In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed‐specific DNA pooling approach (30–35 animals per pool) obtaining an average depth per pool of 42×. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed‐specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production systems.

中文翻译：

---

通过对DNA池进行全基因组测序，可以对欧洲本地和商业猪品种中的拷贝数变异进行全基因组检测，从而确定了具有特征的拷贝数状态。

在这项研究中，我们确定了19种欧洲本地猪种和两个商业品种（意大利大白种和意大利杜洛克）的拷贝数变异（CNV），它们代表了该物种的重要遗传资源。使用特定品种的DNA合并方法（每池30-35只动物）对725头猪的基因组进行测序，平均每池深度为42倍。这种方法最大程度地提高了CNV的发现以及平均表征分析品种的相关拷贝数状态。通过挖掘超过175亿条读数，我们共鉴定了9592个CNV（每个品种约683个CNV）和3710个CNV区域（CNVR；占参考猪基因组的1.15％），平均每个品种77个CNVR被认为是私人的。对一些CNVR进行了更详细的分析，并从测序数据中获得了其他信息。例如，在所分析的品种中，KIT基因与被毛的表型有关，这证实了多拷贝在确定特定品种被毛颜色中的作用。在大多数品种中，覆盖MSRB3基因的CNVR与耳朵大小有关。影响ELOVL6和ZNF622基因的CNVR是分别在立陶宛土著篱和Turopolje猪品种中观察到的私人特征。总体而言，此处揭示的基因组变异性可以解释品种之间的部分遗传多样性，并可能有助于解释其起源，历史以及对各种生产系统的适应性。