Genomic insights into Greek sheep structure and admixture with global domestic breeds

Greece holds a critical geographic position in the introduction of domestic sheep into Europe during Neolithic and post-Neolithic migrations, acting as a bridge with Asia. The genomic profile of Greek sheep remains underexplored compared to global breeds, despite their importance for sustainable livestock production. In this study, we constructed an extensive 50 K SNP data collection from 1,625 Greek indigenous sheep reared in 23 flocks compared to southwest Asian, Asian, south, central and north European populations. We detected a diverse genomic profile for Greek breeds linked to both European and Asian ancestry using PCA, admixture and NeighborNet analyses. The Greek breeds were clearly differentiated at the breed level with close genetic relationships between Greek mainland populations and the Italian Zackel-type sheep. PCA clustering and network topology showed an east-to-west genetic axis extending from Asia to the Iberian Peninsula across the Mediterranean, consistent with the Mediterranean dispersal of domestic sheep, with Greece serving as an interlink between the two continents. The Greek cluster showed the highest reticulation level in the regional phylogenetic analysis, implying recent admixture events compared to other geographic clusters. The average observed heterozygosity in Greek sheep (Ho = 0.358), ranging from 0.326 to 0.376, was comparable to that of Mediterranean breeds (Ho = 0.366). At local scale, the analysis of multiple farms revealed heterogeneous management practices, enabling genetic identification in particular cases as evidenced by the admixture profiles by both between- and within-breed comparisons. Semi-fat-tailed Chios ( F IS = 0.17) and Pelagonia ( F IS = 0.10) sheep displayed higher inbreeding across farms compared to the other Greek sheep attributed to long-lasting selection pressure, conservation efforts and sampling scheme, respectively. Collectively, our findings can be integrated into national conservation actions, especially for endangered populations, to prevent genetic erosion and support sustainable management of local livestock genetic resources.