Genome-wide detection of selection signatures in Edilbay sheep populations from Kazakhstan

Introduction Edilbay sheep represent an important indigenous genetic resource of Kazakhstan, yet genomic differentiation among independently maintained breeding populations remains poorly characterized. This study investigated population structure and signatures of divergent selection in two Edilbay populations from the Azhar and Birlik breeding farms. Methods Following quality control, 588 animals (294 per population) and 24,124 autosomal SNPs were analyzed using PCA, ADMIXTURE, phylogenetic reconstruction, F ST , signed allele-frequency differences, runs of homozygosity (ROH), XP-EHH, and Rsb. Results Despite very low genome-wide differentiation between Azhar and Birlik (F ST =0.0049), population-structure analyses revealed partial separation and greater heterogeneity within Azhar. Localized differentiation and haplotype signals were detected across multiple chromosomes, while ROH patterns indicated broadly similar genomic autozygosity in the two Integration of complementary ROH, F ST , allele-frequency differentiation, and XP-EHH/Rsb signals prioritized a candidate region on OAR10. Coordinate refinement identified an approximately 206-kb convergence core in the genomic neighborhood of PCDH9. The prioritized variants were predominantly non-coding, and neither functional annotation nor regulatory analyses identified a causal variant. Discussion These findings reveal localized genomic differentiation within the Edilbay breed and highlight the OAR10 PCDH9-centered candidate region as a priority for further genomic and functional investigation.