Grapevine field experiments reveal the contribution of genotype, the influence of environment and the effect of their interaction (G×E) on the berry transcriptome

Abstract

Changes in the performance of genotypes in different environments are defined as genotype × environment (G×E) interactions. In grapevine (Vitis vinifera), complex interactions between different genotypes and climate, soil and farming practices yield unique berry qualities. However, the molecular basis of this phenomenon remains unclear. To dissect the basis of grapevine G×E interactions we characterized berry transcriptome plasticity, the genome methylation landscape and within-genotype allelic diversity in two genotypes cultivated in three different environments over two vintages. We identified, through a novel data-mining pipeline, genes with expression profiles that were: unaffected by genotype or environment, genotype-dependent but unaffected by the environment, environmentally-dependent regardless of genotype, and G×E-related. The G×E-related genes showed different degrees of within-cultivar allelic diversity in the two genotypes and were enriched for stress responses, signal transduction and secondary metabolism categories. Our study unraveled the mutual relationships between genotypic and environmental variables during G×E interaction in a woody perennial species, providing a reference model to explore how cultivated fruit crops respond to diverse environments. Also, the pivotal role of vineyard location in determining the performance of different varieties, by enhancing berry quality traits, was unraveled.

Cutting the Gordian Knot of abiotic stress in grapevine: From the test tube to climate change adaptation

“…The relevance of the interactions between genotype and environment was also reported by Dal Santo et al () in berries of ‘Sangiovese’ and ‘Cabernet Sauvignon’ grown in Central Italy (in Tuscany and on the Adriatic coast). This study confirms that there is a huge berry transcriptomic plasticity, reflecting locations and vintages and that gene expression is differentially modulated in response to environmental cues (Dal Santo et al ).…”

“…This study confirms that there is a huge berry transcriptomic plasticity, reflecting locations and vintages and that gene expression is differentially modulated in response to environmental cues (Dal Santo et al ). In both studies, the location of the vineyard had a minor impact on the extent of transcriptome changes in grapes, while qualitative traits, such as the accumulation of secondary metabolites related to wine aroma and color, were significantly affected by the location (Dal Santo et al , ).…”

Same same but different: Cluster architecture variation in five ‘Pinot Noir’ clonal selection lines correlates with differential expression of three transcription factors and further growth related genes

“…Samples from the pre-bloom time showed less variation related to cluster architecture and more variation due to location and season (Figure 6, Online resource 8), than at the later stage. This corresponds to the observation of Dal Santo et al (2018), who identified the factors “developmental stage”, “season” and “location” to affect the overall transcriptional variation over three seasons in two grapevine cultivars.…”

The Rpv3-3 haplotype and stilbenoid induction mediate downy mildew resistance in a grapevine interspecific population

“…In addition, it is worth noting that the WRKY factor VvWRKY28 already found co-expressed with VvSTS transcripts in root and leaves (Corso et al, 2015) was here associated with cis-resveratrol content extending the list of WRKY factors identified as involved in the regulation of stilbenoid metabolism. It has recently been shown that the expression level of several members of the stilbene synthase gene family and genes responsible of the oxidative polymerization of phenolic compounds in the phenylpropanoid pathway is highly influenced by the "location" variable in a G×E interaction study (Dal Santo et al, 2018).…”