Integration of RNAseq and WGCNA to study phenotypic plasticity in wine grape cultivars grown in central-southern Italy

Phenotypic plasticity is the ability of plants to express different phenotypes from the same base genotype depending on the growing environment. Studying plasticity in gene expression in natural systems is crucial for predicting and managing the effects of climate change on plant species. In this context, post-genomic era studies can provide a wide and unbiased view of plant physiology in different environmental conditions. Grapevine (Vitis spp., family Vitaceae) is characterized by a pronounced influence by the external conditions in terms of variability of the metabolic composition of the berries determining a broad phenotypic plasticity. In this work, we aimed to investigate the genotype × environment (G×E) interactions of two red grape cultivars, the international ‘Cabernet Sauvignon’ and the indigenous ‘Aglianico’, at berry commercial maturity, in three different environments of central-southern Italy: Sicilia, Molise and Campania. Taking advantage of a previously performed transcriptome analysis (RNAseq), gene expression was correlated with quality traits using WGCNA. The analysis revealed highly co-expressed clusters of genes (modules). Interestingly, the analysis suggested that quality traits such as total soluble solid (TSS) and polyphenols (PP) correlated with the expression of a limited group of genes, mainly involved in signaling, regulation of transcription and transport, thus indicating the crucial role of these biological processes in establishing the G×E interaction. These results can contribute to an advanced understanding on the relationship between genotype and environment in wine grape also leading to the identification of the best performing genotype for each latitude in terms of TSS and PP content.