Global DNA Methylation Patterns Can Play a Role in Defining Terroir in Grapevine (Vitis vinifera cv. Shiraz)

Abstract

Understanding how grapevines perceive and adapt to different environments 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. To study the genetic and epigenetic diversity across 22 vineyards planted with the cultivar Shiraz in six wine sub-regions of the Barossa, South Australia. Methylation sensitive amplified polymorphisms (MSAPs) were used to obtain global patterns of DNA methylation. 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. Pairwise epigenetic distances between vineyards indicate that the main contributor (23–24%) to the detected variability is associated to the distribution of the vineyards on the N–S axis. Analysis of the methylation profiles of vineyards pruned with the same system increased the positive correlation observed between geographic distance and epigenetic distance suggesting that pruning system affects inter-vineyard epigenetic differentiation. Finally, methylation sensitive genotyping by sequencing identified 3,598 differentially methylated genes in grapevine leaves that were assigned to 1,144 unique gene ontology terms of which 8.6% were associated with response to environmental stimulus. Our results suggest that DNA methylation differences between vineyards and sub-regions within The Barossa are influenced both by the geographic location and, to a lesser extent, by pruning system. Finally, we discuss how epigenetic variability can be used as a tool to understand and potentially modulate terroir in grapevine.

Salt Stress Induces Non-CG Methylation in Coding Regions of Barley Seedlings (Hordeum vulgare)

“…Our findings and those of others [76] do not support this stance, with non-CG types of methylation, such as m CCGG, being found frequently in transcribed regions from DNA isolated from both leaves and roots of barley. It is, however, still open to question whether these markers, like m CG, play roles in regulating gene expression [77].…”

Accumulation of mutations in genes associated with sexual reproduction contributed to the domestication of a vegetatively propagated staple crop, enset

“…Genotyping-by-sequencing was conducted for 149 enset samples (125 domestic and 24 wild; Supplementary Table 2) that were selected to capture the genetic diversity shown by AFLP. The GBS library preparation was carried out as described by Xie et al (2017) including a water negative control as described by Konate et al (2018). The DNA concentration of each individual library was normalized to 5 ng/μl.…”

Linking epigenetics and biological conservation: Towards a conservation epigenetics perspective

“…These environmentally sensitive labile marks hence constitute good molecular biomarkers to evaluate environmental stress experienced by organisms (Mirbahai & Chipman, 2014). The usefulness of epigenetic biomarkers was recently highlighted in an agronomic context for plant cultivars, whereby the pruning systems used in vineyards induce detectable DNA methylation signatures in vines even at narrow geographical scales (Xie et al, 2017). Based on these findings, specific DNA methylation profiles patterns could be used as biomarkers to characterize "terroirs" not only by allocating the geographical and genetic origin of vines but also by determining the pruning systems used in vineyards.…”