Analysis of genetic variability within and among Italian sheep breeds reveals population stratification and suggests the presence of a phylogeographic gradient

Italy has a long history of sheep breeding and, despite a dramatic number contraction occurred in the last century, still counts several local sheep breeds that may represent a unique source of genetic diversity. Here we present the results from the genetic characterization of seven Italian dairy sheep breeds by 19 STR markers. High levels of polymorphism were generally detected, with 16.2 average alleles per locus and an average gene diversity of 0.79. The within-breed analysis highlighted, in six out of the seven breeds, a remarkable proportion of loci displaying significant heterozygote deficit. Moreover, within-breed percentages of locus pairs with significant genotypic disequilibrium were, for all breeds, markedly higher than expected by chance thus suggesting the presence of population stratification. The subdivision was particularly evident for the Leccese sheep breed and was confirmed by the STRUCTURE analysis. On the contrary, results generally highlighted Sarda as the most homogeneous, but less inbred, population, consistently with its large census size and longstanding effective genetic management practices. Both STRUCTURE analysis and measures of genetic distance, with the exception of those based on allele sharing, suggested the presence of a phylogeographic gradient, with Sarda as the most differentiated breed and continental breeds from the same region tending to group closer to each other.Taken together, the results highlighted that all the Italian breeds display a genetic variability content comparable to other European breeds, thus demonstrating their importance as genetic reservoir for future selection options. However, management actions should be more effectively implemented in local endangered breeds in order to reduce inbreeding and within-breed sub-structuring.