Genotype data of Karacabey Merino, Middle Anatolian Merino (Oamer), Akkaraman, HASMER, and HASAK sheep breeds.

This study aimed to comparatively detect genomic signatures of selection in indigenous and crossbred Turkish sheep breeds using high-density SNP genotyping. A total of 1,612 individuals were analyzed, comprising the indigenous Akkaraman breed and four crossbreds: Karacabey Merino, Oamer, Hasak, and Hasmer. PCA revealed clear genetic separation of Akkaraman, partial overlap between Karacabey Merino and Oamer, and distinct variation in the small Hasak and Hasmer populations. Genetic diversity metrics indicated moderate and relatively homogeneous diversity across breeds, with slightly negative FIS, reflecting heterozygote excess. Selection signatures were identified using ROH, iHS, and Tajima’s D statistics. ROH analysis highlighted breed-specific candidate genes associated with growth (e.g., BGLAP, MYF6, GHR), milk production (PRL, LTF, casein cluster), immune response (TLR2, TLR5, IL15), and reproduction (FSHB, BMPR1B). iHS detected additional loci under positive selection, including MSTN, POU1F1, LEPR, and LALBA, while Tajima’s D identified selective sweeps in genes related to muscle development (CAPN2, CAST), reproduction (PAG4), and immune function (IRF2, ITGB2). Fifty candidate genes were shared among all breeds, whereas others were breed-specific, suggesting both common and unique adaptive pathways. These findings provide valuable insights into the genomic architecture and adaptive evolution of indigenous and crossbred Turkish sheep, with implications for conservation and breeding strategies.