Profiling the transcriptional regulatory network reveals putative shared regulatory elements within homoeologs in polyploid Brassica napus

BACKGROUND: Regulatory elements and their interactions underpin transciptional control and are essential for plant growth and development. Yet, in the allopolyploid crop Brassica napus, the global regulatory landscape and the architecture of its complex regulatory networks remain elusive. RESULTS: Here we integrate chromatin accessibility and DNA methylation profiles from four representative accessions to generate a comprehensive atlas of 38,068 regulatory elements in Brassica napus. By coupling these regulatory features with expression quantitative trait locus data, we construct a genome-wide regulatory network comprising 24,541 regulatory elements and 791,512 associations between regulatory elements and genes during seed development. Incorporating 3D genome data reveals that spatial proximity promotes co-expression of cross-chromosomal homoeologous gene pairs through putative shared regulatory elements. Moreover, we uncover pronounced subgenome asymmetry, with the regulatory elements on the An subgenome exerting a disproportionately stronger regulatory influence than those on the Cn subgenome. CONCLUSIONS: This study provides valuable resources for studying the intricate regulatory network governed by regulatory elements and sheds new light on exploring the cross-chromosomal regulation in polyploid plants.