determine the transcriptomic traits common to all varieties, thus defining the core transcriptome of berry development, as well as the transcriptional dynamics underlying differences between red and white berry varieties. A greater variation among the red cultivars than between red and white cultivars at the transcriptome level was revealed, suggesting that anthocyanin accumulation during berry maturation has a direct impact on the transcriptomic regulation of multiple biological processes. The expression of genes related to phenylpropanoid/flavonoid biosynthesis clearly distinguished the behavior of red and white berry genotypes during ripening but also reflected the differential accumulation of anthocyanins in the red berries, indicating some form of cross talk between the activation of stilbene biosynthesis and the accumulation of anthocyanins in ripening berries.

Genetic, epigenetic and genomic effects on variation of gene expression among grape varieties

“…Within each sampling stage, we scheduled the day of sampling in a genotype‐specific manner, in order to collect berries synchronized by phenology across genotypes. Shifts in phenology among genotypes widened as berry development progressed (Massonnet et al ., ). At P and PV stages, the interval of sampling spanned 3 and 4 days, respectively.…”

“…Experimental conditions for gene expression analyses are described in Massonnet et al . (). RNA‐seq raw reads are stored in NCBI Gene Expression Omnibus (GEO) under accession numbers and .…”

The study of hormonal metabolism of Trincadeira and Syrah cultivars indicates new roles of salicylic acid, jasmonates, ABA and IAA during grape ripening and upon infection with Botrytis cinerea

“…3). Content in anthocyanins has been 2 0 described as a reliable indicator of the ripening stage [42]. Additionally, recent 2 1 metabolomics data did not show significant differences in the main ripening parameters 2 2 between control berries of the two cultivars (data not shown).…”

Iso-Seq allows genome-independent transcriptome profiling of grape berry development

“…Grape berries undergo a series of complex physiological and biochemical changes during their development that determine their characteristics at harvest (Kuhn et al 2014). Genome-wide expression studies using microarray and, more recently, RNA sequencing (RNA-seq) revealed that berry development involves the expression and modulation of approximately 23,000 genes (Massonnet et al 2017a) and that the ripening transition is associated with a major transcriptome shift (Fasoli et al 2012). Transcriptomic studies characterized the ripening program across grapevine cultivars (Venturini et al 2013;Da Silva et al 2013;Jiao et al 2015;Massonnet et al 2017a),…”

“…identifying key ripening related genes (Palumbo et al 2014;Massonnet et al 2017a) and determining the impact of stress and viticultural practices on ripening (Deluc et al 2009;Pastore et al 2013;Xi et al 2014;Blanco-Ulate et al 2015Corso et al 2015;Hopper et al 2016;Savoi et al 2016;Zenoni et al for any grape cultivar. Although the V. vinifera genome is relatively small (~487Mb) (Lodhi and Reisch 1995;Jaillon et al 2007) and as repetitive as other plant genomes of similar size (41.4%) (Jaillon et al 2007;Michael and Jackson 2013), it is highly heterozygous (~13%) (Jaillon et al 2007;Velasco et al 2007).…”