Abstract：
Structural variants (SVs), such as deletions (DELs) and insertions (INSs), contribute substantially to pig genetic diversity and phenotypic variation. Using a library of SVs discovered from long-read primary assemblies and short-read sequenced genomes, we map pig genomic SVs with a graph-based method for re-genotyping SVs in 402 genomes. Our results demonstrate that those SVs harboring specific trait-associated genes may greatly shape pig domestication and local adaptation. Further characterization of SVs reveals that some population-stratified SVs may alter the transcription of genes by affecting regulatory elements. We identify that the genotypes of two DELs (296-bp DEL, chr7: 52,172,101-52,172,397; 278-bp DEL, chr18: 23,840,143-23,840,421) located in muscle-specific enhancers are associated with the expression of target genes related to meat quality (FSD2) and muscle fiber hypertrophy (LMOD2 and WASL) in pigs. Our results highlight the role of SVs in domestic porcine evolution, and the identified candidate functional genes and SVs are valuable resources for future genomic research and breeding programs in pigs.
摘要：
结构变体(SV)，如删除(DEL)和插入(INS)，对猪遗传多样性和表型变异有很大贡献。使用从长读取（LR）初级组装和短读取（SR）测序的基因组中发现的SV文库，我们使用基于图形的方法对402个基因组中的SVs进行重新基因分型来定位猪基因组SVs。我们的结果表明，那些具有特定性状相关基因的SVs可能会极大地影响猪的驯化和局部适应。对SV的进一步表征表明，一些群体分层的SV可能通过影响调控元件来改变基因的转录。我们确定了两个DEL的基因型(296-bpDEL，chr7：52,172,101-52,172,397；278-bpDEL，chr18：23,840,143-23,840,421）位于肌肉特异性增强子中，与猪的肉质（FSD2）和肌纤维肥大（LMOD2和WASL）相关的靶基因的表达有关。我们的结果强调了SVs在家猪进化中的作用，鉴定出的候选功能基因和SVs是未来猪基因组研究和育种计划的宝贵资源。
