Harnessing clonal diversity in grapevine: from genomic insights to modern breeding applications

Abstract

Grapevine has been clonally propagated for thousands of years. Though clonal propagation aims at maintaining varietal identity, somatic mutations and epigenetic modifications accumulated over hundreds to thousands of years lead to intra-varietal diversity. This intra-varietal variation is a very valuable resource in grapevine breeding, as it creates the opportunity to improve important traits related to yield, phenology, stress tolerance, and quality without altering the varietal identity which is extremely important for the industry. Recent advances in genomics, epigenetics, and phenotyping technologies are providing completely new opportunities to gain functional insights into the drivers underlying trait variation and to explore this for accelerated grapevine breeding. This review discusses the interaction between somatic mutations, epigenetic regulation, and emerging breeding technologies. We begin by exploring the phenotypic variation observed within clonal populations across various commercially important varieties, focusing on both agronomic and winemaking-related traits. Next, we examine the extent of genomic and epigenomic variation among clones, highlighting known mutations responsible for somatic variants. We also address how grapevine clonal populations serve as an advantageous model for understanding how genetic and epigenetic variants shape complex trait variation. Given recent advances, we discuss the potential of predictive breeding strategies to accelerate clonal evaluation and how genome editing technologies open new opportunities for targeted genetic improvements without passing through the tedium and unpredictability of clonal selection, driven by natural mutation. Ultimately, these new breeding technologies enable the integration of advanced methods into breeding programmes, optimizing grapevine performance while preserving the unique heritage of historic cultivars.

Fig. 1

Schematic representation of how repeated cycles of clonal propagation in grapevine can generate diverse clonal lineages. Note that vegetative propagation of many important cultivars, such as Pinot noir or White Riesling, has been practiced over hundreds to thousands of years of propagation cycles. Green symbols represent beneficial molecular variants, while red symbols indicate negative ones. Crossed-out vines are not propagated as part of maintenance selection to preserve desirable traits. Molecular variants can arise through both genetic mutations and epigenetic modifications, contributing to the diversity observed in clonally propagated grapevine cultivars

Fig. 2

Schematic overview of the grapevine clonal selection pipeline, from initial germplasm exploration to commercial release. The diagram illustrates two main phases: germplasm selection (approximately 5 years) and phenotypic evaluation and selection of superior clones (up to 15 years). The process begins with exploration and identification of promising grapevine clones from old vineyards. Selected clones undergo phytosanitary checks and are subsequently propagated in a controlled vineyard (single location) for preliminary evaluation. Superior clones identified through this initial assessment are then evaluated phenotypically across multiple locations and over multiple years to ensure stability and performance. Ultimately, the best-performing clones are registered and released to the grapevine industry. Activities during Germplasm Selection are primarily conducted by grapevine breeding programmes, whereas phenotypic evaluation and final clone registration involve collaboration between grapevine breeders and national varietal offices