Genetic variability of the Sardinian goat population assessed by the GoatSNP50 BeadChip

The current Sardinian goats derive from a crossbreeding between the native population and the Maltese breed, made to improve milk production. This unplanned crossbreeding was performed with different intensities depending on the area. The aim of this work was to compare a breed assignment of Sardinian goats based on the morphological profile and on the breeding history of the whole herd, with the genetic variability at a medium density SNP chip. The herds were divided into native Sardinian (S), crossbred with Maltese (C) and Maltese (M), based on a phenotypic classification of the genetic type, assessed by the farmer and by a classifier specifically trained . The morphological traits considered were: type of ears, presence of horns and type of coat. The lop ears are the most distinctive trait for identifying the presence of Maltese crossbreeding in a herd, because native Sardinian goats usually have small upright ears. 15 animals were assigned to M group, 40 to S group and 41 to C group. DNA samples of these 96 animals were genotyped using the GoatSNP50 BeadChip devised by the International Goat Genome Consortium (IGGC). After standard quality check (SNP call rate > 0.95; Minor Allele Frequency < 0.01; individual genotype call rate < 0.95) Multidimensional scaling plot (MDS plot) and Reynold’s genetic distances between groups were calculated using Plink and JMP®Genomics 6.0 software. The genetic distances of the three groups confirmed that the native Sardinian and the Maltese groups are the most distant, while the crossbred with Maltese is closer than Maltese to native Sardinian. The crossbred goats overlap to native Sardinian animals in MDS plot, suggesting that crossbred herds still contain a high portion of native Sardinian genome. These results show that this method of breed assignment can be used in conservation programs to identify native Sardinian herds. However, the high portion of native Sardinian genome observed in the crossbred herds, indicates that these population should also be considered to preserve the genetic variability of the Sardinian goat.