BMC Genomics 2006, 7:12 http://www.biomedcentral.com/1471-2164/7/12 IFnitgeugraete7d genetic and local physical map spanning the complex locus VvF3'5'H on LG6 Integrated genetic and local physical map spanning the complex locus VvF3'5'H on LG6. Contigs were assembled using FPC and BAC clones were further aligned using BES-derived markers. Contigs were anchored to the 'Cabernet Sauvi- gnon' and the V. vinifera consensus genetic maps using cross-referenced SSR markers. The orientation of each contig is arbi- trary. Genetic and physical distances are not drawn to scale. Names written in horizontal refer to BAC clones and contigs; those written in vertical refer to markers and genes. The presence of a given marker on a BAC clone is highlighted with a sym- bol and different SSCP haplotypes for each marker are shown with different symbols (■ ● ❍ ). The symbol 'X' stands for lack of amplification of a given marker in the corresponding BAC clone. BAC clones missing any symbols were not tested with the corresponding marker. Physical localisation of VvF3'5'H-1 and VvF3'5'H-2 loci is shown in grey boxes. era consensus map [A. Doligez, unpublished data] by the SSR markers VrZag30, VMC3a8 and VMC3f12, respec- tively. The region spanned 3.0 cM and the median VMC3a8 marker was settled 0.6 cM and 2.4 cM away from VrZag30 and VMC3f12, respectively (Figure 7). The BES of positive BAC clones provided new markers that were closely linked to the flavonoid 3',5'-hydroxylase gene copies and served to characterize that region more precisely. The marker BES9C17-FM was located on the physical map downstream of SSR VrZag30 and identified only BAC clones belonging to the contig ctg313. BES38C24-RM matched uniquely the BAC clones 38C24 and 21H16 belonging to ctg1320. Conversely, BES40A22- FM and BES38C24-FM primers were designed on BES belonging to ctg313 and ctg1320, respectively, but cross- identify BAC clones assembled in both contigs. SSCP analysis of BES40A22-FM and BES38C24-FM fragments revealed that for each marker two haplotypes are present in ctg313 and two different haplotypes are present in ctg1320. Yet, marker BES17K04-FM matched BACs 6H20, 9C17 and 31P20 of ctg313 and BACs 29J23, 38C24, 4K10, 30K14 of ctg1320. SSCP analysis identified four dif- ferent haplotypes at the regions amplified by BES17K04- FM primers: two haplotypes were detected in the BAC clones of ctg1320, one more different haplotype was present in ctg313, and yet another SSCP haplotype was found in both BAC17K04 and BAC24N06 belonging to ctg2373. The occurrence of more than two haplotypes of the flavonoid 3',5'-hydroxylase gene fragments and of the BES markers in a diploid genotype confirmed the presence of paralogous copies of the flavonoid 3',5'-hydroxylase genes and rule out the possibility that the individual con- tigs represent allelic regions that have not been properly Page 10 of 17 (page number not for citation purposes)