A dense single-nucleotide polymorphism-based genetic linkage map of grapevine (Vitis vinifera L.) anchoring Pinot Noir bacterial artificial chromosome contigs

Abstract

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 1245 cM with an average distance of 1.3 cM between adjacent markers, the map was generated from the segregation of 483 single-nucleotide polymorphism (SNP)-based genetic markers, 132 simple sequence repeats (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 that are included in a physical map produced from the same clone of Pinot Noir and covering 352 Mbp. On the basis of 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, are useful for evolutionary studies, and 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.

Figure 1.—

Consensus linkage map of Vitis vinifera from the Syrah × Pinot Noir cross. Linkage groups are numbered according to the V. vinifera map of Adam-Blondon et al. (2004). Markers from EST and from coding BES regions are shown in blue, noncoding BESs in green, SSRs in red, and AFLP markers in black. Loci with a distorted segregation ratio are marked by asterisks (*P < 0.05; **P < 0.01; ***P < 0.001). Distances of markers from the top are indicated on the left in centimorgans. Linked markers that excessively increased the linkage group end distances or that affected the order of neighbors in the group were not included in the map and are listed below each linkage group.

Figure 1.—

Consensus linkage map of Vitis vinifera from the Syrah × Pinot Noir cross. Linkage groups are numbered according to the V. vinifera map of Adam-Blondon et al. (2004). Markers from EST and from coding BES regions are shown in blue, noncoding BESs in green, SSRs in red, and AFLP markers in black. Loci with a distorted segregation ratio are marked by asterisks (*P < 0.05; **P < 0.01; ***P < 0.001). Distances of markers from the top are indicated on the left in centimorgans. Linked markers that excessively increased the linkage group end distances or that affected the order of neighbors in the group were not included in the map and are listed below each linkage group.

Figure 1.—

Consensus linkage map of Vitis vinifera from the Syrah × Pinot Noir cross. Linkage groups are numbered according to the V. vinifera map of Adam-Blondon et al. (2004). Markers from EST and from coding BES regions are shown in blue, noncoding BESs in green, SSRs in red, and AFLP markers in black. Loci with a distorted segregation ratio are marked by asterisks (*P < 0.05; **P < 0.01; ***P < 0.001). Distances of markers from the top are indicated on the left in centimorgans. Linked markers that excessively increased the linkage group end distances or that affected the order of neighbors in the group were not included in the map and are listed below each linkage group.

Figure 1.—

Consensus linkage map of Vitis vinifera from the Syrah × Pinot Noir cross. Linkage groups are numbered according to the V. vinifera map of Adam-Blondon et al. (2004). Markers from EST and from coding BES regions are shown in blue, noncoding BESs in green, SSRs in red, and AFLP markers in black. Loci with a distorted segregation ratio are marked by asterisks (*P < 0.05; **P < 0.01; ***P < 0.001). Distances of markers from the top are indicated on the left in centimorgans. Linked markers that excessively increased the linkage group end distances or that affected the order of neighbors in the group were not included in the map and are listed below each linkage group.