Detection of genomic signatures of selection in the North African Brune de l’Atlas cattle

Abstract

The identification of signatures of selection in indigenous livestock genome is able to elucidate the adaptive mechanisms allowing them to cope with environmental pressures. In the present study, we used genotyping data from 106 Brune de l’Atlas cattle individuals and tests based on the extent of haplotype homozygosity (EHH) to look for footprints of natural selection. We identified 17 genomic regions displaying strong signal of selection (p-value <10-6) overlapping with previously described QTL regions affecting many traits such as meat and milk composition, tuberculosis susceptibility, tick and mastitis resistance. Some of these highly significant candidate regions overlap with four previously described copy number variation regions (CNVRs) suggesting a possible involvement of these CNVRs in local adaptation of the Brune de l'Atlas population. Twelve candidate genes located within 25 kb of the most significant SNPs of the highly significant regions, were identified. Their physiological functions were mainly related to protein methylation, regulation of transcription, immune system homeostasis, ATP transport and regulation of GTPase activity. Our results represent the first study providing evidence for selection footprints in the North African cattle and could help to emphasize the importance to preserve local breeds to cope with challenges related to climate change