Study of 206 Riesling clones links seasonal variability to epigenomic patterns

Nine seasons of clonal data

The study, posted to bioRxiv on November 6, was led by scientists at Hochschule Geisenheim University in Germany, with collaborators in Australia and at the University of Hohenheim. The researchers examined 206 Riesling clones over nine growing seasons, assessing traits associated with production and juice quality.¹

Their central question concerned genotype-by-environment interaction: the possibility that a clone performing strongly in one season may occupy a different relative position in another as weather and other environmental conditions change. This instability is particularly important in perennial crops because grapevines remain in vineyards for many years and clonal selection decisions can be costly and difficult to reverse.¹

Genomic and epigenomic profiles

Using UMR-seq, the team produced paired genomic and epigenomic profiles from the same sample library. The genomic layer recorded DNA sequence variation, including single-nucleotide polymorphisms, while the epigenomic layer identified unmethylated regions—signals related to DNA methylation and gene regulation that do not change the underlying genetic code.¹

When the statistical models did not explicitly incorporate genotype-by-environment interaction, environmental and residual effects represented the largest portions of variation, and the main clonal effect was comparatively small. Genomic relationships accounted for most clonal variance in four of the five traits, while adding an epigenomic relationship matrix produced little change.¹

Epigenomic contribution to seasonal shifts

The results differed when the models directly considered year-specific interaction effects. In that analysis, epigenomic relationships accounted for a substantial portion of genotype-by-environment interaction variance and contributed more than genomic relationships in four of the five traits. The result indicates that epigenomic information may be particularly relevant to understanding why the same clone changes its performance between seasons.¹

The two layers did not merely reproduce the same patterns. According to the authors, genomic and epigenomic relationships captured different forms of clone re-ranking from year to year, identifying distinct changes in relative performance. The strongest estimated genomic and epigenomic effects also generally occurred in different genomic windows, with no more overlap than would be expected by chance.¹

Potential uses and unresolved questions

The findings do not establish that epigenetic markers alone can predict stable vineyard performance, and the paper offers no direct method for selecting clones. If the results are confirmed, however, combining genomic and epigenomic information could eventually help breeders and nurseries assess clones for vineyards exposed to variable conditions. More consistent yield and must composition would be relevant to both grape supply and wine quality, but any practical application remains tentative and requires validation beyond this preprint.¹

The study does not determine how long epigenomic signals persist, whether its findings extend beyond Riesling, the study site and the examined traits, or whether comparable patterns occur in other grape varieties and perennial crops. Its main conclusion is therefore not that epigenomics replaces genomics: genomic relationships were more informative for the main clonal effect in most traits, whereas epigenomic relationships explained a larger part of the year-to-year interaction pattern.¹

Because the work has not undergone peer review, its methods and interpretation still require independent scrutiny. Nevertheless, the dataset—206 Riesling clones observed across nine seasons—is unusually extensive for a vineyard clone study and provides an early basis for investigating the molecular causes of genotype-by-environment interaction and testing whether paired genomic and epigenomic data can improve selection for variable environments.¹