Exploring intra-varietal variation for complex traits in grapevine (Vitis vinifera L.)

Centuries of clonal propagation have shaped remarkable intra-varietal genetic diversity in grapevine, offering valuable opportunities to dissect complex traits and accelerate genetic improvement while safeguarding varietal integrity. Climate change poses significant challenges to global grapevine (Vitis vinifera L.) production, highlighting the urgent need for adaptive breeding strategies to accelerate genetic improvement. While clonal propagation preserves varietal identity and heterozygosity, it also limits the rate of genetic gain due to prolonged breeding cycles. This study assessed phenotypic and genetic variation within eight clonal populations of key grapevine varieties (Pinot Blanc, Pinot Gris, Pinot Noir, Pinot Noir Précoce, Riesling, Müller-Thurgau, Auxerrois, and Savagnin Rose) using 14 years of data collected in Germany across six agronomic, quality, and disease-related traits. Estimates of broad-sense heritability, genetic correlations, and key variance components were derived using linear mixed models. Substantial intra-varietal phenotypic variation was observed across all traits, with moderate to high heritability estimates, confirming that a meaningful proportion of the phenotypic variation can be attributed to the genetic differences among clones. Substantial year and year-by-field variance and interaction components were found to contribute to the total phenotypic variance for most traits, aligning with previous reports of substantial genotype-by-environment interaction in clonal grapevine populations. Genetic correlations revealed both strong positive and strong negative trait relationships, emphasising the importance of informed multi-trait selection strategies. The results highlight considerable potential to enhance clonal selection by integrating predictive breeding tools such as genomic and phenomic selection. Optimisation-based multi-trait selection approaches also offer promising alternatives to traditional index methods, particularly in the context of negative trait correlations. Ultimately, the high intra-varietal genetic variation uncovered in this study represents a valuable resource for improving adaptation to future environments while maintaining varietal integrity in grapevine.