A genome-wide perspective on the population structure of Italian cattle breeds

Despite the growing diffusion of cosmopolite specialized breeds, several autochthonous populations are still farmed in Italy. The aim of this study was to provide a high-resolution picture of the genome-wide diversity and population structure of Italian local cattle breeds using medium-density genome-wide SNP markers. After data editing, the dataset included 800 samples from 32 breeds that were genotyped for 31,013 SNPs. For several breeds we observed a low level of polymorphism and genetic diversity that confirmed threat of extinction. Shared ancestry, admixture events, and reticulations observed on the phylogenetic tree between some breeds, all suggest high levels of gene flow. Clear clusters and relationships between breeds that originated from the same geographical area were detected. However, in spite of the complex admixture history, many of the local Italian cattle breeds have retained unique identities and are clearly differentiated breeds. Differences in their origin, in climate characteristics of farming areas, the genetic isolation, and the inbreeding can be the main reasons for such differentiation. This study represents the first exhaustive genome-wide analysis of Italian cattle diversity. The results largely agreed with the breeding history of the Italian cattle breeds. The population structure and the low genetic diversity presented here for several breeds should be evaluated in adopting conservation strategies. Thus, efforts should be made to improve genetic diversity in these breeds. Control of inbreeding, breeding stations development and improvement of recording system are strategies to conserve these breeds under in situ conservation situation, and in this context, genomic information may play a crucial role for the preservation and management of these populations.