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

Brassica napus is a globally important allotetraploid oilseed crop with a complex genome and extensive structural diversity that remains incompletely characterized. Here, we present gap-free reference genome assemblies for Zhongshuang 11 (ZS11) and Westar, and assemble six additional accessions. We harmonize gene annotations across 22 genomes and develop BnaScope (https://rgmi.hzau.edu.cn/bnascope), a gene-centric functional genomics platform. Gene-based and graph-based pan-genomes identify 123,107 non-redundant gene clusters and 188,218 structural variants, including 112,417 transposable element-mediated structural variants (TEMSVs). TEMSVs show asymmetric distributions between An and Cn subgenomes and are associated with increased homoeolog expression imbalance, particularly for CDS-TEMSVs. SV-based genome-wide association analyses identify candidate genes underlying seed quality traits, and functional analyses demonstrate that BnaPYRDs negatively regulate seed glucosinolate content. These findings establish structural variation as an important contributor to homoeolog regulation and seed-quality variation in B. napus. This study develops a comprehensive pan-genome resource for Brassica napus and reveals how structural variations shape gene regulation and seed quality traits. The findings provide insights into genome diversity and crop improvement.