Genomic characterisation of local sheep breeds of the Eastern Alps

This study presents a comprehensive genomic characterisation and assessment of genetic erosion in four local sheep breeds from the Alpine Veneto region of Italy: Alpagota, Brogna, Foza and Lamon. Using a combination of principal component analysis, ADMIXTURE, and Fst distances, we identified genomic differentiation among the breeds, despite their shared ancestral origin—likely a result of long-term isolation between valleys. Notably, their genomic profiles exhibited greater affinity with Northern European breeds than with other Italian breeds, reflecting historical patterns of migration and trade. Analyses of effective population size (Ne), linkage disequilibrium (LD) and inbreeding levels revealed varying degrees of genetic diversity and erosion risk among the breeds. The Lamon and Foza populations showed critically low Ne, elevated LD and high inbreeding levels, indicating a heightened risk of genetic erosion—particularly for Foza. In contrast, Brogna and Alpagota maintained Ne estimates above 100, suggesting they are not currently at critical risk, though they still warrant proactive conservation measures to preserve genetic health. In conclusion, this study reveals distinct genomic patterns and differing conservation priorities among four Alpine Veneto sheep breeds. Genomic data proved essential in identifying breeds at critical risk—particularly Foza and Lamon—and in guiding tailored conservation strategies. Continued monitoring and proactive management are key to preserving their genetic integrity and long-term viability. The four Veneto breeds displayed genetic differences compared to other European breeds, likely as a result of long-term geographic isolation.Despite their relatedness, each breed remains genetically distinct.There is an urgent need for conservation actions, particularly for the highly vulnerable Foza population. The four Veneto breeds displayed genetic differences compared to other European breeds, likely as a result of long-term geographic isolation. Despite their relatedness, each breed remains genetically distinct. There is an urgent need for conservation actions, particularly for the highly vulnerable Foza population.