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.

A genome wide scan using the Illumina Ovine beadChip 50 K was performed on DNA of 100 dairy sheep to identify key genes affecting milk fat and protein content. The markers with allele frequency significantly different between the high fat content and the low fat content sheep (62 markers) were different from the markers discriminating the sheep on the basis of milk protein percentage (207 markers). The genes in proximity of these markers were explored in the Ovine Genome Assembly OARv3.1, then mapped to known pathways of the Gene Ontology to determine which ones were most represented. Our results indicated that the genes influencing protein content were mainly involved in basic cellular processes, like regulation of transcription, RNA metabolic processes and nucleoside binding, and were many more (641) than the genes (165) which potentially affect fat content, which were mainly represented in the lipid binding, the macromolecule processing and in the plasma membrane categories. No significant markers affecting protein content were detected in proximity of the previously reported QTL on chromosome 6; on the other hand, significant markers were identified on chromosome 3 which might support the previously identified QTL on chromosome 3.