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Identification of signatures of positive selection that have shaped the genomic landscape of South African pig populations
Hlongwane, Nompilo; Dzomba, Edgar F.; Hadebe, Khanyisile; Van der Nest, Magrieta Aletta; Pierneef, Rian Ewald; Muchadeyi, Farai C.
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 identified
regions included quantitative loci (QTLs) associated with economically important traits. For example,
meat and carcass QTLs were prevalent in all the populations, showing the potential of village and
indigenous populations’ ability to be managed and improved for such traits. Results of this study
therefore increase our understanding of the intricate interplay between selection pressures, genomic
adaptations, and desirable traits within South African pig populations.
Description:
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.