Prediction of Genetic Resistance for Scrapie in Ungenotyped Sheep Using a Linear Animal Model.

Mohammed Boareki,Flavio Schenkel,Angela Cánovas,Delma Kennedy

doi:10.3390/genes12091432

Mohammed Boareki, Flavio Schenkel + Show 2 more

Open Access

https://doi.org/10.3390/genes12091432

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Abstract

Selection based on scrapie genotypes could improve the genetic resistance for scrapie in sheep. However, in practice, few animals are genotyped. The objectives were to define numerical values of scrapie resistance genotypes and adjust for their non-additive genetic effect; evaluate prediction accuracy of ungenotyped animals using linear animal model; and predict and assess selection response based on estimated breeding values (EBV) of ungenotyped animals. The scrapie resistance (SR) was defined by ranking scrapie genotypes from low (0) to high (4) resistance based on genotype risk groups and was also adjusted for non-additive genetic effect of the haplotypes. Genotypes were simulated for 1,671,890 animals from pedigree. The simulated alleles were assigned to scrapie haplotypes in two scenarios of high (SRh) and low (SRl) resistance populations. A sample of 20,000 genotyped animals were used to predict ungenotyped using animal model. Prediction accuracies for ungenotyped animals for SRh and SRl were 0.60 and 0.54, and for allele content were from 0.41 to 0.71, respectively. Response to selection on SRh and SRl increased SR by 0.52 and 0.28, and on allele content from 0.13 to 0.50, respectively. In addition, the selected animals had large proportion of homozygous for the favorable haplotypes. Thus, pre-selection prior to genotyping could reduce genotyping costs for breeding programs. Using a linear animal model to predict SR makes better use of available information for the breeding programs.

Highlights

In the typical form of scrapie, the risk of infection is determined by variation in amino acid sequence encoded in the PrP gene [1,2,3,4]
The Pearson’s correlation coefficients between estimated breeding values (EBV) and the trait true genetic value are shown in Table 6 for ungenotyped animals
The current study showed that selecting ungenotyped sheep based on EBV could increase scrapie resistance traits (SR) (Tables 7 and 8) and ARR allele frequency and its homozygous genotype frequency (Figures 3 and 4), what could reduce typical scrapie prevalence in sheep

Summary

Introduction

In the typical form of scrapie, the risk of infection is determined by variation in amino acid sequence encoded in the PrP gene [1,2,3,4]. There are five common haplotypes (ARR, AHQ, ARH, ARQ, and VRQ) associated with the scrapie risk of infection; in which the haplotype ARR is associated with lowest risk, and the haplotype VRQ is associated with highest risk of scrapie infection [2,5,6,7]. A total of 15 common possible genotype combinations are associated with five risk groups (R1, R2, R3, R4, and R5), in which R1 genotypes are associated with low risk for scrapie infection (i.e., the most favorable genotypes) and R5 are associated with highest risk of infection [3,8,9]. Due to the association of genotypes with the risk of scrapie, the use of genotyping for breeding programs is appealing for scrapie eradication programs [5,8,10,11]. Gengler et al [12] proposed the use of a practical method to predict the allele content of bi-allelic locus in ungenotyped animals by using the Best Linear Unbiased Predictor (BLUP), in which the number of observed alleles in the genotype (0, 1, or 2) are used as a response variable, assuming complete heritability

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