Poor Genetic Structure in Local Goat Breeds from Central and Southern Continental Italy

As a follow-up activity within the frame of the Italian Goat Consortium (http://www.goatit.eu), a total of 190 samples from 8 small population size goat breeds from central and southern continental Italy, i.e. Bianca (24), Capestrina (22), Facciuta (24), Fulva (22), Garganica (24), Ciociara Grigia (24), Montefalcone (23) and Teramana (24), was genotyped using the Illumina Goat 60K SNP BeadChip. After pruning (--mind 0.1 --geno 0.02 --maf 0.01), 48,655 loci and 187 animals were left. Unsupervised Bayesian clustering highlighted, at K=2, no significant sub-structuring, with the exception of six Garganica animals, that were found to have rather high inbreeding coefficients (inbreeding bias). At K=3, the Teramana animals partly clustered in a separate group (N=11), partly fell in the general group (N=8), the remaining animals presenting signals of admixture between these two clusters (N=5). At the best K value (K=4), identified using the ADMIXTURE cross-validation procedure, a further cluster appeared, represented by few Bianca, few Capestrina and very few Grigia animals. The latter three breeds are all from the same region (Lazio), hence the observed results may suggest that recent short-range admixture practices may have influenced the current genetic make-up of these breeds. MDS analysis corroborated the above results. Meta-analysis of our genotypic dataset with data available from previous studies will allow to get better insights on the generally weak genetic structure observed in this study, likely arising from extensive remote and recent admixture practices and/or a common ancestral genetic stock.