The dynamics of ACR and DNA methylation impact asymmetric subgenome dominance in allotriploid Brassica species

Polyploidy plays a crucial role in the evolution and diversification of eukaryotes, often leading to structural and functional imbalances as multiple subgenomes merge. Numerous studies have demonstrated the phenomenon of asymmetric subgenome dominance in polyploid species. However, the subgenomic dominance resulting from interspecific hybridization with accessible chromatin regions (ACRs) and DNA methylation remains largely unexplored in allotriploids. We generated two allotriploid hybrids of Brassica species (ArAnCn) by crossing the allotetraploid Brassica napus (AnAnCnCn) with the diploid Brassica rapa (ArAr). Our results revealed that the An subgenome exhibits the highest levels of gene expression among the three subgenomes (Ar, An, and Cn) in F1 hybrids. However, the Cn subgenome that actually exerts dominance over An and Ar, as evidenced by the abundance of dominant triplet homologous genes. We found that the Cn subgenome contains a significantly higher density of ACRs than An and Ar subgenomes, and the expression levels of dominant triplet homologous genes are closely associated with the presence of ACRs in proximal and genic. Interestingly, variations in DNA methylation levels alone do not fully explain the expression advantages observed in F1 hybrids. We then discovered that reduced CHH methylation in F1 hybrids might be associated with decreased expression of BnaDCL3 and BnaDRM2 in the RNA-directed DNA methylation pathway. Furthermore, the mutants Bnadcl3CR and Bnardr2CR exhibited a selective preference for 24-nt small RNA and non-CG methylation in the An and Cn subgenomes. Overall, this study elucidates the relationship between ACRs, DNA methylation, and asymmetric subgenome dominance in resynthesis allotriploid species.