Genome-wide analysis reveals differential admixture dynamics and historical demographic contractions in African cattle

The rich cattle genetic diversity in Africa has been supporting livelihoods for centuries, providing food and nutrition security, income, and socio-cultural values. Understanding the genetic architecture of African cattle is essential for conservation and sustainable breed improvement. This study assessed genome-wide diversity, population structure, admixture patterns, and gene flow in 44 cattle populations across West, East, and Southern Africa, utilizing 63,655 medium-density SNP markers. Comparative analyses incorporated South Asian zebu and European taurine breeds for reference. Genetic diversity, estimated via observed heterozygosity and inbreeding coefficients (F_ROH), indicated higher variability in African zebu and admixed populations compared to African taurine cattle. Trypanotolerant taurine breeds such as N'Dama and Lagunaire exhibited low observed heterozygosity and high inbreeding, consistent with historical isolation and natural selection in tsetse-endemic regions. Principal component analysis and ADMIXTURE clustering revealed region-specific patterns of taurine-indicine admixture. West African taurine breeds retained high taurine ancestry, while West and East African zebu breeds showed extensive indicine introgression. Southern African cattle exhibited moderate admixture, with Nguni cattle retaining a distinct Sanga genetic signature. Effective population size (Ne) estimates revealed historical bottlenecks across all regions, temporally coinciding with the nineteenth century rinderpest pandemic. Contemporary Ne values indicated small effective sizes in several taurine and localized zebu populations, warranting conservation attention. This study provides genomic insights into patterns of admixture, gene flow, and demographic variations shaping African cattle diversity. The findings emphasize the need for regionally tailored breeding and conservation strategies to sustain the genetic diversity and adaptive potential of African cattle under evolving climatic and production challenges.