Natural and artificial directional selection in cosmopolitan and autochthonous pig breeds and wild boars have shaped their genomes and resulted in a reservoir of animal genetic diversity. Signatures of selection are the result of these selection events that have contributed to the adaptation of breeds to different environments and production systems. In this study, we analysed the genome variability of 19 European autochthonous pig breeds (Alentejana, Bísara, Majorcan Black, Basque, Gascon, Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda, Krškopolje pig, Black Slavonian, Turopolje, Moravka, Swallow-Bellied Mangalitsa, Schwäbisch-Hällisches Schwein, Lithuanian indigenous wattle and Lithuanian White old type) from nine countries, three European commercial breeds (Italian Large White, Italian Landrace and Italian Duroc), and European wild boars, by mining whole-genome sequencing data obtained by using a DNA-pool sequencing approach. Signatures of selection were identified by using a single-breed approach with two statistics [within-breed pooled heterozygosity (HP) and fixation index (FST)] and group-based FST approaches, which compare groups of breeds defined according to external traits and use/specialization/type. We detected more than 22 million single nucleotide polymorphisms (SNPs) across the 23 compared populations and identified 359 chromosome regions showing signatures of selection. These regions harbour genes that are already known or new genes that are under selection and relevant for the domestication process in this species, and that affect several morphological and physiological traits (e.g. coat colours and patterns, body size, number of vertebrae and teats, ear size and conformation, reproductive traits, growth and fat deposition traits). Wild boar related signatures of selection were detected across all the genome of several autochthonous breeds, which suggests that crossbreeding (accidental or deliberate) occurred with wild boars. Our findings provide a catalogue of genetic variants of many European pig populations and identify genome regions that can explain, at least in part, the phenotypic diversity of these genetic resources.

中文翻译：

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欧洲本地和商业猪品种的全基因组测序可以检测选择的特征，以使遗传资源适应不同的育种和生产系统。

大都会和本地猪品种和野猪的自然和人工定向选择已经塑造了它们的基因组，并导致了动物遗传多样性的积累。选择的标志是这些选择事件的结果，这些事件促使品种适应不同的环境和生产系统。在这项研究中，我们分析了19种欧洲本土猪的基因组变异性（Alentejana，Bísara，Majorcan Black，Basque，Gascon，Apulo-Calabrese，Casertana，Cinta Senese，Mora Romagnola，Nero Siciliano，Sarda，Krškopolje猪，Black Slavonian，来自9个国家/地区的Turopolje，Moravka，燕腹Mangalitsa，Schwäbisch-HällischesSchwein，立陶宛土特产和立陶宛白旧类型，三种欧洲商业品种（意大利大白，通过挖掘使用DNA池测序方法获得的全基因组测序数据，从而获得意大利长白和意大利杜洛克以及欧洲野猪。通过使用具有两种统计数据的“单品种方法” [品种内混合杂合度（HP）和固定指数（FST）]和基于组的FST方法来鉴定选择的特征，该方法比较了根据外部性状和用途定义的品种组/专业化/类型。我们在23个比较人群中检测到超过2200万个单核苷酸多态性（SNP），并确定了359个显示选择特征的染色体区域。这些区域包含已知的基因或正在选择并与该物种的驯化过程相关的新基因，这些基因会影响几种形态和生理特征（例如 毛色和图案，身体大小，椎骨和乳头的数量，耳朵的大小和构造，生殖性状，生长和脂肪沉积性状）。在几个本地种的所有基因组中都检测到与野猪有关的选择特征，这表明野猪发生了杂种（偶然或故意）。我们的发现提供了许多欧洲猪种群遗传变异的目录，并确定了至少可以部分解释这些遗传资源表型多样性的基因组区域。这表明野猪杂交（偶然或故意）。我们的发现提供了许多欧洲猪种群遗传变异的目录，并确定了可以至少部分解释这些遗传资源表型多样性的基因组区域。这表明野猪杂交（偶然或故意）。我们的发现提供了许多欧洲猪种群遗传变异的目录，并确定了可以至少部分解释这些遗传资源表型多样性的基因组区域。