A genome wide scan highlights differences in the genetic architecture of fat and protein contents in dairy sheep

•Fat and protein are of great importance in determining sheep cheese production.•A genome wide scan showed that fat percentage is controlled by fewer genes than protein.•Gene Ontology analysis indicated that the genes influencing protein content were involved in basic cellular processes, mainly transcription regulation.•The genes influencing fat content were involved in macromolecule processing and in the plasma membrane categories.•Significant markers identified on chromosome 3 might support the identified QTL on OAR 3.