Hybrid epigenome unveils parental genetic divergence shaping salt‐tolerant heterosis in Brassica napus

Heterosis holds great potential for improving yield, quality, and environmental adaptability in crop breeding, which suggests that hybrids can exhibit better performance in adapting to extreme environments. However, the epigenetic mechanisms of salt-tolerant heterosis in allopolyploid crop Brassica napus (AACC, 2n = 38), particularly chromatin accessibility, remain largely unexplored. We investigated the dynamics of chromatin accessibility and transcriptional reprogramming during a time course of salt exposure in Brassica napus hybridization. We observed the importance of epigenetic and transcriptional regulation in plant resilience. The chromatin accessibility and transcriptome rapidly changed within a short time frame of salt exposure. Hybrid possessed more accessible chromatin and more active transcriptome than that of parents driven by epigenetic aggregation and genetic complementation. Broader and more flexible genomic resources enabled hybrid preferentially unitized advantageous alleles for salt stress adaptation. Meanwhile, these salt stress-responsive genes in hybrid exerted various heterotic effects, with non-additive genetic effects, including full-dominance, partial-dominance, and overdominance effects, playing a crucial role in salt stress adaptation. Our results expanded the heterosis hypothesis from an epigenetic perspective and emphasized how the combined effects of genetic and epigenetic factors enable hybrid to better withstand salt stress.