Structural variations (SVs) have significant impacts on complex phenotypes by rearranging large amounts of DNA sequence. We present a comprehensive SV catalog based on the whole-genome sequence of 1060 pigs (Sus scrofa) representing 101 breeds, covering 9.6% of the pig genome. This catalog includes 42,487 deletions, 37,913 mobile element insertions, 3308 duplications, 1664 inversions, and 45,184 break ends. Estimates of breed ancestry and hybridization using genotyped SVs align well with those from single nucleotide polymorphisms. Geographically stratified deletions are observed, along with known duplications of the KIT gene, responsible for white coat color in European pigs. Additionally, we identify a recent SINE element insertion in MYO5A transcripts of European pigs, potentially influencing alternative splicing patterns and coat color alterations. Furthermore, a Yorkshire-specific copy number gain within ABCG2 is found, impacting chromatin interactions and gene expression across multiple tissues over a stretch of genomic region of ~200 kb. Preliminary investigations into SV’s impact on gene expression and traits using the Pig Genotype-Tissue Expression (PigGTEx) data reveal SV associations with regulatory variants and gene-trait pairs. For instance, a 51-bp deletion is linked to the lead eQTL of the lipid metabolism regulating gene FADS3, whose expression in embryo may affect loin muscle area, as revealed by our transcriptome-wide association studies. This SV catalog serves as a valuable resource for studying diversity, evolutionary history, and functional shaping of the pig genome by processes like domestication, trait-based breeding, and adaptive evolution.

中文翻译：

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1060 个猪基因组结构变异的绘图和功能表征

结构变异 (SV) 通过重新排列大量 DNA 序列，对复杂表型产生重大影响。我们基于代表 101 个品种的 1060 头猪 (Sus scrofa) 的全基因组序列提出了一个全面的 SV 目录，覆盖了猪基因组的 9.6%。该目录包括 42,487 个删除、37,913 个移动元素插入、3308 个重复、1664 个倒位和 45,184 个断裂末端。使用基因型 SV 对品种祖先和杂交的估计与单核苷酸多态性的估计非常一致。观察到地理分层缺失以及已知的 KIT 基因重复，该基因导致欧洲猪的白毛颜色。此外，我们在欧洲猪的 MYO5A 转录本中发现了最近的 SINE 元件插入，可能影响替代剪接模式和毛色变化。此外，在 ABCG2 中发现了约克郡特有的拷贝数增加，影响了约 200 kb 基因组区域内多个组织的染色质相互作用和基因表达。使用猪基因型组织表达 (PigGTEx) 数据对 SV 对基因表达和性状的影响进行了初步调查，揭示了 SV 与调控变异和基因性状对的关联。例如，51 bp 缺失与脂质代谢调节基因 FADS3 的先导 eQTL 相关，正如我们的全转录组关联研究所揭示的，FADS3 在胚胎中的表达可能会影响腰部肌肉区域。该 SV 目录是研究猪基因组多样性、进化历史和通过驯化、基于性状的育种和适应性进化等过程的功能塑造的宝贵资源。