A Novel EPGV Workflow for a Successful Design of 13K SNPs for High Throughput Genotyping on Illumina Array in an Polyploid Species: Rapeseed (Brassica napus L)

We have designed a high-throughput genotyping 20K InfiniumHD iSelect beadchip for the Brassica napus(DARMOR-bzh line) genome sequencing project to validate and refine the assembly of the polyploid genome.

The EPGV workflow efficiently demonstrates the selection and the design of the most informative SNPs onto the 20K InfiniumHD beads. The critical strategy of the process was the selection of unique SNPs overcoming the constraints of a highly similar homoelogous nature of this polyploid genome.The relevance of the selection process has been validated first by an efficient clustering with the GenomeStudio software and secondly by the construction of a cluster file containing 87% of successful SNPs.

Furthermore, the genetic mapping with three offsprings from five parental lines leads to a high level of genotype detection (>90% of the SNPs for 95% of individuals). The on-going analysis with a panel of 120 diverse rapeseed lines confirms the usefulness of these SNPs for association genetics analyses as we have found more than 75% of SNPs with a minor allele frequency greater than 5%. We will present the EPGV work-flow and the preliminary results obtained.