Genomic and Epigenomic Relationships Capture Different Patterns of Genotype-by-Environment Interaction in Grapevine Clones

In 206 Riesling (Vitis vinifera) clones across nine growing seasons, epigenomic relationships captured a substantial share of genotype-by-environment interaction, exceeding genomic contribution in four of five traits.

• Why it matters: GEI limits consistent selection in clonally propagated perennials, and it is unclear whether genetic or epigenetic variation better explains year-to-year clone performance.
• What they did: Paired genomic SNPs and unmethylated-region profiles were generated with UMR-seq, then genomic and epigenomic relationship matrices were used to partition clonal variance and GEI under models with and without explicit GEI.
• The result: Without explicit GEI, environmental and residual effects dominated and genomic main effects were modest; with factor-analytic GEI covariance, epigenomic effects drove most GEI variance and differed in clone re-ranking and genomic-window localization.

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