Chromosomal Rearrangements Cause Divergence of the Brassica B Genome from its Closely Related A and C Genomes and Limit Homoeologous Recombination

Of the three Brassica diploid genomes (AA, BB and CC, each represented in B. rapa, B. nigra and B. oleracea respectively) the B genome has evolved separately from the A/C lineage for some 6 million years. The B genome is recognized as an important source of useful genes for Brassica crop improvement, yet thus far has not been as extensively studied as its relatives. The B genome shows limited homoeologous recombination with the A and C genome chromosomes and it’s not yet known if this lack of recombination is controlled by genetic factors or caused by structural divergence.

A Bacterial Artificial Chromosome (BAC) library of B. nigra was screened to make a physical map of regions homologous to a 222 kb segment of A. thaliana chromosome 4 (At4), which was also duplicated on At5. Fingerprinting of 483 BACs defined six physical contigs for this region in B. nigra as expected if the B genome shared the whole genome triplication event previously identified in the Brassiceae tribe.  Sequencing of representative BACs from each physical region elucidated micro-scale rearrangements across the three paleopolyploid Brassica genomes. Extensive conservation of gene content and sequence identity was found with one large-scale chromosomal rearrangement differentiating the genomes. These findings suggest such events are the main force in the speciation of B. nigra limiting recombination between the B genome and the genomes of the closely related A/C lineage.