Geographical patterning of sixteen goat breeds from Italy, Albania and Greece assessed by Single Nucleotide Polymorphisms

Abstract

Background: SNP data of goats of three Mediterranean countries were used for population studies and reconstruction of geographical patterning. 496 individuals belonging to Italian, Albanian and Greek breeds were genotyped to assess the basic population parameters.

Results: A total of 26 SNPs were used, for a total of 12,896 genotypes assayed. Statistical analysis revealed that breeds are not so similar in terms of genetic variability, as reported in studies performed using different markers. The Mantel test showed a strongly significant correlation between genetic and geographic distance. Also, PCA analysis revealed that breeds are grouped according to geographical origin, with the exception of the Greek Skopelos breed.

Conclusion: Our data point out that the use of SNP markers to analyze a wider breed sample could help in understanding the recent evolutionary history of domestic goats. We found correlation between genetic diversity and geographic distance. Also PCA analysis shows that the breeds are well differentiated, with good correspondence to geographical locations, thus confirming the correlation between geographical and genetic distances. This suggests that migration history of the species played a pivotal role in the present-day structure of the breeds and a scenario in which coastal routes were easier for migrating in comparison with inland routes. A westward coastal route to Italy through Greece could have led to gene flow along the Northern Mediterranean.

Figure 1

Principal component analysis (PCA) of allele frequencies from twenty three SNP loci genotyped in the sixteen goat breeds. Projection on axis 1 and axis 2, which cumulatively explained 52% of the total inertia contained in the data set. Breeds acronyms as in Table 1. Albanian breeds, green; North Italian breeds, blue; South Italian breeds, red; Greek breeds, pink.

Figure 2

Principal component analysis (PCA) of allele frequencies from twenty six SNP loci genotyped in the sixteen goat breeds. Projection on axis 1 and axis 2, which cumulatively explained 56.8% of the total inertia contained in the data set. Breeds acronyms as in Table 1. Albanian breeds, green; North Italian breeds, blue; South Italian breeds, red; Greek breeds, pink.

Figure 3

Rearing area of each analysed breed.