Dairy sheep production in Mediterranean countries is based on the regional exploitation of a great variety of breeds, whose milk is processed into high quality cheese. The maintenance of these local breeds is strategically important from genetic diversity and environmental perspectives. Modern molecular genetics tools can be used to increase the efficiency of classic breeding programs in dairy sheep. Previously to the development of effective marker- or gene-assisted protocols, it was necessary to identify the genes controlling the production traits considered as selection targets. This project will increase the density of genetic markers at a QTL region influencing milk fat percentage in a commercial population of Churra sheep, a Spanish indigenous breed highly specialized in milk production. A combined linkage analysis and linkage disequilibrium analysis will subsequently be applied to refine the QTL position, enabling the identification of positional and functional candidate genes included in the refined QTL region. The strongest candidate genes and also inter-genic regions will be characterised further by sequence analysis for SNP discovery. The allelic variants identified will then be tested for possible relationships with milk fat percentage. This project will represent the first attempt to move genetic mapping in DAIRY sheep, from low-density linkage studies to high-density linkage disequilibrium and association methods. The project will take advantage of the information derived from the latest release of the Bovine Genome sequence (comparative approach) and the Virtual Sheep Genome sequence. This is a novel approach to gene identification in dairy sheep, which has only just become possible with the increased available information on the sheep and cattle genomes. The successful fulfilment of the project objectives may lead to the implementation of molecular information into the classic breeding program currently running in the Churra population.