Functional Population Genomics of African and South American Cattle

This thesis presents a comprehensive analysis of the genetic history and evolutionary dynamics of cattle breeds across Africa and South America. Through a series of detailed investigations, I explored the genetic structure, adaptive traits, and evolutionary history of these breeds, focusing on their responses to a wide range of environmental conditions. Using advanced genomic techniques, my research elucidated the intricate patterns of admixture and selection in African cattle. Similarly, I investigated the genetic diversity of Latin American Criollo cattle, assessing their adaptability and resilience across diverse agroecological niches. The findings provide critical insights into the role of genetic ancestry and admixture in cattle adaptability, highlighting the importance of genetic conservation in the face of climate change and ecological challenges. In Chapter 2, I investigated the mitonuclear dimension in African cattle. The phenotypic diversity of African cattle reflects adaptation to a wide range of agroecological conditions, human-mediated selection preferences, and complex patterns of admixture between the humpless Bos taurus (taurine) and humped Bos indicus (zebu) subspecies, which diverged 150–500 thousand years ago. Despite extensive admixture, all African cattle possess taurine mitochondrial haplotypes, even populations with significant zebu biparental and male uniparental nuclear ancestry. My research involved assessing whether mitonuclear interactions affect nuclear genes in these cattle. I found evidence for mitonuclear coevolution, with an increase in taurine ancestry at mitochondrially targeted nuclear genes, supporting the hypothesis of incompatibility between taurine mitochondrial and zebu nuclear genomes. In Chapter 3, I investigated the genetic diversity of Criollo cattle, descendants of Iberian breeds in the Americas. These cattle have adapted to the diverse environments of Latin America and the Caribbean, showing traits like disease resistance and heat tolerance. My study involved analyzing three Criollo breeds using whole-genome sequencing to examine population structure and admixture. I found evidence of gene flow from African taurine and Asian zebu populations, and identified genes linked to adaptive traits like thermotolerance and immunity. The study highlights Criollo cattle's adaptability and genetic potential in the context of climate change and disease challenges. In Chapter 4, I explored the population structure, genetic diversity, and functional genomics of West African cattle, a crucial component of the continent’s agricultural and cultural heritage. Using WGS data, I generated detailed insights into the levels of taurine and zebu ancestry across West African cattle, identifying breeds with pure African taurine ancestry and those showing significant admixture. I employed population branch statistics (PBS) and the MOSAIC tool for local ancestry analysis to pinpoint genomic regions exhibiting evidence of selection, thereby identifying signatures of adaptation in both pure African taurine and admixed West African cattle. These work revealed important genetic adaptations underpinning immune response mechanisms and environmental resilience, and emphasising the adaptive significance of taurine ancestry in the African context. Moreover, I screened the cattle DNA samples for the presence of genomic DNA from Trypanosoma spp., the protozoan parasites that cause African animal trypanosomiasis (AAT). This research work not only provides a comprehensive understanding of the genetic makeup and evolutionary history of West African cattle but also highlights the importance of preserving their unique genetic heritage.