Genomic and epigenomic contributions to trait variation, genotype-by-environment interactions, and stability in grapevine clones

Abstract

Clonal selection remains central to grapevine improvement, yet consistent yield and fruit quality across vintages are challenged by pronounced genotype-by-environment interactions (G×E). While genomic markers are increasingly used to characterise clonal diversity, the extent to which epigenomic variation contributes to trait performance and stability in grapevine remains unclear.

Here, we integrate genomic (SNP) and epigenomic (DNAmethylation-derived) features with 11 years of phenotypic data from 210 Riesling clones to quantify their relative contributions to yield and juice quality traits. Genomic and epigenomic relationship structures differed substantially, indicating that methylation profiles capture patterns of clonal relatedness not fully explained by DNAsequence variation.

Multi-kernel linear mixed modelling and subsequent variance partitioning revealed that epigenomic features contributed strongly to trait variation and explained a greater proportion of G×E interaction variance than genomic markers for yield and key fruit quality traits. Notably, the two molecular layers exhibited distinct G×E patterns, with epigenomic features explaining a greater proportion of interaction variance, indicating that they capture components of performance not fully represented by genomic markers.

Aggregating marker effects to genomic regions identified segments associated with both high mean performance and reduced year-to-year variability, providing a framework to prioritise stability-associated regions in clonal selection.

These findings demonstrate that integrating epigenomic information can enhance the dissection of trait stability in grapevine and offers new opportunities to refine clonal selection strategies for consistent performance under variable growing conditions.