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dc.contributor.author | Hlongwane, Nompilo![]() |
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dc.contributor.author | Dzomba, Edgar F.![]() |
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dc.contributor.author | Hadebe, Khanyisile![]() |
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dc.contributor.author | Van der Nest, Magrieta Aletta![]() |
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dc.contributor.author | Pierneef, Rian Ewald![]() |
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dc.contributor.author | Muchadeyi, Farai C.![]() |
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dc.date.accessioned | 2024-08-01T10:22:46Z | |
dc.date.available | 2024-08-01T10:22:46Z | |
dc.date.issued | 2024-01-02 | |
dc.description | DATA AVAILABILITY STATEMENT : The datasets that were analysed during the current study are available from the corresponding author upon reasonable request. | en_US |
dc.description | 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. | en_US |
dc.description.abstract | 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. | en_US |
dc.description.department | Biochemistry | en_US |
dc.description.department | Genetics | en_US |
dc.description.department | Microbiology and Plant Pathology | en_US |
dc.description.sdg | SDG-02:Zero Hunger | en_US |
dc.description.sponsorship | The Agricultural Research Council (ARC)—Professional Development Program, the National Research Foundation and the ARC-Biotechnology Platform. | en_US |
dc.description.uri | https://www.mdpi.com/journal/animals | en_US |
dc.identifier.citation | Hlongwane, N.L.; Dzomba, E.F.; Hadebe, K.; van der Nest, M.A.; Pierneef, R.; Muchadeyi, F.C. Identification of Signatures of Positive Selection That Have Shaped the Genomic Landscape of South African Pig Populations. Animals 2024, 14, 236. https://doi.org/10.3390/ani14020236. | en_US |
dc.identifier.issn | 2076-2615 (online) | |
dc.identifier.other | 10.3390/ani14020236 | |
dc.identifier.uri | http://hdl.handle.net/2263/97396 | |
dc.language.iso | en | en_US |
dc.publisher | MDPI | en_US |
dc.rights | © 2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). | en_US |
dc.subject | Genetic signatures | en_US |
dc.subject | HapFLK | en_US |
dc.subject | Pigs | en_US |
dc.subject | Gene enrichment analyses | en_US |
dc.subject | Integrated haplotype score (iHS) | en_US |
dc.subject | Cross-population extended haplotype homozygosity (XP-EHH) | en_US |
dc.subject | SDG-02: Zero hunger | en_US |
dc.subject | Quantitative trait loci (QTLs) | en_US |
dc.title | Identification of signatures of positive selection that have shaped the genomic landscape of South African pig populations | en_US |
dc.type | Article | en_US |