Abstract
This study aimed to elucidate the genetic architecture and selection signatures in two prominent Iraqi fat-tailed sheep breeds, Awassi and Hamdani. One hundred forty animals were genotyped using the Illumina Ovine SNP50K BeadChip, providing genome-wide coverage with approximately 53,714 SNP markers. To uncover candidate genomic regions under selection, we employed three complementary approaches: integrated haplotype score (iHS), runs of homozygosity (ROH) and Tajima's D analyses. The iHS analysis identified 69 candidate genes in Awassi sheep and 286 in Hamdani sheep, whereas ROH analysis revealed 190 and 277 candidate genes in the respective breeds. Tajima's D corroborated these findings with one gene in Awassi and four in Hamdani sheep. Population structure was rigorously assessed using ADMIXTURE, principal component analysis (PCA) and neighbour-joining phylogenetic tree reconstruction, collectively demonstrating a distinct genetic separation of the Awassi breed and a more admixed genetic profile for the Hamdani breed. Functional enrichment analysis of candidate genes implicated several biological processes and pathways, including immune response, hormone regulation and cellular signalling, underscoring their potential roles in adaptation and disease resistance. Overall, our findings provide novel insights into the genetic differentiation and adaptive evolution of Iraqi fat-tailed sheep, offering a valuable resource for future breeding and conservation programmes.