Unravelling the genetic structure and genetic relationships of indigenous Greek sheep breeds using SNP markers

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.

Genome-wide analyses evaluating 46,733 SNPs and 4347 multi-allelic haplotype blocks revealed a distinct ascertainment bias affecting Western and Eastern breeds differently. Mitigating this bias via the block-based approach demonstrated that Greek sheep breeds/populations retain high genetic diversity, despite pronounced heterogeneity. Breeds such as Lesvos, Vlahiko, and Karagouniko exhibited high heterozygosity, low inbreeding, and relatively large effective population sizes, whereas Thraki, Agrinio, Katafygio, Serres, and Argos showed low diversity, elevated inbreeding, and small recent effective population sizes. Greek breeds/populations occupied an intermediate position between Western European and Southwest Asian groups, reflecting their geographic location and historical role in early dispersal routes. Island populations (Cretan breeds, Kasos and Karpathos) formed a cohesive genetic cluster shaped by long-term isolation, while semi-fat-tailed Greek breeds showed close affinities with Middle Eastern and North African populations. Introgression from East Friesian sheep strongly influenced the genomic profile of the Arta breed.

This study provides a comprehensive genomic baseline for indigenous Greek and Cypriot sheep, highlighting their high genetic diversity and complex demographic histories. While several breeds represent valuable reservoirs of adaptive variation, others face immediate risk of genetic erosion. These findings provide essential guidance for prioritizing conservation actions and integrating genomic information into sustainable management and breeding strategies.