Calculation of PrP genotype and NSP type probabilities in Slovenian sheep | Izračun verjetnosti genotipov PrP in skupin NSP pri ovcah v Sloveniji

anglais. The PrP genotype probabilities in non genotyped Slovenian sheep were calculated. Altogether 36 083 ewes and rams of various breeds were included into analysis. The PrP genotype was known for 10 504 animals. Five different PrP alleles were present in the data set. Pedigree and genotype data structure differed between breeds. Iterative allelic peeling with incomplete penetrance model was used for the calculation of genotype probabilities for each animal given the genotype data of relatives. Analyses were performed for each breed separately. Additionally, NSP (National Scrapie Plan) type probabilities and the average NSP value were calculated from the genotype probabilities. Results were presented for live animals only. There were no animals with additionally identified PrP genotype or NSP type with certainty. The PrP genotype was additionally identified with 95% probability for 0.0 to 5.7% animals of different breeds. NSP type was additionally identified with the same probability for 0.0 to 34.9% animals of different breeds. We assume that the low number of additional identifications was due to: a large number of alleles, intermediate allele frequencies, data structure, a uniform prior, and the use of incomplete penetrance model. Additional identifications provided some cost savings, but did not prove useful in the selection for scrapie resistance of the entire population. The average NSP value should be used instead, since it can be calculated for all animals and encompasses all information from genotype probabilities.

slovène. Izračunali smo verjetnosti genotipov PrP za negenotipizirane ovce v Sloveniji. V analizo smo zajeli 36 083 ovc in ovnov različnih pasem. Genotip PrP je bil znan za 10 504 živalih. V podatkih je bilo prisotnih pet različnih alelov PrP. Struktura porekla in podatkov o genotipu PrP se je med pasmami razlikovala. Z metodo alelnega lupljenja in modelom nepopolne penetrance, smo na podlagi genotipa sorodnikov iterativno izračunali verjetnosti genotipov PrP za vse živali. Analize smo opravili za vsako pasmo posebej. Iz verjetnosti genotipov smo preračunali verjetnosti za skupine NSP (National Scrapie Plan) ter iz teh povprečno vrednost NSP. Rezultate smo predstavili le na živih živalih. Prav nobeni živali nismo uspeli z gotovostjo dodatno določiti genotipa PrP ali skupine NSP. Za 0,0 do 5,7 % živali različnih pasem smo lahko dodatno določili genotip PrP s 95 % verjetnostjo, medtem ko smo lahko z enako verjetnostjo dodatno določili skupino NSP za 0,0 do 34,9 % živali različnih pasem. Menimo, da so vzroki za majhno število dodatnih določitev genotipa PrP sledeči: veliko število alelov, intermediarne frekvence alelov, struktura podatkov, uniformna apriorna verjetnost in uporaba modela nepopolne penetrance. Dodatne določitve genotipa PrP in skupine NSP predstavljajo prihranek za rejski program. Zaradi majhnega števila dodatnih določitev metoda ni uporabna za selekcijo celotnih populacij na odpornost proti praskavcu. V ta namen lahko uporabimo povprečno vrednost NSP, saj ta parameter združuje vse verjetnosti genotipov PrP in ga lahko izračunamo za vse živali.