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.

非洲本土牛品种在非洲大陆已被驯养数千年之久。由于其演化所处的热带环境条件严苛——例如严重的疾病与寄生虫侵染、高温、饲料与水源匮乏——这些牛品种已演化出不同程度的热带环境适应性状。为探究非洲牛的热带环境适应基因组特征，本研究采用XP-EHH与XP-CLR群体统计方法，对东非瘤牛品种与欧洲、亚洲普通牛品种的全基因组进行了比对分析。通过全基因组分析，本研究共鉴定出多个参与各类生物学过程与通路的基因，这些过程与通路涵盖驯化与行为调控（多巴胺能与谷氨酸能突触）、采食与代谢（胃酸分泌、代谢通路）、耐热性（鞘脂与Wnt信号通路）、免疫应答（T细胞受体信号通路）以及生长与繁殖（成骨细胞分化、成纤维细胞迁移）等方面。此外，本研究还鉴定出与蜱虫及寄生虫抗性性状相关的基因，包括角蛋白基因、胶原蛋白基因、钙信号通路相关基因以及肿瘤坏死因子蛋白编码基因。本研究鉴定的基因与通路，加深了我们对非洲瘤牛热带环境适应生物学机制的认知，可为其应用于基因组选择育种项目提供支撑。本研究结果可为后续相关研究奠定基础，并有助于开发针对蜱虫与胃肠道寄生虫侵染的疫苗。