Final Activity Report Summary - SHEEPHEALTHGENETICS (Development of methodologies for sheep health genetics) Transmissible spongiform encephalopathies (TSE) are fatal neurodegenerative diseases occurring in mammalian species, such as scrapie affecting sheep and BSE affecting cattle. Susceptibility to scrapie is partly depending on the inherited alleles of the prion protein (PrP) gene. Generally the PrP alleles are described for three codons named after the amino acids they encode: 136 (Alanine or Valine; A,V), 154 (Histidine or Arginine; H,R) and 171 (Glutamine, Arginine or Histidine; Q,R,H) which are related with scrapie susceptibility. At these codons, the following five alleles are commonly distinguished: ARR, AHQ, ARH, ARQ and VRQ in order of increasing susceptibility.If found that BSE can be transmitted from cattle to sheep then the effects would be huge due to the known effect of BSE causing Creutzfeldt-Jakob disease in humans. To avoid any risk of scrapie or BSE in sheep to humans the EU decided that selection against susceptible PrP alleles should be implemented. This means that all susceptible PrP alleles should be eradicated from the EU sheep population. Effective selection against PrP alleles or for other traits of interest depends strongly on good pedigree information. In sheep, pedigree information is often missing due to natural insemination using multiple sires joining a flock of ewes. The need to obtain PrP allele information can be used to obtain information on more loci and enable pedigree verification.In the first year of the project SHEEPHEALTHGENETICS, results of the investigations on PrP allele frequencies in the Sicilian dairy sheep populations were obtained. For this purpose three Sicilian populations have been genotyped for the PrP gene. These populations were: Valle del Belice (8 flocks with 1088 animals), Comisana, (3 flocks with 1141 animals) and a number of Sicilian flocks with scrapie outbreaks, in which the animals where indigenous Sicilian dairy sheep which often were cross-bred (5 flocks with 1762 animals). Furthermore a computer program 'Pedverif' was developed to verify pedigree information.DNA was isolated from blood and amplified using PCR to obtain sufficient DNA for allele determination. Valle del Belice allele frequencies were ARR (32,4 %), AHQ (6,5 %), ARH (1,1 %), ARQ (58,7 %) and VRQ (1,4 %). Comisana allele frequencies were ARR (39,4 %), AHQ (2,9 %), ARH (2,9 %), ARQ (50,9 %) and VRQ (3,9 %). In the infected indigenous flocks the allele frequencies were ARR (32,8 %), AHQ (2,4 %), ARH (1,7 %), ARQ (59,1 %) and VRQ (3,9 %). ARQ and secondly ARR were the most common alleles in all three populations. The most susceptible allele VRQ and also ARH appear to have a low frequency and therefore can be eradicated fast. The second most susceptible allele ARQ is however the allele most frequently found. This allele can only be removed in several generations. The highly susceptible genotypes VRQ/AHQ, VRQ/ARH, VRQ/ARQ and VRQ/VRQ together include 2,7 %, 7,7 % and 7,8 % of the Valle del Belice, Comisana and infected indigenous populations respectively. The resistant animals are ARR/ARR, ARR/AHQ, ARR/ARH and ARR/ARQ, which together comprises Valle del Belice (54,3 %), Comisana (60,1 %) and infected indigenous flocks (51,5 %) of the same populations. In total, 55,3 %, 63,0 % and 54,4 % carry an ARR allele. Verification of the Hardy-Weinberg genotype equilibrium showed that selection so far does not strongly affect the PrP locus.Pedverif is aimed at populations with parental uncertainty. Main complications are:- More pathways need to be recursively verified to avoid pedigree loops.- Combinations of candidate parents need to be reported and not single candidate parents, otherwise there will be impossible combinations between possible parents.- A combination of candidate parents for an individual might be possible but maybe not in combination with a combination of candidate parents for other individuals.In conclusion, the eradication of undesired alleles can be achieved by using only ARR/ARR sires. Several generations will be needed.