A population-scale analysis of genetic, epigenetic, and phenotypic variation in Pinot clonal populations

Abstract

Clonal selection has been used for centuries to improve major grapevine varieties, yet the molecular mechanisms responsible for phenotypic variation among clones remain poorly understood. While somatic mutations accumulate during vegetative propagation, recent evidence suggests that epigenetic variation, particularly stable DNAmethylation changes, may be an equally important and heritable source of clonal diversity. Understanding the relative contributions of genetic and epigenetic variation to agronomic and oenological performance is essential for developing molecular breeding strategies in clonally propagated crops.

In this ongoing work, we have performed Oxford Nanopore long-read sequencing of 202 clones from the Pinot family (P. noir, P. blanc, P. gris, and P. précoce) to characterize somatic genetic variation, including SNPs and structural variants, alongside single-base DNAmethylation patterns. These molecular data were integrated with extensive two-year field evaluations of phenology, proximal sensing-derived cluster, berry architectural traits and fruit quality parameters. To the best of our knowledge, this represents the most extensive integration of genomic, epigenomic and phenotypic data within a single grapevine cultivar group to date. In ongoing analyses, we dissect the relative contributions of somatic mutations and stable DNAmethylation differences to key agronomic traits. This allows us to resolve molecular drivers of clonal diversity within the Pinot family and to quantify trait variation that cannot be explained by genetic sequence differences alone. By linking specific molecular features to agronomic performance, this work provides a foundation for incorporating epigenetic information into clonal evaluation and selection, and for defining molecular targets that can inform precision breeding strategies in grapevine and other vegetatively propagated crops.