SummaryTo cope with the challenges facing agriculture, speeding-up breeding programs is a worthy endeavor, especially for perennials, but requires to understand the genetic architecture of important traits. To go beyond QTL mapping in bi-parental crosses, we exploited a diverse panel of 279 Vitis vinifera L. cultivars. This panel planted in five blocks in the vineyard was phenotyped over several years for 127 traits including yield components, organic acids, aroma precursors, polyphenols, and a water stress indicator. Such an experimental design allowed us to reliably assess the genotypic values for most traits. The panel was genotyped for 60k SNPs by combining an 18K microarray and sequencing (GBS). Marker densification via GBS markedly increased the proportion of genetic variance explained by SNPs, and two multi-SNP models identified QTLs not found by a SNP-by-SNP model. This led to 489 reliable QTLs using the combined microarray-GBS SNPs for 41% more response variables than a SNP-by-SNP model applied to microarray-only SNPs, and many QTLs were new compared to the results from bi-parental crosses. Prediction accuracy ranging from 0.14 to 0.84 for 80% of the response variables was promising for genomic selection, and provided insights into the genetic architecture of each trait when put in perspective with the number of QTLs and heritability.