Genome-Wide Footprints of Pig Domestication and Selection Revealed through Massive Parallel Sequencing of Pooled DNA

BackgroundArtificial selection has caused rapid evolution in domesticated species. The identification of selection footprints across domesticated genomes can contribute to uncover the genetic basis of phenotypic diversity.
Methodology/Main FindingsGenome wide footprints of pig domestication and selection were identified using massive parallel sequencing of pooled reduced representation libraries (RRL) representing ∼2% of the genome from wild boar and four domestic pig breeds (Large White, Landrace, Duroc and Pietrain) which have been under strong selection for muscle development, growth, behavior and coat color. Using specifically developed statistical methods that account for DNA pooling, low mean sequencing depth, and sequencing errors, we provide genome-wide estimates of nucleotide diversity and genetic differentiation in pig. Widespread signals suggestive of positive and balancing selection were found and the strongest signals were observed in Pietrain, one of the breeds most intensively selected for muscle development. Most signals were population-specific but affected genomic regions which harbored genes for common biological categories including coat color, brain development, muscle development, growth, metabolism, olfaction and immunity. Genetic differentiation in regions harboring genes related to muscle development and growth was higher between breeds than between a given breed and the wild boar.
Conclusions/SignificanceThese results, suggest that although domesticated breeds have experienced similar selective pressures, selection has acted upon different genes. This might reflect the multiple domestication events of European breeds or could be the result of subsequent introgression of Asian alleles. Overall, it was estimated that approximately 7% of the porcine genome has been affected by selection events. This study illustrates that the massive parallel sequencing of genomic pools is a cost-effective approach to identify footprints of selection.

研究背景
人工选择已使驯化物种发生快速演化。鉴定驯化基因组中的选择印记，有助于揭示表型多样性的遗传基础。

材料与方法/主要发现
本研究通过对野猪以及4个经过肌肉发育、生长、行为和毛色强选择的家猪品种（大白猪（Large White）、长白猪（Landrace）、杜洛克猪（Duroc）、皮特兰猪（Pietrain））的混合简化基因组文库（RRL，约覆盖基因组2%）进行大规模平行测序，鉴定了猪驯化与选择的全基因组印记。本研究采用专门开发的统计方法，该方法可校正DNA混合测序、低平均测序深度以及测序误差带来的影响，从而获得猪全基因组范围内的核苷酸多样性与遗传分化估计值。研究发现了广泛的正选择与平衡选择信号，其中在皮特兰猪中检测到最强的选择信号——该品种是针对肌肉发育进行高强度选育的品种之一。多数选择信号具有群体特异性，但所影响的基因组区域均富集了参与若干共同生物学类别的基因，包括毛色、脑发育、肌肉发育、生长、代谢、嗅觉与免疫功能。与单个家猪品种与野猪之间的遗传分化相比，肌肉发育与生长相关基因所在区域的遗传分化在不同家猪品种间更高。

结论与意义
本研究结果表明，尽管各驯化品种经历了相似的选择压力，但选择作用于不同的基因。这一现象可能反映了欧洲家猪品种的多次驯化事件，或是后续亚洲等位基因渐渗的结果。总体而言，据估计约7%的猪基因组受到选择事件的影响。本研究证实，基因组混合文库的大规模平行测序是一种经济高效的选择印记鉴定方法。