Physical anchoring and integrated geneting mapping among five elite cultivars of Vitis vinifera L.

The aim of the present work was to develop an integrated gene map among five élite cultivars of Vitis vinifera: ‘Syrah’, ‘Pinot Noir’, ‘Grenache’, ‘Riesling’, and ‘Cabernet Sauvignon’, parents of three crosses analyzed. A novel mapping software tool, which takes into account genotyping errors, was used for the segregation data and linkage analysis. Our integration strategy led to 33.4% of the markers being common to at least two crosses. A new source of markers, single nucleotide polymorphisms (SNPs) identified in coding sequences and unique BAC-end sequences (BESs), was added to the available IGGP reference set of SSRs. The complete integrated map comprises 1,131 loci (349 AFLPs, 331 BESs, 169 ESTs, 282 SSRs) spanning 1,442.5 cM over 19 linkage groups (LGs) and shows a mean distance between neighbor loci of 1.27 cM. A total of 259 SSRs are common to a previous grapevine integrated map based on microsatellites. Marker order was mainly conserved between the integrated map and the highly dense ‘Syrah’ x ‘Pinot Noir’ map except for a few inversions. Of 1,131 markers, 668 were suitable for genetically anchoring 381 contigs of the physical map produced from ‘Pinot Noir’ (covering 360.8 Mbp) and 164 markers were also used to anchor 122 contigs of the physical map produced from ‘Cabernet Sauvignon’ (covering 102 Mbp). Since this integrated linkage map anchors the two existing grapevine physical maps, the development of this unique and useful genetic and genomic tool represents an important resource for the whole grapevine research community.