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Hlongwane NL, Dzomba EF, Hadebe K, van der Nest MA, Pierneef R, Muchadeyi FC. Identification of Signatures of Positive Selection That Have Shaped the Genomic Landscape of South African Pig Populations. Animals (Basel) 2024; 14:236. [PMID: 38254405 PMCID: PMC10812692 DOI: 10.3390/ani14020236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/17/2023] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
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.
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Affiliation(s)
- Nompilo L. Hlongwane
- Agricultural Research Council, Biotechnology Platform, Private Bag X5, Onderstepoort 0110, South Africa; (K.H.); (R.P.); (F.C.M.)
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville 3209, South Africa;
| | - Edgar F. Dzomba
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville 3209, South Africa;
| | - Khanyisile Hadebe
- Agricultural Research Council, Biotechnology Platform, Private Bag X5, Onderstepoort 0110, South Africa; (K.H.); (R.P.); (F.C.M.)
| | - Magriet A. van der Nest
- Agricultural Research Council, Biotechnology Platform, Private Bag X5, Onderstepoort 0110, South Africa; (K.H.); (R.P.); (F.C.M.)
- Hans Merensky Chair in Avocado Research, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa;
| | - Rian Pierneef
- Agricultural Research Council, Biotechnology Platform, Private Bag X5, Onderstepoort 0110, South Africa; (K.H.); (R.P.); (F.C.M.)
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
| | - Farai C. Muchadeyi
- Agricultural Research Council, Biotechnology Platform, Private Bag X5, Onderstepoort 0110, South Africa; (K.H.); (R.P.); (F.C.M.)
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Chen Y, Wu X, Wang J, Hou Y, Liu Y, Wang B, Hu X, Zheng X, Zhang X, Ding Y, Yin Z. Detection of Selection Signatures in Anqing Six-End-White Pigs Based on Resequencing Data. Genes (Basel) 2022; 13. [PMID: 36553577 DOI: 10.3390/genes13122310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/02/2022] [Accepted: 12/04/2022] [Indexed: 12/14/2022] Open
Abstract
As a distinguished Chinese indigenous pig breed that exhibits disease resistance and high meat quality, the Anqing six-end-white (AQ) pig represents a valuable germplasm resource for improving the quality of the pig breeding industry. In this study, 24 AQ pigs that were distantly blood-related and 6 Asian Wild Boar (AWB) were selected for 10× deep-genome resequencing. The signatures of the selection were analyzed to explore the genetic basis of their germplasm characteristics and to identify excellent germplasm-related functional genes based on NGS data. A total of 49,289,052 SNPs and 6,186,123 indels were detected across the genome in 30 pigs. Most of the genetic variations were synonym mutations and existed in the intergenic region. We identified 275 selected regions (top 1%) harboring 85 genes by applying a crossover approach based on genetic differentiation (FST) and polymorphism levels (π ratio). Some genes were found to be positively selected in AQ pigs' breeding. The SMPD4 and DDX18 genes were involved in the immune response to pseudorabies virus (PRV) and porcine reproductive and respiratory syndrome virus (PRRSV). The BCL6 and P2RX6 genes were involved in biological regulation of immune T cells and phagocytes. The SLC7A4 and SPACA4 genes were related to reproductive performance. The MSTN and HIF1A genes were related to fat deposition and muscle development. Moreover, 138 overlapping regions were detected in selected regions and ROH islands of AQ pigs. Additionally, we found that the QTLs with the most overlapping regions were related to back fat thickness, meat color, pH value, fatty acid content, immune cells, parasitic immunity, and bacterial immunity. Based on functional enrichment analysis and QTLs mapping, we conducted further research on the molecular genetic basis of germplasm traits (disease resistance and excellent meat quality). These results are a reliable resource for conserving germplasm resources and exploiting molecular markers of AQ pigs.
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Wang Z, Sun H, Chen Q, Zhang X, Wang Q, Pan Y. A genome scan for selection signatures in Taihu pig breeds using next-generation sequencing. Animal 2019; 13:683-93. [PMID: 29987993 DOI: 10.1017/S1751731118001714] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Taihu pig breeds are the most prolific breeds of swine in the world, and they also have superior economic traits, including high resistance to disease, superior meat quality, high resistance to crude feed and a docile temperament. The formation of these phenotypic characteristics is largely a result of long-term artificial or natural selection. Therefore, exploring selection signatures in the genomes of the Taihu pigs will help us to identify porcine genes related to productivity traits, disease and behaviour. In this study, we used both intra-population (Relative Extend Haplotype Homozygosity Test (REHH)) and inter-population (the Cross-Population Extend Haplotype Homozygosity Test (XPEHH); F-STATISTICS, F ST ) methods to detect genomic regions that might be under selection process in Taihu pig breeds. As a result, we found 282 (REHH) and 112 (XPEHH) selection signature candidate regions corresponding to 159.78 Mb (6.15%) and 62.29 Mb (2.40%) genomic regions, respectively. Further investigations of the selection candidate regions revealed that many genes under these genomic regions were related to reproductive traits (such as the TLR9 gene), coat colour (such as the KIT gene) and fat metabolism (such as the CPT1A and MAML3 genes). Furthermore, gene enrichment analyses showed that genes under the selection candidate regions were significantly over-represented in pathways related to diseases, such as autoimmune thyroid and asthma diseases. In conclusion, several candidate genes potentially under positive selection were involved in characteristics of Taihu pig. These results will further allow us to better understand the mechanisms of selection in pig breeding.
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