Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus

Interspecific hybridization and allopolyploidization merge evolutionarily distinct parental genomes (subgenomes) into a single nucleus. A frequent observation is that one subgenome is \"dominant” over the other subgenome, having a greater number of retained genes and being more highly expressed. Which subgenome becomes dominantly expressed in allopolyploids remains poorly understood. Here we “replayed the evolutionary tape” with six isogenic resynthesized Brassica napus (rapeseed) allopolyploid lines and investigated subgenome dominance patterns over the first ten generations post merger. We found that the same subgenome was consistently more dominantly expressed in all lines and generations and that >70% of biased gene pairs showed the same dominance patterns across all lines and an in silico hybrid of the parents. Gene network analyses indicated an enrichment for network interactions and several biological functions for the Brassica oleracea derived 'BnC' subgenome biased pairs, but...