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

Changes in the performance of genotypes in different environments are defined as genotype x environment (G x E) interactions. In grapevine (Vitis vinifera), complex interactions between different genotypes and cli- mate, soil and farming practices yield unique berry qualities. However, the molecular basis of this phe- nomenon remains unclear. To dissect the basis of grapevine G x 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 geno- type, and GxE-related. The GxE-related genes showed different degrees of within-cultivar allelic diversity in the two genotypes and were enriched for stress responses, signal transduction and secondary metabo- lism categories. Our study unraveled the mutual relationships between genotypic and environmental vari- ables during GxE 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 deter- mining the performance of different varieties, by enhancing berry quality traits, was unraveled.