Pigs are one of the earliest domesticated animals and multiple breeds have been developed to meet the various demands of consumers. EigenGWAS is a novel strategy to identify candidate genes that underlying population genetic differences and to infer candidate regions under selection as well. In this study, EigenGWAS and F _st analyses were performed using the public re‐sequencing data of three typical commercial pig breeds, Duroc, Landrace and Yorkshire. The intersection of genome‐wide significant SNPs detected by EigenGWAS and top‐ranked 1% SNPs of F _st results were treated as signals under selection. Using the data of all three breeds, 3062 signals under selection were detected and the nearby genomic regions within 300 kb upstream and downstream covered 6.54% of whole genome. Pairs of breeds were analysed along with the pathway analysis. The gene function enrichment results indicated that many candidate genes located in the genomic regions of the signals under selection were associated with biological processes related to growth, metabolism, reproduction, sensory perception, etc. Among the candidate genes, the FSHB , AHR , PTHLH , KDR and FST genes were reported to be associated with reproductive performance; the KIT , KITLG , MITF , MC1R and EDNRB genes were previously identified to affect coat colour; the RETREG1 , TXNIP , BMP5 , PPARD and RBP4 genes were reported to be associated with lipid metabolism and growth traits. The identified genetic differences across the three commercial breeds will advance understanding of the artificial selection history of pigs and the signals under selection will suggest potential uses in pig genomic breeding programmes.

中文翻译：

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通过EigenGWAS和Fst分析发现了杜罗克，长白猪和约克郡猪品种的选择驱动遗传差异。

猪是最早的驯养动物之一，已经开发出多种品种来满足消费者的各种需求。EigenGWAS是一种新颖的策略，用于识别潜在的群体遗传差异的候选基因，并推断出正在选择的候选区域。在本研究中，使用三个典型商品猪品种Duroc，Landrace和Yorkshire的公共重测序数据进行了EigenGWAS和F _st分析。EigenGWAS检测到的全基因组重要SNP与F _st排名最高的1％SNP的交集结果被视为选择信号。利用这三个品种的数据，检测到了3062个信号被选择，上游和下游300 kb内的附近基因组区域覆盖了整个基因组的6.54％。分析了成对的品种以及途径分析。基因功能富集结果表明，位于选择信号的基因组区域中的许多候选基因与与生长，代谢，繁殖，感官知觉等有关的生物学过程有关。在候选基因中，FSHB，AHR，PTHLH，据报道，KDR和FST基因与生殖性能有关。在KIT，先前已鉴定出KITLG，MITF，MC1R和EDNRB基因会影响毛色。据报道，RETREG1，TXNIP，BMP5，PPARD和RBP4基因与脂质代谢和生长特性有关。在三个商业品种之间确定的遗传差异将促进对猪的人工选择历史的了解，选择中的信号将暗示在猪基因组育种计划中的潜在用途。