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

Despite the growing diffusion of cosmopolite specialized breeds, several autochthonous cattle breeds and populations are still bred 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 together with the small effective population sizes confirmed threat of extinction. According to the runs of homozygosity analysis, evidence of recent inbreeding was strong in some breeds. Low pair-wise genetic differentiation values, 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 region or area were detected. However, in spite the complex admixture history of most breeds, many of the local Italian cattle breeds have retained unique identities and are differentiated breeds, and this can be due to differences in the origin, differences in climate, genetic isolation and inbreeding. This study represents the first exhaustive 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 useful in creating conservation strategies. If reproductive isolation within groups of the same herd and area is maintained in subsequent generations, the short-term rate of inbreeding will increase dangerously, resulting in a decrease in the effective population size and seriously damaging the breeds future. Thus, efforts should be made to improve genetic diversity in these breeds. In particular, mating decisions will play an important role in limiting inbreeding and will increase the size of these local breeds.