Understanding the genetic determinism of crop yield, grape quality traits and adaptation potential is of paramount importance both for practical viticulture and for breeding new varieties to face future climate change challenges. The rapid development of advanced phenotyping and genotyping technologies will provide the information needed to cope with the efficient analysis of these complex traits by the use of relatively low-cost and robust systems. Here, we report the use of genotyping-by-sequencing (GBS, Keygene patents) to a large half-diallel grapevine population (N ~ 600) from 10 connected segregating progenies. The approach was useful to identify a total of 71,720 genetic polymorphisms, including biallelic SNPs and multiallelic markers. A subset of fully-informative and/or common markers to all (or 9) progenies were selected for the subsequent genetic grouping and mapping within each progeny. This process led to individual consensus maps with similar length than those previously published, but higher marker density. Individual maps were then merged to create a high-density grapevine integrated genetic map, with high informative content and acceptable marker order agreement between progenies. On the other hand, novel image-based phenotyping systems are designed for the automatic and non-destructive estimation of flower number, berry number and berry size, and available high-throughput phenotyping technologies are used to evaluate stress indicators of photosystems in selected individuals from the population. This novel genetic and phenotypic information will be integrated to identify QTLs and candidate genes involved in the genetic determinism of these relevant grapevine traits.