ArticleGenetics, selection, evolution : GSE2023
Mapping restricted introgression across the genomes of admixed indigenous African cattle breeds.
Article in Genetics, selection, evolution : GSE, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed, 10 citations in OpenAlex.
- Integrative Genomics Identifies Candidate Genes Underlying Trypanotolerance in Hybrid African Cattle.Evolutionary applications · 2026Article
- Genomic signals on the X chromosome reveal local adaptations in Ethiopian cattle.BMC genomics · 2026Article
- Distinct adaptation and ancestral retention signals in African and European indigenous cattle genomes.Communications biology · 2026Article
- Genetic admixture and adaptive signatures of Guanling cattle revealed by whole-genome sequence.BMC genomics · 2026Article
- Comparative detection of selection signatures in indigenous and crossbred Turkish sheep breeds.Scientific reports · 2025Article
- PopCluster Improves Accessibility, Speed and Accuracy of Available Genotypic Clustering Software.Molecular ecology resources · 2025Article
- Genomic diversity of Cameroonian Gudali and Gudali-cross cattle.Scientific reports · 2025Article
- Genome-wide local ancestry and the functional consequences of admixture in African and European cattle populations.Heredity · 2025Article
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Authors and funding
13 authors at 8 institutions in 7 countries.
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Abstract
backgroundThe genomes of indigenous African cattle are composed of components with Middle Eastern (taurine) and South Asian (indicine) origins, providing a valuable model to study hybridization and to identify genetic barriers to gene flow. In this study, we analysed indigenous African cattle breeds as models of hybrid zones, considering taurine and indicine samples as ancestors. In a genomic cline analysis of whole-genome sequence data, we considered over 8 million variants from 144 animals, which allows for fine-mapping of potential genomic incompatibilities at high resolution across the genome.
resultsWe identified several thousand variants that had significantly steep clines ('SCV') across the whole genome, indicating restricted introgression. Some of the SCV were clustered into extended regions, with the longest on chromosome 7, spanning 725 kb and including 27 genes. We found that variants with a high phenotypic impact (e.g. indels, intra-genic and missense variants) likely represent greater genetic barriers to gene flow. Furthermore, our findings provide evidence that a large proportion of breed differentiation in African cattle could be linked to genomic incompatibilities and reproductive isolation. Functional evaluation of genes with SCV suggest that mitonuclear incompatibilities and genes associated with fitness (e.g. resistance to paratuberculosis) could account for restricted gene flow in indigenous African cattle.
conclusionsTo our knowledge, this is the first time genomic cline analysis has been applied to identify restricted introgression in the genomes of indigenous African cattle and the results provide extended insights into mechanisms (e.g. genomic incompatibilities) contributing to hybrid differentiation. These results have important implications for our understanding of genetic incompatibilities and reproductive isolation and provide important insights into the impact of cross-breeding cattle with the aim of producing offspring that are both hardy and productive.
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