Italian Goat Consortium: a first overview of genetic variability using a medium density single nucleotide polymorphism array

The Italian Goat Consortium was established from the Innovagen Project to join local efforts and resources for the genomic characterisation of Italian goat breeds. Thirteen Italian goat breeds (Valdostana, Saanen, Orobica, Bionda dell'Adamello, Val Passiria, Grigia Ciociara, Teramana, Nicastrese, Aspromontana, Girgentana, Argentata dell'Etna, Sarda and Maltese - the latter sampled in Sardinia and Sicily) for a total of 350 animals (15-32 per breed) were analysed using a medium density SNP array. Data editing was based on the following thresholds: MAF <1%; Missing SNP >5%; Missing animal >5%; HW within breed FDR >20%. After filtering, a total of 51,136 SNPs were retained, showing that the adopted SNP chip is highly informative for the characterization of Italian goat breeds. Population structure and breed distinctiveness were investigated with the software Admixture, that revealed the best fitting solution at K=11 partitions. The software also highlighted variable levels of admixture and an early differentiation of Val Passiria, Orobica, Valdostana, Teramana, Girgentana and Sarda breeds. Within MDS plot, some breeds are clearly appreciable as distinct: Girgentana, Teramana, Orobica and Maltese. PCA analysis revealed a gradient of diversity North (from alpine breeds) - South (to Sicilian breeds) and East (from Val Passiria breed) - West (to Valdostana breed) in the Alps. The calculation of Fis index indicated little or no inbreeding, while LD analysis in Chromosome 6 showed levels of disequilibrium much lower than cattle at short physical distance.