Genome-wide reprogramming of sRNA and lncRNA in the epigenetic regulation following interspecific hybridization in the Brassica species

Interspecific hybridization has a significant impact on the inheritance of non-coding RNAs (ncRNAs), resulting in alterations in gene expression and phenotypic variation. However, the mechanisms behind interspecific hybridization-mediated ncRNA regulation and its interaction with epigenetic pathways are not well understood. We examined ncRNA profiles in two F 1 hybrids of Brassica napus and Brassica rapa (Hybrid-sh and Hybrid-yh). Regulatory differences in small RNAs (sRNAs) between hybrids were mainly driven by maternal inheritance, with Hybrid-sh exhibiting more substantial maternal influence and Hybrid-yh showing transgressive regulation, while 24-nt siRNAs were directly involved in methylation control. We identified 47,855 lncRNA transcripts exhibiting more pronounced non-additive expression patterns during interspecific hybridization than protein-coding mRNAs. Intergenic lncRNAs maintained higher methylation levels across CG/CHG/CHH contexts but had less chromatin accessibility than antisense lncRNAs. Notably, lncRNA0410 , a conserved antisense transcript from CP12-1 's 5′-region, contained a chromatin-accessible site in Hybrid-yh with limited conservation beyond crucifers. It enhanced flavonol biosynthesis by activating BnaA03.MYB12 , improving drought tolerance. Intriguingly, dosage-sensitive lncRNAs exhibited unique epigenetic signatures, including siRNA enrichment, methylation, and chromatin accessibility features that influence transcriptional responses. This research sheds light on the roles of ncRNA in hybrid vigor and genome stability, revealing key epigenetic regulatory mechanisms in plant hybridization.