Exploring the genomes of East African Indicine cattle breeds reveals signature of selection for tropical environmental adaptation traits

African indigenous cattle breeds have been reared within the continent for millennia. Due to the harsh tropical environmental conditions (e.g. sever disease and parasite prevalence, high temperature, feed and water scarcity) where they evolved, they have developed various levels of tropical environment adaptation attributes. In order to explore the genomic signatures of tropical environment adaptation in African cattle, we compared the whole genomes of East African Indicus cattle breeds with European and Asian Taurine cattle breeds using XP-EHH and XP-CLR population statistical methods. Several genes involved in various biological processes and pathways related to domestication and behavior (dopaminergic and glutamatergic synapse), feeding and metabolism (gastric acid secretion, metabolic pathways), thermotolerance (sphingolipid and Wnt signaling), immune system response (T cell receptor signaling), and growth and reproduction (osteoblast differentiation, fibroblast migration) were identified from our genome analysis. Genes associated with tick and parasite resistance traits such as keratin genes, collagen genes, calcium signaling, and tumor necrosis factor proteins were also identified. The genes and pathways identified in this study improve our understanding of the biological mechanisms of tropical environment adaptation of African Indicus cattle breeds, which may allow us to use them for genomic selection programs. This result presents a basis for further study and may help to develop vaccines for tick and gastrointestinal parasite challenge.