Grapevine field experiments reveal the contribution of genotype, the influence of environment and the effect of their interaction (GXE) on the berry transcriptome [array]

Changes in the performance of genotypes in different environments are defined as genotype 3 environment (G3E) 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 G3E 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 G3E-related. The G3E-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 G3E 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. Vitis vinifera berries from Sangiovese and Cabernet Sauvignon cultivars were harvested at four different developmental stages (i.e., pea size (PS), pre-veraison (PV), mid-ripening (MR) and fully ripe (FR)), in three central Italian locations (i.e., Bolgheri in the Tuscany coast, Montalcino in the Tuscany Appennines and Riccione in the Adriatic coast) (Fig. 1a, Supplementary Tables 1-2) during two consecutive growing seasons (2011 and 2012) in biological triplicates for a total of 144 samples.