Exploring Chromosome Interactions in Higher Ploidy Brassica Populations Using the Infinium 60K SNP Chip

The Brassica genus provides a versatile model for investigating chromosome interactions in polyploids. Six species contain the AA, BB, CC, AABB, AACC and BBCC genome combinations, and these species can be hybridised to produce a variety of genome configurations with comparative ease.  We are investigating basic questions about how meiotic chromosome behaviour links to sequence similarity,  genome dosage and genome differentiation by molecular karyotyping of interspecific hybrid populations using the recently released Illumina Brassica Infinium 60K SNP chip. Much has been discovered previously by genotyping such populations using hybridisation- or PCR-based markers. However, the arrival of the Infinium 60K SNP chip for the Brassica A and C genomes provides a powerful genotyping tool with unprecedented resolution to detect genome interactions in experimental populations. We show examples of how the Infinium 60K chip is allowing us to understand how polyploidy, speciation and genome differentiation affect chromosome behaviour in Brassica.