A major aim in modern grapevine (Vitis vinifera L.) breeding programs is the introgression of disease resistance genes along with desired cultural and oenological traits. Understanding the genetic links between resistance genes and agro-oenological traits is a crucial issue for grapevine breeders. We studied the genetic determinism of a wide range of agro-oenological traits in a complex interspecific hybrid population and identified two cases of colocalizations with disease resistance quantitative trait loci (QTL). The species of origin of chromosomal regions in the off-springs were determined thanks to in silico chromosome painting. The linkage drag around resistance genes from primary gene pool was assessed as low due to a good recombination rate with V. vinifera. We established that wild Vitis species are, apart from their interest in disease resistance, essential resources for improving the cultural characteristics of grapevine.