Indigenous sheep of Greece represent important genetic resources shaped by long-term adaptation to diverse environments. However, many populations face demographic decline, genetic erosion, and their genomic diversity remains inadequately characterized. This study presents a comprehensive genome-wide analysis of both recognized and previously uncharacterized indigenous Greek sheep. Newly genotyped data from 36 Greek breeds/populations, one Cypriot breed and one outgroup (Cypriot Mouflon) were combined with previously published genotypes from 85 international breeds and four additional outgroups, analyzing 127 ovine populations in total. To mitigate commercial BeadChip ascertainment bias when evaluating these uncharacterized populations, we utilized genome-wide SNP blocks to assess genetic diversity, reconstruct population structure, estimate effective population sizes, and place them within a broad comparative framework encompassing European, Southwest Asian, and North African breeds.

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