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In this study we used a medium density panel of SNP markers to perform population genetic analysis in five Italian cattle breeds. The BovineSNP50 BeadChip was used to genotype a total of 2,935 bulls of Piedmontese, Marchigiana, Italian Holstein, Italian Brown and Italian Pezzata Rossa breeds. To determine a genome-wide pattern of positive selection we mapped the F ST values against genome location. The highest FST peaks were obtained on BTA6 and BTA13 where some candidate genes are located. We identified selection signatures peculiar of each breed which suggest selection for genes involved in milk or meat traits. The genetic structure was investigated by using a multidimensional scaling of the genetic distance matrix and a Bayesian approach implemented in the STRUCTURE software. The genotyping data showed a clear partitioning of the cattle genetic diversity into distinct breeds if a number of clusters equal to the number of populations were given. Assuming a lower number of clusters beef breeds group together. Both methods showed all five breeds separated in well defined clusters and the Bayesian approach assigned individuals to the breed of origin. The work is of interest not only because it enriches the knowledge on the process of evolution but also because the results generated could have implications for selective breeding programs. © The Author(s) 2014.

Italy represented a crucial zone for migration and formation of sheep breeds. However, few data on Italian breeds have been published so far. We analysed seven Italian sheep breeds using mitochondrial DNA (mtDNA) sequencing to gain information on their genetic diversity and history. A 721 bp mtDNA control region fragment was amplified and sequenced in a total of 138 samples belonging to seven breeds and to Italian mohuflon (Ovis orientalis musimon) to investigate genetic diversity and phylogenetic evolution. We retrieved 68 variable sites and 79 haplotypes. The sheep breeds in our study are quite diverse, and phylogenetic analyses resulted in 3.6% of the samples belonging to A, 2.2% to D and 94.2% to B mtDNA haplogroups. Principal Component Analysis (PCA) showed a separation of breeds on both dimensions. The results of this study provide data on Italian breeds, presently scarcely investigated, and contribute to the knowledge of Italian sheep breeds and will be useful to the understanding of population genetics and breed evolution.

We employed mtDNA and nuclear SNPs to investigate the genetic diversity of sheep breeds of three countries of the Mediterranean basin: Albania, Greece, and Italy. In total, 154 unique mtDNA haplotypes were detected by means of D-loop sequence analysis. The major nucleotide diversity was observed in Albania. We identified haplogroups, A, B, and C in Albanian and Greek samples, while Italian individuals clustered in groups A and B. In general, the data show a pattern reflecting old migrations that occurred in postneolithic and historical times. PCA analysis on SNP data differentiated breeds with good correspondence to geographical locations. This could reflect geographical isolation, selection operated by local sheep farmers, and different flock management and breed admixture that occurred in the last centuries., c