Identification of signatures of positive selection that have shaped the genomic landscape of South African pig populations

DATA AVAILABILITY STATEMENT : The datasets that were analysed during the current study are available from the corresponding author upon reasonable request. ; SUPPLEMENTARY MATERIAL : TABLE S1: Summaries of the number of potential regions detected in iHS; TABLE S2: List of selected regions and candidate genes detected in iHS method associated with each pig population; TABLE S3: Summaries of the number of potential regions for XPEHH; TABLE S4: Genomic regions under divergent selection identified by XP-EHH method and associated candidate genes; TABLE S5: Genomic regions under divergent selection identified by HapFLK method and associated candidate genes; TABLE S6: Enriched pathways for significant genes identified using iHS, XP-EHH and HapFLK; TABLE S7: Enriched pathways identified for XP-EHH. ; South Africa boasts a diverse range of pig populations, encompassing intensively raised commercial breeds, as well as indigenous and village pigs reared under low-input production systems. The aim of this study was to investigate how natural and artificial selection have shaped the genomic landscape of South African pig populations sampled from different genetic backgrounds and production systems. For this purpose, the integrated haplotype score (iHS), as well as cross population extended haplotype homozygosity (XP-EHH) and Lewontin and Krakauer’s extension of the Fst statistic based on haplotype information (HapFLK) were utilised. Our results revealed several population-specific signatures of selection associated with the different production systems. The importance of natural selection in village populations was highlighted, as the majority of genomic regions under selection were identified in these populations. Regions under natural and artificial selection causing the distinct genetic footprints of these populations also allow for the identification of genes and pathways that may influence production and adaptation. In the context of intensively raised commercial pig breeds (Large White, Kolbroek, and Windsnyer), the ...