This study provides new evidence in UK goats for an association of Prnp gene polymorphisms with low disease incidence and probably with partial resistance to classical scrapie. In contrast there is no indication for gene variants associated with increased susceptibility to classical scrapie, such as the one found for codon 136 valine polymorphism of ovine Prnp. Our genetic analysis of classical scrapie cases from dairy goats in two UK herds collected within a period of about 3 years reveals for the first time an association of codon 127 serine with a decreased probability to develop clinical scrapie, but not with susceptibility to infection and accumulation of PrPd. The development of clinical signs is a measure of incubation period length and defines the age-of-onset in natural scrapie cases, our data imply that S127 is a modulator of pathogenesis, similar to other Prnp alleles in ruminants, eg. H154 in sheep or 132L in deer . Whether goats with S127 containing genotypes are lifelong subclinical carriers of infectivity or have a very extended incubation period remains to be investigated.
A similar association was observed with the codon 142 methionine carriers, where the frequency of clinical positive M142 carriers is lower than compared to the frequency of PrPd-positive, preclinical M142 carriers. But for both, clinical and preclinical, the frequency is significantly lower than for II142 genotypes. There was no susceptibility difference between M142/wt-S and M142/wt-P genotypes as has been suggested in studies by Barillet et al. .
Reported classical scrapie cases have been absent from the UK goat population for more than 10 years before these four affected herds emerged . Little is known about the origin of these scrapie outbreaks and they represent for the time being the only UK herds to study Prnp disease association. Our data are therefore subject to the relative small number of cases and confirmation of the described genetics, particularly for S127 will depend on further outbreaks or experimental challenges. However, our findings regarding the M142 allele are in agreement with previous publications [14, 20, 21].
Of the ten Prnp coding region polymorphisms that were observed in our herds, three (Q101R, R154H and N146S) are described for the first time in the UK goat population. There are important differences in the frequencies of these polymorphisms between the various breeds. The M142 allele is less prominent in the meat and fibre breeds; to our best knowledge these breeds have never reported scrapie cases in the UK. However the Boer goats showed high frequency of the polymorphism N146S which has been shown in the Cypriot Damascus breed to increase scrapie resistance [16, 17]. This polymorphism was also reported in Boer goat in Chinese populations, in which the S146 allele is the more frequent (57.4%). Only the Cashmere goats carried the I218L polymorphism, which is consistent with data from Chinese studies which showed this polymorphism in Liaoning Cashmere and Beijing Native goats at frequencies of 13.3% and 62.5%, respectively . The Prnp analysis suggest that the UK meat and fibre breeds are closer to each other than they are to dairy breeds, which is supported by other breed characteristics. The H154 allele, which is proposed to increase the susceptibility to atypical scrapie, was not observed in the dairy breeds, which make up the majority of UK goats. In contrast, the S127 allele was found almost exclusively in dairy goats where it showed high variation between herds (2.5%-25%), although the mean was similar to populations in some other countries.
The frequencies of some of the Prnp alleles in the UK compared to some other countries are quite different (Table 4) with the exception of the wildtype alleles. This is an important issue when breeding strategies are to be considered, which are dependent on allele selection and potential QTL linkage. Almost all UK dairy goat herds had a high percentage (≥ 20%) of the M142 allele, which is three times higher than for herds from France and Italy [14, 26]. The fact that this allele is found at this high frequency in the UK goat population is surprising as it could suggest a selective advantage. However, it would be very speculative to assume that this resistance-related allele is present and maintained at that level due to previous or current scrapie epidemics. It should be noted here that before Prnp genotype-based breeding was introduced into the UK sheep population the resistance related R171 allele was also already frequent , which may have been due to balancing selection . The association of the M142 allele with partial resistance and its high frequency would make it a candidate for breeding programmes to reduce scrapie prevalence in the short term.
A marked difference was found in polymorphisms R211Q and Q222K which were four times and ten times less common, respectively, in British herds than in French and Italian herds. Because of the very high resistance to TSEs conferred by the K222 allele, it presents a good candidate allele to select for in genetic scrapie eradication programmes. Our data show that 33% of dairy herds contain at least one K222 carrier, whereas none were found in the herds of the meat and fibre breeds. With a K222 allele frequency of less than 1% on average, natural breeding to high levels will remain a long term aim rather than a immediate solution for the UK. However dairy goats in Western European countries are less diversified into breeds than sheep and the utilization of European breeding stock with the K222 allele through artificial insemination may be a viable option.
It has been reported that human and sheep Prnp are under balancing selection [25, 28], which may or may not be related to TSEs. A consequence of this would be the maintenance of a larger number of Prnp variants in the population than under purifying selection, which has been suggested to constrain bovine Prnp variability  and may underlie wild populations such as chamois and deer [30, 31]. It appears that domestic goat populations maintain a number of Prnp polymorphisms as might be expected from balancing selection and the majority of these polymorphisms is associated with a degree of protection against TSEs compared to the wildtype. We were interested to see if a goat population from a region which had never any confirmed scrapie outbreaks would show equally diverse Prnp genetics as the UK or other scrapie affected countries. We selected herds of Mexican Criollas goats, a breed of European linage that was introduced several hundred years ago into the Americas. These goats would most likely not have been under TSE-related selection. The fact that we found five polymorphisms at frequencies ≥ 3% and a novel F201L polymorphism in fewer than 200 animals leads us to argue that TSE epidemics are not the exclusive reason for high genetic variability of the Prnp in livestock species such as sheep and goats. Interestingly, the K222 allele most closely associated with high scrapie resistance in French flocks  was not detected in Mexican Criollas goats, whereas the S146 allele -associated with scrapie resistance in Cypriot flocks [16, 17]-was present at 5% level.
This study confirmed that the UK goat population contains resistance associated alleles at various frequency levels, some of which could be used for long term breeding programmes for a reduction of classical scrapie cases.