Plant & Animal Genomes XIII Conference Plant & Animal Genomes XIII ConferenceJanuary 15-19, 2005
Town & Country Convention Center
San Diego, CA
Gregor Durstewitz , Joerg Plieske , Andreas Polley , Eva-Maria Graner , Hartmut Luerssen , Dagmar Kulosa , Martin W. Ganal
SNPs are the most frequent type of genetic polymorphism and expectations are high for association and linkage studies using SNPs as genetic markers. SNP-based DNA fingerprints can further be useful for variety identification, phylogenetic analysis and the assessment of genetic diversity.
We have started a project aimed at SNP discovery, validation, mapping and genotyping. This project utilizes an integrated platform for large scale SNP discovery. Our strategy for SNP discovery is based on comparative sequencing of EST amplicons in a test panel of Brassica varieties. This Brassica panel is designed to represent the entire range of genetic diversity in allopolyploid rapeseed with a focus on economically important lines and includes the diploid parental genomes of cabbage (Brassica oleracea, C genome) and bird rapeseed (Brassica rapa, A genome). Actual (as opposed to in silico) sequencing produces a wealth of supplementary data. This includes A/C-genome differentiation as well as access to flanking sequence and neighboring polymorphism data for custom assay design. In addition, data from this SNP pipeline include information on PCR conditions, detected SNP markers, mapping data, allele frequencies in relevant populations and actual SNP genotypes of tested varieties.
Using this approach, we have investigated approximately 2.500 ESTs from Brassica. SNPs have been identified in more than 1.000 genes. Several hundred of the investigated genes have been mapped through Pyrosequencing onto our integrated rapeseed map containing approximately 1.000 microsatellite markers.