Figure 2

Analysis of BAC pools and Brassica accessions with oligonucleotide pool assays. The sequences represent those that were established for the genes found in the Express genome unless indicated otherwise. Panel (A) shows the results for SNP assay #52 which was specific for BnaA.PKp3.a. In this intragenomic SNP assay oligonucleotide 1 corresponds to an allele which was found for example in the genotypes Express and Tapidor, whereas oligonucleotide 2 matched the allele present in the Ningyou7 genome. The darker colored regions in the graphs correspond to genotype call areas which were defined by GenomeStudio Data Analysis Software v2011.1, in the red and blue areas all plants homozygous for the Express and Ningyou7 alleles were found, respectively. Heterozygous plants showed up in the purple area. The results for SNP assays #51 and #47 are displayed in panels (B) and (C), respectively. Oligonucleotides 1 and 2 of intergenomic assays #51 and #47 discriminated between homoeologous genes BnaA.PKp3.a and BnaC.PKp3.a. In all graphs the data points for the BAC pools were color-coded according to the information which was deduced from the BAC coordinates that had been identified via colony hybridization and locus assignment studies. The dashed lines and boxed values correspond to the thresholds which were implemented for the optimized scoring method.