Data from: Genetic diversity, breed composition and admixture of Kenyan domestic pigs

The genetic diversity of African pigs, whether domestic or wild has not been widely studied and there is very limited published information available. Available data suggests that African domestic pigs originate from different domestication centers as opposed to international commercial breeds. We evaluated two domestic pig populations in Western Kenya, in order to characterize the genetic diversity, breed composition and admixture of the pigs in an area known to be endemic for African swine fever (ASF). One of the reasons for characterizing these specific populations is the fact that a proportion of indigenous pigs have tested ASF virus (ASFv) positive but do not present with clinical symptoms of disease indicating some form of tolerance to infection. Pigs were genotyped using either the porcine SNP60 or SNP80 chip. Village pigs were sourced from Busia and Homabay counties in Kenya. Because bush pigs (Potamochoerus larvatus) and warthogs (Phacochoerus spp.) are known to be tolerant to ASFv infection (exhibiting no clinical symptoms despite infection), they were included in the study to assess whether domestic pigs have similar genomic signatures. Additionally, samples representing European wild boar and international commercial breeds were included as references, given their potential contribution to the genetic make-up of the target domestic populations. The data indicate that village pigs in Busia are a non-homogenous admixed population with significant introgression of genes from international commercial breeds. Pigs from Homabay by contrast, represent a homogenous population with a “local indigenous’ composition that is distinct from the international breeds, and clusters more closely with the European wild boar than African wild pigs. Interestingly, village pigs from Busia that tested negative by PCR for ASFv genotype IX, had significantly higher local ancestry (>54%) compared to those testing positive, which contained more commercial breed gene introgression. This may have implication for breed selection and utilization in ASF endemic areas. A genome wide scan detected several regions under preferential selection with signatures for pigs from Busia and Homabay being very distinct. Additionally, there was no similarity in specific genes under selection between the wild pigs and domestic pigs despite having some broad areas under similar selection signatures. These results provide a basis to explore possible genetic determinants underlying tolerance to infection by ASFv genotypes and suggests multiple pathways for genetically mediated ASFv tolerance given the diversity of selection signatures observed among the populations studied.

无论家猪还是野生猪类，非洲猪群的遗传多样性尚未得到广泛研究，已发表的相关资料亦极为有限。现有数据显示，与国际商用猪品种不同，非洲家猪起源于多个独立的驯化中心。为了在已知为非洲猪瘟（African Swine Fever, ASF）流行区的区域内，解析当地猪群的遗传多样性、品种构成与遗传混合特征，我们对肯尼亚西部的两个家猪种群开展了评估。针对这两个特定种群开展特征分析的重要原因之一在于，已有部分本地猪群的非洲猪瘟病毒（African Swine Fever Virus, ASFv）检测结果呈阳性，但未表现出任何临床症状，这提示它们对病毒感染存在一定程度的耐受性。本次研究采用猪单核苷酸多态性（Single Nucleotide Polymorphism, SNP）60芯片或SNP80芯片对猪只进行基因分型。家猪样本采集自肯尼亚的布西亚（Busia）县与霍马湾（Homabay）县。由于已知薮猪（*Potamochoerus larvatus*）和疣猪属（*Phacochoerus* spp.）对ASFv感染具有耐受性（感染后无临床症状），因此将它们纳入研究，以评估家猪是否存在类似的基因组特征。此外，为了参考可能对目标家猪种群遗传组成产生贡献的欧洲野猪与国际商用品种，我们也纳入了这两类样本作为对照群体。数据显示，布西亚县的家猪种群为非均质的混合种群，存在来自国际商用品种的显著基因渐渗现象。与之形成鲜明对比的是，霍马湾县的猪群为均质种群，其“本地土著”遗传组成与国际商用品种截然不同，且聚类结果更接近欧洲野猪，而非非洲野生猪类。值得注意的是，在布西亚县的家猪中，经PCR检测ASFv基因型IX呈阴性的个体，其本地祖先占比（>54%）显著高于检测呈阳性的个体——后者携带更多的商用品种基因渐渗痕迹。这一发现对ASF流行区的猪品种选育与利用具有潜在的参考价值。全基因组扫描发现，布西亚县与霍马湾县的猪群分别存在多个受到优先选择的基因组区域，二者的选择印记差异极为显著。此外，尽管野生猪与家猪在部分宽泛的选择区域存在相似的选择印记，但二者受选择的具体基因并无重合。本研究结果为探索ASFv感染耐受性背后的潜在遗传决定因素提供了重要基础，同时鉴于所研究种群间观察到的选择印记多样性，提示存在多条受遗传调控的ASFv耐受通路。