Development and application of single nucleotide polymorphism markers in the polyploid Brassica napus by 454 sequencing of expressed sequence tags

Single nucleotide polymorphisms (SNPs) are currently the important classes of genetic markers for major crop species. It has the abundant polymorphism, however, is not widely applicable for genetic linkage mapping. In this study, methods for developing SNP markers in polyploid rapeseed by incorporation of expressed sequence tag (EST) redundancy, quality index and lines information between parents in the absence of reference genomic sequence data are demonstrated. For the development of SNP markers, ESTs were generated from two rapeseed parents ZY036 and 51070. Putative SNPs were computationally identified using 201 190 high-quality 454 ESTs from the two parents. A total of 655 putative SNPs were detected, among which transition changes accounted for 56% and transversion changes accounted for 44%. Of 50 randomly selected, putative SNPs 42 could be successfully validated, and six of these were successfully mapped in an F2 population from the two parents that were used for generating the EST libraries. These results demonstrate the usefulness of our approach for SNP marker development.