Progress in Genomic Analysis of Italian Goat Population

A total of 354 unrelated animals from 14 Italian breeds have been genotyped with the Illumina goat SNP50 BeadChip by Italian Goat Consortium. Population structure, analyzed with a Bayesian approach (Admixture software) and a multivariate approach (Principal Component Analysis, PCA), revealed variable levels of genetic admixture and a clear geographical distribution of diversity, from North to South along the peninsula and from East to West in the Alps. Genetic gradients of variation along geographic clines may derive both from isolation by distance or local adaptation to different environments. Therefore we used the Lositan software to identify and investigate separately neutral loci from those under directional and balancing selection. The three datasets were analysed with i) Neighbor-net, reconstructed from a Reynolds distance matrix between breeds, ii) Bayesian clustering and iii) PCA. Neutral and directionally selected loci showed the same geographic pattern observed when using the entire dataset, while markers under balancing selection were unable to clearly separate breeds. Genetic signals of demographic and selection histories seem tightly intertwined in Italian goats. Future analyses will focus on reconstructing the demographic history of individual breeds and on identifying genomic regions under positive selection using a range of different methodologies.