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Background  Transmissible spongiform encephalopathies (TSE) are fatal neurodegenerative diseases of several mammalian species, including humans. In Italy, the active surveillance through rapid tests on brain stem from small ruminants started in 2002 on randomly selected samples of healthy slaughtered animals. Sampling number was proportionally related to the regional small ruminant population. Of the twenty Italian regions, Sicily has the second largest population of small ruminants which is mainly constituted by crossbreed animals (>70 %). Sicily contains also three native sheep breeds  Pinzirita ,  Comisana  and  Valle del Belice.  Native goat breeds are  Girgentana ,  Messinese ,  Argentata dell’Etna, Maltese  and  Rossa Mediterranea.  The polymorphisms of prion protein gene ( PRNP)  may influence disease susceptibility and breeding programs for genetic TSE resistance are being applied in sheep. Protective alleles have been recently reported for goats also. These differ from those in sheep and may allow breeding programs in the near future.  In this paper the data of active surveillance for scrapie control in general population of small ruminants in Sicily are reported together with the analysis on the polymorphism of  PRNP  in a number of Sicilian autochthonous breeds. The evaluation of the frequency of protective alleles is fundamental for the implementation of a TSE resistance breeding program.    Results  TSE surveillance in small ruminants in Sicily showed a of total fifty seven scrapie outbreaks from 1997 to 2014 involving mainly crossbreed animals. The  PRNP  polymorphism analysis in autochthonous breeds showed protective allele frequencies of 30–40 % ARR in sheep and 12–18 % K222 in three of the four goat breeds; these breeds are distributed over limited areas of the island.    Conclusion  The study on  PRNP  polymorphisms in Sicilian small ruminant population showed higher frequency of the protective alleles compared to most other European breeds. Our results suggest that  PRNP  genetic variety in Sicilian sheep and goats can be a resource for TSE resistance breeding programmes while maintaining the conservation of endangered breeds and valorisation of their typical food products.    Electronic supplementary material  The online version of this article (doi:10.1186/s12917-016-0766-9) contains supplementary material, which is available to authorized users.

Scrapie incidence and PRNP polymorphisms: rare small ruminant breeds of Sicily with TSE protecting genetic reservoirs