Signatures of Adaptive Selection in Indigenous Pigs: Implications for African Swine Fever (ASF)

African Swine Fever (ASF) has emerged as a major threat to pig enterprises in Africa, especially following the use of improved genetics that are susceptible to African Swine Fever Virus (ASFv) infections. Anecdotal evidence suggests that some indigenous pigs in Africa are less susceptible to ASFv and characterization of susceptibility could contribute to food security in Africa and beyond. The aim of the research was to characterize the genetic of indigenous Kenyan pigs and understand whether infected but tolerant pigs have an identifiable genomic structure that is different from other susceptible pig types. Samples were obtained from a subset of unrelated indigenous pigs, including those seropositive for ASFv. Additional samples were collected from bush pigs and Warthog. All DNA extracted from these samples was analyzed using the Illumina Porcine SNP60 Beadchip. European breeds were included to aid in identification of admixed pigs. The analysis of this mixed population has provided important information regarding the genetic diversity and genomic structure of indigenous East African pigs, and provides evidence of gene flow between indigenous pig populations and bush pigs. In addition, genomic regions with differential allelic enrichment were detected between the exotic, indigenous and wild pigs, suggesting possible positive selection for adaptation related to tolerance to ASFv infections. Our results suggest that it may be possible to obtain Ancestry Informative Markers (AIMs) for accurate estimation of admixture proportions and identification of tolerant pig types.