Meat genomics comes of age: applications over the whole value chains, from animal breeding to meat authentication.

High-throughput sequencing and genotyping technologies have been applied in meat animals for different purposes and from different perspectives. Here, we present different applications of genomic technologies for the sustainable development of meat animal value chains. We have applied genome-wide association studies (GWAS) and candidate gene analyses carried out within breeds or populations to identify genomic regions and markers associated with meat quality and production traits of the animals and novel molecular phenotypes directly or indirectly involved in muscle mass and fat deposition, feed efficiency, welfare of the animals and disease resistance. We have combined GWAS with population genomic analyses across breeds, including autochthonous animal genetic resources, to identify signatures of selection that can be used to identify genomic regions explaining the variability of relevant traits for meat production and adaptation to peculiar production systems in cattle, pigs, and rabbits. We have then applied whole genome sequencing to identify new causative or putative causative mutations affecting the targeted traits in all investigated meat species. We have also applied genomics for the development and implementation of authentication and traceability systems of meat products, including the use of single DNA markers, multiple single nucleotide polymorphism panels, and targeted and untargeted whole DNA sequencing of DNA extracted from complex or simple meat-based matrices. Authentication DNA based approaches have made it possible to strengthen the link between breed-branded meat products and the conservation of animal genetic resources, including autochthonous breeds, and to enlarge the application and sensitivity of the assays that can even easily recover information from the single animals from which the products have been obtained.