Specifications
Organism/cell line/tissue	Vitis vinifera cv. PN40024
Sex	Hermaphrodite
Sequencer or array type	The scaffold sequences were obtained by whole genome sequencing using the Sanger technology on ABI3730xl sequencers (Applied BioSystems) according to the supplementary information of Jaillon et al., Nature, 2007, 449: 463–468, doi: http://dx.doi.org/10.1038/nature06148. Genotype data were obtained from the GrapeReSeq 20K Vitis genotyping chip (https://urgi.versailles.inra.fr/Species/Vitis/GrapeReSeq_Illumina_20K) following the Infinium HD Assay Ultra Protocol (Ilumina Inc.). The V. vinifera cv. Kishmish vatkana mate pair sequences were produced using an Illumina HiSeq 2500 sequencer (Illumina Inc.).
Data format	Analyzed
Experimental factors	Three mapping populations were used: •120 individuals derived from two reciprocal crosses between V. vinifera cv. Riesling cl.49 and V. vinifera cv. Gewürztraminer cl.643 (Ri × Gw) •358 individuals derived from a cross between V. vinifera cv. Chardonnay and Vitis spp. ‘Bianca’ (Ch × Bi) •192 individuals derived from two reciprocal crosses between V. vinifera cv. Syrah and V. vinifera cv. Grenache (Sy × Gr)
Experimental features	Grapevine reference genome assembly and annotation V. vinifera cv. Kishmish vatkana was used for the generation of mate pair sequences.
Consent	Creative commons non copy left (cc-by): the data can be freely re-used at the condition to cite its authors
Sample source location	The Ri × Gw and the Sy × Gr populations were maintained in experimental units of the Institut National de la Recherche Agronomique (INRA), respectively the Service Experimentation Agricole et Viticole (Colmar, France) and the Domaine de Vassal (Marseillan-Plage, France). The Ch × Bi population and the V. vinifera cv. Kishmish vatkana variety (VIVC no. 6277) were maintained in the germplasm collection of the University of Udine at the Experimental Farm A. Servadei (Udine, Italy).