Genetic diversity within and among endangered local cattle breeds from Tuscany (Italy)

Italy has a rich diversity in farm animals. In particular, Tuscany hosts a number of autochthonous bovine breeds that are, or have been, relevant for the economic sustainability of the agriculture, the origin and history of which are still poorly documented. Most of these breeds suffered in the past a dramatic loss of economic importance being substituted by cosmopolite and more productive breeds. The aim of the present study was to analyse levels of genetic diversity and relationship among local cattle breeds from Tuscany (Central Italy) using microsatellite markers. DNA from 194 animals (Calvana, 61; Garfagnina, 43; Pontremolese, 23; Chianina, 67) was analyzed at 22 microsatellite loci. Number of alleles (NA) and allelic frequencies were estimated. Locus by locus FST, exact tests for deviations from the Hardy-Weinberg equilibrium (HWE) and pair-wise linkage disequilibrium (LD) among microsatellite loci were evaluated. In addition, various among-population genetic distances were calculated. The study evidenced a significant departure from Hardy-Weinberg equilibrium in all the analyzed breeds, probably caused by a rather high level of inbreeding for Calvana, Garfagnina and Pontremolese, whereas likely reflecting the results of recent selective processes in Chianina. The overall fixation index was 0.115±0.054. Results obtained in this study suggest that the situation of the analyzed breeds is risky as their variability is compromised by a high level of inbreeding, in particular Pontremolese was the most compromised breed. Several distance metrics highlighted a only moderate differentiation between Chianina and Calvana if compared to values found among the other breeds. Also molecular coancestry and kinship distance supported the hypothesis that Calvana originated from Chianina, whereas Garfagnina and Pontremolese should have different ancestral origins. The low genetic variability suggests the need for a careful genetic management of the breeds, in order to maintain long-term population survival and adaptability and to avoid the risk of more excessive increase in the inbreeding level, which would result in significant inbreeding depression and in significant loss of genetic variation