Environmental conditions and agronomic practices induce consistent global changes in DNA methylation patterns in grapevine (Vitis vinifera cv Shiraz). Huahan Xie 1,2‡ , Moumouni Konate 1,2‡ , Na Sai 1,2,3 , Kiflu Gebremicael Tesfamicael 1,2 , Timothy Cavagnaro 2 , Matthew Gilliham 2,3 , James Breen 4,5 , Andrew Metcalfe 6 , Roberta DeBei 2 , Cassandra Collins 2 , Carlos Marcelino Rodriguez Lopez 1,2 * 1 Environmental Epigenetics and Genetics Group, University of Adelaide, Waite Campus, PMB1 Glen Osmond, SA, 5064. 2 The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, PMB1 Glen Osmond, SA, 5064 3 The ARC Centre of Excellence in Plant Energy Biology, University of Adelaide, Waite Campus, PMB1 Glen Osmond, SA, 5064. 4 Robinson Research Institute, University of Adelaide, Adelaide 5005, Australia 5 University of Adelaide Bioinformatics Hub, School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia 6 School of Mathematical Sciences, University of Adelaide, Adelaide 5005, Australia ‡ Both authors contributed equally. *Corresponding author Correspondence: Dr. Carlos Marcelino Rodriguez Lopez University of Adelaide, Plant Research Centre School of Agriculture, Food and Wine, Waite Campus, Adelaide, SA, 5064, Australia. carlos.rodriguezlopez@adelaide.edu.au Abstract Fruit attributes that affect wine quality are thought to be largely driven by the interaction of grapevine’s genetic characteristics with environmental factors (i.e. climate, soil and topography) 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 will provide us with an insight into how to better manage crop quality. 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 the contribution of DNA methylation to plant performance has been extensively studied in other major crops, very little work has been done in grapevine. Here we used Methylation Sensitive Amplified Polymorphisms to obtain global patterns of DNA methylation, and to identify the main drivers of epigenetic diversity across 22 vineyards planted with the cultivar Shiraz in six distinctive wine areas of a major wine zone, The Barossa, South Australia. The observed epigenetic profiles showed a high level of differentiation that grouped vineyards by their area of provenance despite the low genetic differentiation between vineyards and sub-regions. Furthermore, pairwise epigenetic distances between vineyards with similar management systems showed a significant correlation with geographic distance. Finally, methylation sensitive Genotyping By Sequencing identified 3,598 differentially methylated genes that were assigned to 1,144 unique GO terms of which 8.6% were associated with response to environmental stimulus. Taken together, our results indicate that the intensity and directionality of DNA methylation differentiation between vineyards and wine sub-regions within The Barossa are driven by management and local growing conditions. Finally, we discuss how epigenetic variability can be used as a tool to understand and potentially modulate terroir in grapevine. . CC-BY-NC-ND 4.0 International license certified by peer review) is the author/funder. It is made available under a The copyright holder for this preprint (which was not this version posted April 29, 2017. . https://doi.org/10.1101/127977 doi: bioRxiv preprint