Asymmetric epigenetic modifications and transposable elements contribute to subgenome expression dominance in allotetraploid Brassica juncea

Brassica juncea is a widely cultivated and economically important allotetraploid oilseed and vegetable crop. Subgenome expression dominance is a prevalent phenomenon in allopolyploid plants and plays a pivotal role in metabolic regulation, stress responses, environmental adaptation, and the formation of agronomic traits. However, the relationship between epigenetic modifications, transposable elements (TEs), and subgenome expression dominance in B. juncea remain poorly understood. Here, we examined how subgenome expression dominance in allotetraploid B. juncea is linked to asymmetric epigenetic modifications and TEs. The results showed the A j subgenome as the dominantly expressed subgenome in B. juncea . Epigenetic landscapes constructed for DNA methylation and histone modifications (H3K4me3, H3K9me3, H3K27me3, and H3K27ac) exhibited subgenome asymmetry, with DNA methylation and H3K9me3 modifications showing a bias toward the B j subgenome that closely correlates with subgenome expression dominance. Further analyses revealed that gene expression is jointly regulated by the synergistic and antagonistic interactions among multiple epigenetic modifications. In addition, the number of Class I TEs in the B j subgenome is approximately three times that in the A j subgenome, and compared with the A j subgenome, the B j subgenome harbors higher density of TEs in the gene bodies and a greater number of Class I TEs near genes. These insertional biases of TEs between the subgenomes, together with their association with epigenetic modifications, may be associated with the distinct regulatory landscapes underlying subgenome expression dominance in B. juncea . Taken together, these findings provide valuable insights into the epigenetic regulatory mechanisms underlying subgenome expression dominance in polyploid plants.