A dense SNP-based genetic linkage map of grapevine (Vitis vinifera L.) anchoring Pinot Noir BAC contigs

The construction of a dense genetic map for Vitis vinifera and its anchoring to a BAC-based physical map is described: it includes 994 loci mapped onto 19 linkage groups, corresponding to the basic chromosome number of Vitis. Spanning 1,245 cM with an average distance of 1.3 cM between adjacent markers, the map was generated from the segregation of 483 SNP-based genetic markers, 132 SSRs, and 379 AFLP® markers in a mapping population of 94 F 1 individuals derived from a V. vinifera cross of the cultivars Syrah and Pinot Noir. Of these markers, 623 were anchored to 367 contigs which are included in a physical map produced from the same clone of Pinot Noir and covering 352 Mbp. Based on contigs containing two or more genetically mapped markers, region-dependent estimations of physical and recombinational distances are presented. The markers used in this study include 118 SSRs common to an integrated map derived from five segregating populations of V. vinifera. The positions of these SSR markers in the two maps are conserved across all Vitis linkage groups. The addition of SNP-based markers introduces polymorphisms that are easy to database, useful for evolutionary studies and that significantly increase the density of the map. The map provides the most comprehensive view of the Vitis genome reported to date and will be relevant for future studies on structural and functional genomics and genetic improvement. AFLP® is a registered trademark and the AFLP® technology is covered by patents and patent applications of Keygene N.V.