Genetic diversity and structure of Italian sheep breeds inferred by genome-wide SNP analysis:overview of the “Italian Project for Sheep Biodiversity

So far, genetic diversity within and among Italian sheep breeds has been investigated almost exclusively by microsatellite markers and never at national scale. Recently, high density Single Nucleo - tide Polymorphism (SNP) arrays have been developed for the major livestock species, including sheep. In the second half of 2010, a large national collaborative project was launched, within the context of the International Sheep Genome Consortium (ISGC), aiming at characterizing at the genomic level the main Italian sheep breeds, together with some endangered local breeds. Around 500 animals evenly distributed among 19 Italian breeds (Alpagota, Altamurana, Appenninica, Bagnolese, Bergamasca, Biellese, Comisana, Delle Langhe, Fabrianese, Gentile di Puglia, Laticauda, Leccese, Massese, Pecora Nera di Arbus, Pinzirita, Sambucana, Sarda, Sopravissana, Valle del Belice) have been genotyped using a 50K SNP array. Molecular data have been pruned according to SNP minor allele frequency (MAF<0.01), frequency of missing genotypes (Geno>0.1) and linkage disequilibrium (r2 > 0.5) using the PLINK software package. The subsequent analysis of the massive data generated by genome-wide SNP genotyping will pinpoint the genetic distinctiveness and levels of admixture of Italian breeds, thus unraveling new aspects of the breed formation process. In addition, comparative analysis of conserved haplotypes will identify genomic segments under selection pressure, highlighting interesting genomic regions. Data analysis will also be useful to select SNP loci suitable for parentage and identity DNA test in Italian breeds