Genetic structure and diversity of Santa Inês sheep flocks in Brazilian Mid-North

The genetic structure and diversity of Santa Inês sheep flocks from the Mid-North sub-region of Brazil were assessed using microsatellite markers.A total of 257 DNA samples from animals raised in six farms were genotyped using a panel of 20 microsatellite loci. Different programs were used to assess the influence of null alleles on genetic differentiation estimates, the probability of loci being under selection, and to calculate different parameters to assess the genetic variability and the power of markers to determine the kinship among flocks. Deviations from the Hardy-Weinberg equilibrium and linkage disequilibrium were tested using the R package genepop. A Bayesian clustering analysis was performed using the STRUCTURE program. The R packages poppr, adegenet, ape, polysat, and ggplot2 were used to construct a dendrogram and perform the principal coordinates analysis (PCoA). The Wilcoxon sign-rank test was conducted to detect population bottlenecks. Network graphics were constructed to assess the bidirectional distribution of the gene flow among flocks.The average values obtained for the number of alleles per locus, expected heterozygosity (He), polymorphism information content (PIC), discriminatory capacity, the combined probability of identity, and the probability of exclusion for the markers were 15.4, 0.886, 0.877, 0.954, 0.025, and 0.920, respectively. The lowest degree of genetic variability was observed in Farm 6, i.e. He (0.700), PIC (0.653), and allelic richness (Ar) (3.760), whereas Farm 1 had the highest values of He (0.890), PIC (0.882), and Ar (4.690). Signals of genetic bottleneck and moderate genetic differentiation were observed in all flocks. The migration rates in all flocks were high, with a trend towards Farm 1.There is moderate structuring and high genetic diversity in the flocks evaluated. It is necessary to review the management strategies, because of the signals of bottleneck and genetic erosion.