Multi-Omics Data Integration for Genome by Environment Interactions Analysis in Vitis vinifera

Fruit traits affecting wine quality are driven by the interaction of the grapevine’s genome with environmental factors and vineyard management. All these variables, in conjunction with the wine making process, give a wine its distinctive character. Understanding how grapevines perceive and adapt to a changing environment can provide us with an insight to better manage crop quality as we can capture a ‘plant’s perspective of its growing environment’. Mounting evidence suggests that epigenetic mechanisms are a key interface between the environment and the genotype that ultimately affect the plant’s phenotype. Moreover, it is now widely accepted that epigenetic mechanisms are a source of useful variability during crop varietal selection that could affect crop performance. While DNA methylation has been deeply studied in other crops, very little work has been done to understand its contribution to plant performance in grapevine. Here we used epigenomics, transcriptomics, metagenomics and metabolomics to dissect what are the main drivers of epigenetic diversity across 22 vineyards planted with the cultivar Shiraz in five wine subregions of the Barossa Valley (Australia). Interestingly, although the genetic differentiation between vineyards and regions was very low, the observed epigenetic and transcription profiles showed a high level of differentiation that grouped vineyards by subregion. Furthermore, pairwise epigenetic distances between vineyards with similar management systems showed a significant correlation with geographic distance. Taken collectively, our results indicate that plant age, management and local growing conditions are the main drivers of epigenetic differentiation between vineyards and wine subregions within the Barossa Valley.