Genetic diversity and selection signatures in the Cornigliese sheep breed

The Cornigliese sheep is an Italian local breed experiencing a reduction in population size. The present study aims to investigate genetic diversity and selection patterns in the Cornigliese sheep breed using an integrated approach based on pedigree and genomic data. We used pedigree information from 5,784 animals and genomic data from 293 individuals genotyped with the Ovine 50K SNP chip. A total of 42 individuals from the Bergamasca breed were genotyped with the same SNP and included as a reference population, given the documented historical introgression of Bergamasca genetics into the Cornigliese breed. Pedigree completeness was low (CGE = 2.23), limiting the reliability of pedigree-based estimates, whereas genomic inbreeding (FROH = 8%–11%) was consistent with values reported for other Italian local breeds. 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.