Detecting Homoeologous Recombination Events in Cultivated Using a Genome-Wide SNP Array.

The heavy selection pressure due to intensive breeding of has created a narrow gene pool, limiting the ability to produce improved varieties through crosses between cultivars. One mechanism that has contributed to the adaptation of important agronomic traits in the allotetraploid has been chromosomal rearrangements resulting from homoeologous recombination between the constituent A and C diploid genomes. Determining the rate and distribution of such events in natural will assist efforts to understand and potentially manipulate this phenomenon. The Brassica high-density 60K SNP array, which provides genome-wide coverage for assessment of recombination events, was used to assay 254 individuals derived from 11 diverse cultivated spring type These analyses identified reciprocal allele gain and loss between the A and C genomes and allowed visualization of homoeologous recombination events across the genome. The events ranged from loss/gain of 0.09 Mb to entire chromosomes, with almost 5% aneuploidy observed across all gametes. There was a bias toward sub-telomeric exchanges leading to genome homogenization at chromosome termini. The A genome replaced the C genome in 66% of events, and also featured more dominantly in gain of whole chromosomes. These analyses indicate homoeologous recombination is a continuous source of variation in established and the rate of observed events appears to vary with genetic background. The Brassica 60K SNP array will be a useful tool in further study and manipulation of this phenomenon.