Uncovering the genetic basis of agronomic traits in over 1,000 grapevine genotypes derived from a disease resistance breeding program

European viticulture faces two critical challenges currently: climate change and its direct and indirect impacts in the one hand and the need to dramatically reduce pesticide use in the other hand. In response, breeding programs, such as the INRAE-ResDur program, have prioritized the development of grapevine varieties with disease resistance and improved adaptability to climate change. We took the opportunity of the important plant material produced during the INRAE-ResDur program over twenty years to dissect the genetic basis of key agronomic traits using a comprehensive approach. We conducted genome-wide association studies (GWAS) modeling both additive and non-additive genetic effects, alongside classical QTL mapping and a meta-GWAS that integrates data across multiple environments and pleiotropic effects. These analyses identified numerous loci associated with important traits related to yield, phenology, and stress tolerance. Notably, several loci showed significant genotype-by-environment (GxE) interactions, while others showed pleiotropic effects influencing multiple traits. Overall, 39 genomic regions were detected in QTL analysis in biparental populations, GWAS with additive and non-additive effects, and meta-GWAs analysis, accounting for the 13 agronomic traits. These results provide valuable molecular markers that can be applied in marker-assisted selection or knowledge-assisted genomic selection. This study highlights a complex polygenic architecture underlying agronomic traits in grapevine, involving multiple loci with both additive and interaction effects and underscores the need for integrative breeding strategies to achieve sustainable improvements in future viticulture.