Italian Goat Consortium: a collaborative project to study the Italian caprine biodiversity.

The Italian Goat Consortium (IGC), joined the effort of manyUniversities and Research Institutes, in a comprehensivestudy of the Italian goat population genetic makeup using amedium density (54K) SNPs chip. Currently IGC has genotypedmore than 1,000 animals from more than 30 goatbreeds and populations from all Italian geographical and agroecologicalareas of goat rearing.The aim of this work is to obtain a clear picture of the Italiancaprine biodiversity, to reconstruct the ancestry, to disentanglethe genetic background and to assess the relationships amongand within the investigated breeds. To date, the IGC datasetincludes about 50 million genotypes. The data were qualitychecked by excluding markers and individuals on the basis ofmissing genotypes, minor allele frequency and close individualrelatedness. Genetic relationships among and within breedswas investigated by Multi-Dimensional Scaling and PrincipalComponent Analysis. Population structure, ancestry modelsand admixture were estimated by ADMIXTURE andfastSTRUCTURE software. Finally, phylogenic trees were reconstructedwith PHYLIP software suite starting from shared-alleleidentity by state, and Reynolds distance matrices, while pastmigration events were modeled with TreeMix software.The results confirmed high levels of genetic polymorphismand confirmed the North-South geographical pattern of diversity,previously reported on a smaller sample of Italian goatbreeds. The analysis also revealed a pivotal role of CentralItaly in connecting the genetic resources of the northern andsouthern areas of the country, and confirms the genetic isolationof insular breeds. Moreover, some breeds show clearlydistinctive and homogeneous gene pools, whereas otherbreeds present complex and, in some cases, dishomogeneousgenetic background.