Selection Footprints Reflecting Population Stratification of Local Sheep Breeds in the Danube Region

This study investigated genetic diversity, population structure, and selection footprints across 16 local sheep breeds from the Danube region using high-density SNP data. The diversity status was derived from the overall heterozygosity and genomic-based inbreeding coefficients (FHOM and FIS). Population stratification was assessed using principal component analysis, phylogenetic networks, and admixture estimation. Selection footprints were identified based on the genome-wide Wright's fixation index (FST) distribution. Moderate observed and expected heterozygosity levels were found, with the highest values in the Improved Valachian breed (Ho = 0.44±0.10, He = 0.44±0.08) and the lowest in the East Friesian (Ho = 0.37±0.16) breed. Inbreeding coefficients aligned with heterozygosity patterns, indicating an increase in inbreeding in geographically or historically separated breeds and reduced inbreeding in recently developed composite breeds, particularly the Improved Valachian and Slovak Dairy sheep. All approaches testing population structure confirmed breed stratification corresponding to geographic and phylogenetic backgrounds, while admixture analysis revealed the highest proportion of genetic admixture in the composite breeds. A genome-wide scan revealed 24 candidate regions under selection pressure across 15 autosomes, encompassing 48 protein-coding genes, including those related to reproduction (TNP1, AMHR2) and immune response (SLC11A1, IL9, JAK3). Functional enrichment analysis identified overrepresented GO terms related to protein binding, spermatogenesis, hypoxia response, and KEGG pathways such as TGF-beta and VEGF signalling. This study provides insights into breed-specific selection pressures driven by diverse breeding goals and environmental adaptation in sheep breeds in the Danube region. The study also highlights the importance of genomic tools for preserving genetic diversity and supporting sustainable breeding strategies in local populations.