A Pan‐TE Map Reveals the Important Role of Transposable Elements in Gene Expression and Phenotypic Diversity in 2,311 Rapeseed Accessions

Transposable elements (TEs) play an important role in shaping gene transcription regulatory networks and driving genome evolution. However, there is still little understanding for TE polymorphisms at the species level of rapeseed and their impacts on gene expression and phenotypic formation. This study systematically identified 8 268 255 TEs from 14 rapeseed genomes and constructed the first rapeseed pan-TE map and then obtained TE insertion polymorphisms (TIP) in 2311 oilseed rape accessions (Brassica napus). Integrative analysis of transcriptome data suggests TEs modulate transcription by diverse cis-regulatory mechanisms and 67% TEs related to nearby gene promote transcription. TE-GWAS identified 1427 TEs in 80 loci associated with 15 traits. Further multi-omics analysis identified a TE insertion in BnaA03.FLCb. suppresses its transcription and ultimately results in early flowering. Besides, one CACTA-like insertion in BnaA09.CYP78A9 reveals the regulatory mechanism how TE-derived cis-regulatory elements promote gene expression to regulate silique length. These results provide a TIP map at the species level and demonstrate that TEs play an important role in transcription regulatory and breeding improvement in rapeseed.