P0398 High Density SNP Consensus Map a Useful Tool for Rapeseed Genomic

Jerome Pauquet , Biogemma, Mondonville, France
Nicolas Ribière , Biogemma, Mondonville, France
Isabelle André , Biogemma, Mondonville, France
Nicole Lucante , Biogemma, Mondonville, France
Jean-Pierre Martinant , Limagrain, Riom, France
Laurent Hanneton , limagrain, Verneuil L'étang, France
Philippe Blanchard , Euralis, Mondonville, France
Nathalie Rivière , Biogemma, Chappes, France
Clotilde Claudel , Biogemma, Mondonville, France
Bruno Grezès-Besset , Biogemma, Mondonville, France
Over the last few years, the use of SNP (Single Nucleotide Polymorphisms) as the preferred marker system for many species has taken off. In the relatively complex amphidiploid species oilseed rape (Brassica napus), this development has taken longer and only now are we arriving at significant numbers of SNP that can be exploited as markers for the various applications of interest, like QTL-fine-mapping, marker assisted selection or association genetics as well as more fundamental work on e.g. understanding genome organisation or genome assembling. In this study we will present the use of several mapping populations to build a SNP based Brassica napus consensus map. A total of more than 10000 genes, were mapped using the Illumina chemistries. The SNP were mapped on populations independently in two main step i) creation of a robust framework of SNP using Mapmaker 3.0 ii) use of Actionmap (Albini et al, NAR 31: 3815-18, 2003) to assign all the markers to linkage groups.  Finally, Biomercator(Arcade et al., Bioinformatics 20 (14): 2324-2326, 2004) was used to construct the consensus map. For map construction, positions were considered homologous between maps when they derived from the same amplicon and mapped to the equivalent position allowing maximising linked between maps.