Applied genomics in dairy science: from animal breeding to dairy product authentication.

Genomics has changed dairy science introducing new technologies and new approaches in different steps from the value chain, that goes from the breeding and selection of the cattle to the authentication of dairy products. We have applied high-throughput genotyping approaches and whole genome sequencing to characterise the genetic variability of cattle of different breeds and obtain information on genomic regions containing major genes affecting milk quality and production traits, including casein genes. The obtained genomic information has been used to verify or reconstruct the pedigree of some cattle populations and then to redesign optimum contribution selection programs in local breeds. For two cattle breeds (Reggiana and Modenese), we obtained genomic information from almost all animals registered to their herd books. Signature of selection have been also identified in several cattle breeds by combining runs of homozygosity, F statistics and other population genetic approaches. These applications have made it possible to manage the cattle populations and re-define breeding and conservation programs of cattle genetic resources. Then authentication approaches based on DNA analyses have been set up to recover the breed of origin of dairy products, including Parmigiano-Reggiano cheese. Here, targeted PCR- based assays and untargeted next generation sequencing approaches have been set up for monitoring frauds derived from the use of milk of undeclared breeds or species.