The degree and direction of subgenome expression bias in Brassica napus vary between cultivars, tissues and developmental stages.

Most extant plant lineages show evidence of past polyploidisation events in their genomes. Allopolyploids arise from hybridisation, resulting in polyploid genomes comprising subgenomes from different ancestors. Adaptation to their environment, pre- and post-hybridisation and selection for specific traits has led to several allopolyploids exhibiting an unequal contribution from their subgenomes to phenotypic traits. Associated regulatory changes may have given rise to cultivar-specific subgenome dominance that contributes to the diversity of phenotypes. Likewise, different tissues and developmental stages have distinct expression profiles that may exhibit higher contributions from one subgenome relative to the other. Here, we investigate different metrics for quantifying the contribution of each subgenome to expression in cultivars of Brassica napus, in space (tissue) and time (development). Brassica napus inherited two subgenomes, A and C, from its ancestors Brassica rapa (A) and Brassica oleracea (C). We find that the C subgenome has a larger contribution to transcript abundance than the A subgenome, whereas the mean abundance per expressed gene is higher for the A subgenome. Direct comparison of homoeologous pairs reveals higher expression of genes on the C subgenome. We find that the degree and direction of expression bias can change substantially within a homoeologous pair between cultivars, tissues and across development, suggesting that subgenome dominance is highly dynamic. The quantification of expression bias reveals a strong dependence on the metric and on classification thresholds. These findings help explain contradictory reports on expression bias and subgenome dominance.