Poorer resolution of low-density SNP vs. STR markers in reconstructing genetic relationships among seven Italian sheep breeds

Single Nucleotide Polymorphisms (SNPs) are increasingly used in livestock to infer genetic variability and relationship within and among breeds. Since displaying different mutational properties, bi-allelic markers could reconstruct dissimilar scenarios with respect to long-established Short Tandem Repeats (STRs). Here we present the results from the genetic characterization of seven Italian breeds using 111 SNPs, compared to those previously obtained from 19 STR loci typed on the same population sample (Sarda: 97; Comisana: 67; Altamurana: 83; Leccese: 86; Gentile di Puglia: 74; Bagnolese: 33; Laticauda: 30). All the 111 SNP loci resulted to be polymorphic in the total sample, with only six loci being monomorphic in at least one breed. After pruning of loci displaying MAF<0.1, a total of 103 SNPs were left in the overall sample dataset. The overall SNP gene diversity was 0.40 (±0.09). A remarkably low proportion of SNPs (on average 2.2%) displayed significant (P<0.01) deviations from the Hardy–Weinberg equilibrium within the seven breeds. The Leccese breed displayed not only the highest levels of Hardy-Weinberg and gametic disequilibrium (4.9% of SNPs), but also the highest inbreeding coefficient (FIS=0.05) and the highest within-breed allele-sharing distance (D=0.31). These results are consistent with the evidence of sub-structuring within the Leccese breed, as suggested by both the STRUCTURE analysis and the NJ tree based on the inter-individual allele-sharing distance. In addition, the analysis among-breeds highlighted a marked differentiation of Sarda, likely consistent with its insular nature. A more complex scenario was observed when looking at the ability of SNP in reconstructing genetic connections among Italian sheep breeds in comparison to what obtained previously with STR. SNP generally provided poorer resolution in reconstructing the genetic relationships among the seven Italian sheep breeds, likely due to their limited number. Interestingly, the study produced also a first clue of overdominance as shaping the pattern of variability at olfactory receptor genes in the ovine species.