Comprehensive analysis of population structure and genomic diversity in fifteen Anatolian sheep breeds

BACKGROUND: Characterizing genomic diversity and population structure is essential for the conservation and sustainable utilization of indigenous sheep genetic resources. Anatolia represents an important center of sheep diversity, harboring multiple populations shaped by diverse breeding histories, ecological conditions, and management practices. In this study, we performed a comprehensive genome-wide assessment of fifteen Anatolian sheep populations using SNP-based data to investigate their genomic diversity, population structure, and genetic relationships. RESULTS: Genetic diversity indices revealed substantial heterogeneity among populations in terms of heterozygosity, allelic richness, minor allele frequency, proportion of polymorphic loci, and inbreeding coefficients, indicating marked differences in within-population genomic variation. Analysis of molecular variance showed that most of the total genetic variation was distributed within populations, although a significant proportion was also attributable to among-population differences. Pairwise FST estimates and principal component analysis demonstrated a structured yet heterogeneous genomic landscape, with some populations exhibiting clear differentiation and others clustering more closely. Phylogenetic analyses further supported this pattern through differences in monophyletic clustering, branch-length dispersion within populations, and patristic distances between populations. Admixture analysis identified three major ancestry components and revealed population-specific differences in ancestry composition and admixture levels. Runs of homozygosity (ROH) analyses showed considerable variation among populations in both the abundance and length distribution of homozygous segments, which was also reflected in class-specific ROH-based genomic inbreeding coefficient (FROH) profiles. Gene flow estimates additionally indicated heterogeneous connectivity across populations. CONCLUSIONS: Together, these findings demonstrate that Anatolian sheep populations retain diverse and structured genomic backgrounds despite varying levels of differentiation, admixture, and genomic inbreeding. This study provides a robust genomic framework for understanding the evolutionary relationships among Anatolian sheep populations and offers valuable insights to inform future conservation, management, and breeding strategies.