Genome-Wide SNP Scans Reveal Multiple Signatures of Selection in Egyptian Barki Sheep and Goats Raised in Hot Arid Environments

Indigenous African livestock are most often exposed to natural selection for adaptation to their natural production environments. This has most likely left detectable signatures of selection within their genomes. However, so far no study has made an attempt to verify such signatures. Here, we investigated footprints of selection for adaptation to hot arid environments using two complementary approaches, pairwise F_ST and the intergrated haplotype homozygosity score (iHS) to analyze genotype data generated using Illumina’s Ovine and Caprine 50K SNP BeadChips from 68 and 59 Barki sheep and goats that are indigenous to Egypts’ Coastal Zone of the Western Desert. We identified 26 genomic regions displaying highly significant signals of selection in the two species most of which spanned genes involved in multiple signaling pathways that control various cellular processes as well as signal transduction pathways. We identified selection signatures spanning the several genes which either directly or indirectly influence important traits for adaptation to hot arid environments. We further identified a shared consensus selection signature on a conserved syntenic segment on ovine and caprine chromosomes 10 and 12 respectively, providing evidence for selection among ovicaprinae in a common environment. Our study highlights the importance of nondescript African indigenous livestock populations as attractive biological models to study and identify genome wide selection sweeps for adaptation to diverse agro-ecologies and for genome-wide association analysis.