Although individual genomic structural variants (SVs) are known to influence gene expression and trait variation, the extent and scale of SV impact across a species remain unknown. In the present study, we constructed a reference library of 334,461 SVs from genome assemblies of 16 representative morphotypes of neopolyploid Brassica napus accessions and detected 258,865 SVs in 2,105 resequenced genomes. Coupling with 5 tissue population transcriptomes, we uncovered 285,976 SV-expression quantitative trait loci (eQTLs) that associate with altered expression of 73,580 genes. We developed a pipeline for the high-throughput joint analyses of SV-genome-wide association studies (SV-GWASs) and transcriptome-wide association studies of phenomic data, eQTLs and eQTL-GWAS colocalization, and identified 726 SV–gene expression–trait variation associations, some of which were verified by transgenics. The pervasive SV impact on how SV reshapes trait variation was demonstrated with the glucosinolate biosynthesis and transport pathway. The study highlighting the impact of genome-wide and species-scale SVs provides a powerful methodological strategy and valuable resources for studying evolution, gene discovery and breeding.

尽管已知单个基因组结构变异 （SV） 会影响基因表达和性状变异，但 SV 对物种的影响程度和规模仍然未知。在本研究中，我们从 16 种新多倍体甘蓝型油菜种质的代表性形态的基因组组装中构建了一个包含 334,461 个 SVs 的参考文库，并在 2,105 个重测序基因组中检测到 258,865 个 SVs。与 5 个组织群体转录组偶联，我们发现了 285,976 个 SV 表达数量性状位点 （eQTL），这些位点与 73,580 个基因的表达改变相关。我们开发了一个用于 SV 全基因组关联研究 （SV-GWASs） 的高通量联合分析和表型数据、 eQTL 和 eQTL-GWAS 共定位的转录组范围关联研究的管道，并确定了 726 个 SV 基因表达-性状变异关联，其中一些通过转基因验证。硫代葡萄糖苷生物合成和转运途径证明了 SV 对 SV 如何重塑性状变异的普遍影响。该研究强调了全基因组和物种尺度 SV 的影响，为研究进化、基因发现和育种提供了强大的方法策略和宝贵的资源。