Genomic Diversity and Footprints of Selection in Hamdani Sheep

Abstract

Simple Summary Identification of genetic variability and genomic regions under selection pressure has significant potential not only for sustaining animal production but also for comprehensive breeding programs to address future challenges. As one of the native sheep breeds of Iraq, Hamdani (HAM) sheep are also found in neighboring countries, including Türkiye, owing to their high adaptability to harsh environmental conditions and satisfactory production performance. Therefore, HAM sheep represent a valuable breed for gaining deeper insight into genetic diversity and the effects of natural and artificial selection on the genome. To reduce ascertainment bias associated with SNP-array technologies and capture breed-specific genetic variants, we used double-digest restriction site-associated DNA sequencing (ddRADseq) to investigate genetic diversity and footprints of selection in HAM sheep. The HAM population showed high observed heterozygosity (0.323 ± 0.01) and low genomic inbreeding (mean FHOM = 0.029 ± 0.02; FROH = 0.008 ± 0.01). Selection pressure was identified for numerous candidate genomic regions linked to reproductive performance, lipid metabolism, and environmental adaptation. Given the limited sample size, these findings should be considered preliminary genomic knowledge to support future conservation strategies and genome-based breeding programs for the sustainable improvement of the HAM sheep breed.