Vitis vinifera is one of the earliest domesticated crop and it is native of the Mediterranean and Middle East areas. Dioecy and allogamy are found in all wild Vitis vinifera L. subsp. sylvestris and for a successful reproduction, cross-pollination is required while inbreeding leads to severe genetic depression of progeny. However, in the cultivated species (subspecies sativa) hermafroditism and self-pollination were selected during the domestication process to improve berry production. The issues that would arise from this contrast are avoided thanks to the process of vegetative propagation, a procedure that allows to fix favorable genes combinations in selected genotypes, making them virtually immortal and escape the need for sexual reproduction. Consequently, some varieties might be very ancient: Pinot noir, Muscat Blanc à Petits Grains, and Sultanina, for example, date back probably to one or two thousands of years ago (Bowers et al. 1999a; This et al. 2006). Moreover, the population structure of Vitis vinifera generated recently a considerable research interest but it is still debated, mostly because it is not clear how accurately germplasm collection used in these studies represent the real population of this species (Myles et al. 2011; Emanuelli et al. 2013; Bacilieri et al. 2013). Indeed, some researchers believe that few varieties are actually progenitors of most of the relevant cultivated genotypes and such elite cultivars are responsible for the complex and close relationships between the cultivars. (Myles et al. 2011).