Transposable element-mediated structural variations drive gene expression and agronomic trait diversity in Brassica napus

Brassica napus is a globally significant polyploid oilseed crop with a complex genome, harbors substantial yet largely unexplored genetic diversity. In this study, we upgraded the genomes of the elite rapeseed cultivar Zhongshuang 11 (ZS11) and the spring cultivar Westar and their genome annotations. Additionally, we assembled the genomes of six other representative varieties, namely ZS2, Bugle, 352, 862, Ribenyoucai (RB), and Baihua (BH), and constructed a comprehensive pan-genome comprising 101,903 non-redundant pan-gene clusters derived from 22 genomes. Analysis of the pan-genome led to the identification of 124,682 transposable element- mediated structural variations (TEMSVs), which are unevenly distributed among subgenomes and have a significant impact on gene expression. Notably, this uneven distribution correlates with unbalanced expression of homoeologous gene pairs (uHGPs), with the degree of imbalance increasing alongside the number of TEMSVs. These uHGPs consistently exhibit biased expression patterns across different tissues. Furthermore, using structural variation-based genome-wide association studies (SV-GWAS), we identified two candidate genes, BnaA06.PC78 and BnaC03.UCU1 , which are associated with seed oil content and fatty acid composition. This study offers valuable insights and genetic resources for elucidating gene expression dynamics among subgenomes and advancing B. napus breeding.