Genetic diversity and selection signatures in the Cornigliese sheep breed

Population structure analyses highlighted close clustering between Cornigliese and Bergamasca sheep, reflecting their historical exchange. Selection-signature analysis revealed several ROH islands, containing genes and QTLs associated with growth, meat, milk and adaptation traits. Candidate genes related to body size and growth, including NCAPG, PLAG1 and FAM184B, were identified.

Additional genes, such as LAP3, LOXL2 and MEPE, have previously been associated with milk production and milk composition traits, while genes DNAJB5, PEBP4, HERC2 and MLANA suggest possible selection for environmental adaptation, immune response, parasite resistance and pigmentation traits. Our results identify genomic regions that may have been shaped by both historical and ongoing selective pressures and provide insights to support conservation measures and future genomic selection strategies for this endangered breed.</p> <p></p><p>Integration of pedigree (5,784 animals) and genomic SNP data (50K chip) showed that pedigree‑based inbreeding underestimates true autozygosity.

In contrast, genomic inbreeding estimated from Runs of Homozygosity (FROH ≈ 8%–11%) provides a more accurate representation of realised homozygosity, highlighting discrepancies between the two metrics.</p><p>PCA and FST analyses revealed a close genetic relationship between Cornigliese and Bergamasca sheep.</p><p>ROH islands contain genes and QTLs associated with production, fertility and adaptation traits, providing targets for conservation and future genomic selection strategies.</p><p></p> <p>Integration of pedigree (5,784 animals) and genomic SNP data (50K chip) showed that pedigree‑based inbreeding underestimates true autozygosity.

In contrast, genomic inbreeding estimated from Runs of Homozygosity (FROH ≈ 8%–11%) provides a more accurate representation of realised homozygosity, highlighting discrepancies between the two metrics.</p> <p>PCA and FST analyses revealed a close genetic relationship between Cornigliese and Bergamasca sheep.</p> <p>ROH islands contain genes and QTLs associated with production, fertility and adaptation traits, providing targets for conservation and future genomic selection strategies.</p>