High-Density SNP Markers Based Map Construction and Genome-Wide Linkage Analysis in Brassica napus

The 5306 validated SNP markers were genotyped using 139 individuals of a doubled haploid population derived from a cross between Skipton and Ag-Spectrum. A genetic linkage map based on 1341 SNP, DArT, SSR, SRAP and candidate gene markers was constructed and further utilised to identify loci associated with flowering time and resistance to blackleg disease, caused by the fungus Leptosphaeria maculans. A total of 809 SNP markers were mapped to unique positions on the A and C genomes and provided a framework genetic linkage map. A QTL analysis revealed that a single major locus Rlm4 controls resistance to L. maculans isolate 04MGPS021 and is located on chromosome A7. Several SNPs along with other markers were mapped within 1 cM of the Rlm4 locus. SNP markers associated with QTL for flowering time were also identified on chromosome A2, A3, and A7. Alignments of SNP and other markers with the reference genomes of Brassica rapa and Brassica oleracea allowed identification of candidate genes for resistance to blackleg and flowering time. To test the usefulness of SNP markers we are currently investigating genome-wide associations for various target traits important to Australian B. napus breeding programs. Genome wide identification and validation of SNP markers in conjunction with high throughput genotyping will enable genomic selection for qualitative and quantitative traits to be used in B. napus improvement programs.