Genomic Scan to Detect Selection Footprints in African Cattle Populations Adapted to Different Agro-Ecologies

Natural selection has shaped the genetic diversity of African indigenous cattle genetic resources. This diversity is detectable in the form of diseases resistance and tolerance to extrem  climatic conditions. Adaptive traits are critical for sustainable livelihood support under low input production areas where the majority of livestock keepers cannot sustain high input-high output systems. Nevertheless, the unique genetic composition of African indigenous cattle breeds has not yet been well understood. Breakthrough in the development of high density molecular markers has noticeably facilitated genomic scan to detect selection footprints in domestic livestock species. Genomic scan for ecological adaptation between breeds adapted to specific ecological conditions could help to elucidate the genomic bases of local adaptation. To spot genomic regions under selection in Ethiopian cattle populations, we have genotyped 126 (n = 52 from highland agro-ecology, n = 74 from lowland-agro ecology) animals using Bovine SNP 80 K chip derived from the indicine breeds. In comparison of populations sampled from different landscapes, we identified genes which are involved in energy metabolism and homeostasis (PDE3B, SLCO1C1 and FIG4), reproduction (THBS2 and MIR2483), regulation of cell differentiation and survival, apoptosis and stress response (DNHD1, SMAD3, MOSPD2 and DNHD1). The genes identified in this study may have important implications for further understanding of the genetics of adaptation of the target cattle breeds under heterogeneous landscapes.

Key words: Adaptation, Ethiopian cattle, selection signatures, genomic scan