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.

非洲家猪与野猪的遗传多样性尚未得到广泛研究，已发表的相关资料十分有限。现有数据表明，与国际商业培育品种不同，非洲家猪起源于多个驯化中心。本研究对肯尼亚西部的两个家猪种群开展评估，旨在解析该非洲猪瘟（African Swine Fever, ASF）流行区域内家猪的遗传多样性、品种构成及基因混合与渐渗特征。开展此类特定种群解析的原因之一在于，有部分本土猪的非洲猪瘟病毒（African Swine Fever Virus, ASFv）PCR检测呈阳性，但未表现出临床症状，提示其存在某种形式的感染耐受性。本研究采用猪SNP60或SNP80芯片对受试猪进行基因分型，村落家猪样本采集自肯尼亚的布西亚（Busia）与霍马湾（Homabay）两县。由于薮猪（Potamochoerus larvatus）和疣猪（Phacochoerus spp.）已被证实对ASFv感染具有耐受性（感染后无临床症状），本研究将其纳入实验，以评估家猪是否存在相似的基因组特征。此外，为探究欧洲野猪与国际商业培育品种是否对目标家猪种群的遗传构成存在潜在贡献，本研究也将此类样本作为参照纳入实验。数据显示，布西亚县的村落家猪为非均质混合种群，存在大量国际商业培育品种的基因渐渗。与之形成对比的是，霍马湾县的家猪为均质种群，其遗传构成属于"本土土著"类型，与国际商业品种截然不同，且聚类结果更接近欧洲野猪，而非非洲野猪。值得注意的是，布西亚县中经PCR检测为ASFv IX型阴性的村落家猪，其本地祖先占比（＞54%）显著高于检测呈阳性的个体，后者携带更多商业品种的基因渐渗片段。这一发现对于ASF流行区域的品种选育与利用具有参考意义。全基因组扫描检测到多个受优先选择的基因组区域，布西亚与霍马湾家猪的选择特征存在显著差异。此外，尽管野生猪与家猪在部分宽泛的选择区域存在相似特征，但二者受选择的具体基因并无重叠。上述研究结果为探究ASFv基因型感染耐受性的潜在遗传决定因子提供了基础，且鉴于所研究种群间选择特征的多样性，提示存在多条遗传介导的ASFv耐受通路。