The Italian Goat Consortium (IGC), joined the effort of many
Universities and Research Institutes, in a comprehensive
study of the Italian goat population genetic makeup using a
medium density (54K) SNPs chip. Currently IGC has genotyped
more than 1,000 animals from more than 30 goat
breeds and populations from all Italian geographical and agroecological
areas of goat rearing.
The aim of this work is to obtain a clear picture of the Italian
caprine biodiversity, to reconstruct the ancestry, to disentangle
the genetic background and to assess the relationships among
and within the investigated breeds. To date, the IGC dataset
includes about 50 million genotypes. The data were quality
checked by excluding markers and individuals on the basis of
missing genotypes, minor allele frequency and close individual
relatedness. Genetic relationships among and within breeds
was investigated by Multi-Dimensional Scaling and Principal
Component Analysis. Population structure, ancestry models
and admixture were estimated by ADMIXTURE and
fastSTRUCTURE software. Finally, phylogenic trees were reconstructed
with PHYLIP software suite starting from shared-allele
identity by state, and Reynolds distance matrices, while past
migration events were modeled with TreeMix software.
The results confirmed high levels of genetic polymorphism
and confirmed the North-South geographical pattern of diversity,
previously reported on a smaller sample of Italian goat
breeds. The analysis also revealed a pivotal role of Central
Italy in connecting the genetic resources of the northern and
southern areas of the country, and confirms the genetic isolation
of insular breeds. Moreover, some breeds show clearly
distinctive and homogeneous gene pools, whereas other
breeds present complex and, in some cases, dishomogeneous
genetic background