Abstract
The genetic underpinnings of calf mortality can be partly polygenic and partly due to deleterious effects of recessive lethal alleles. Prediction of the genetic merits of selection candidates should thus take into account both genetic components contributing to calf mortality. However, simultaneously modeling polygenic risk and recessive lethal allele effects in genomic prediction is challenging due to effects that behave differently. In this study, we present a novel approach where mortality risk probabilities from polygenic and lethal allele components are predicted separately to compute the total risk probability of an individual for its future offspring as a basis for selection. We present methods for transforming genomic estimated breeding values of polygenic effect into risk probabilities using normal density and cumulative distribution functions and show computations of risk probability from recessive lethal alleles given sire genotypes and population recessive allele frequencies. Simulated data were used to test the novel approach as implemented in probit, logit, and linear models. In the simulation study, the accuracy of predicted risk probabilities was computed as the correlation between predicted mortality probabilities and observed calf mortality for validation sires. The results indicate that our novel approach can greatly increase the accuracy of selection for mortality traits compared with the accuracy of predictions obtained without distinguishing polygenic and lethal gene effects.
Highlights
Important fractions of deleterious mutations segregating in diploid organisms are recessive alleles that cause fatal effects when present in a homozygous state
The accuracies obtained with the novel approach were significantly higher (P < 0.001) than those obtained with the conventional approach
We present an efficient approach for predicting the total risk probabilities for future offspring of selection candidates by predicting risk probabilities from polygenic and recessive lethal components separately
Summary
Important fractions of deleterious mutations segregating in diploid organisms are recessive alleles that cause fatal effects when present in a homozygous state. Recessive lethal alleles are of considerable economic consequence in the dairy industry because they cause calf and young stock mortality as well as reproductive inefficiency (e.g., Cole et al 2016). The most practiced approach in dairy breeding is to limit carrier-to-carrier mating (Charlier et al 2008) While such an approach might be feasible with few lethal alleles segregating in the population, it is becoming considerably more difficult with the increasing number of detected recessive lethal alleles (VanRaden et al 2011; Fritz et al 2013; Sahana et al 2013, 2016; Kadri et al 2014; Hoff et al 2017). Genomic prediction of breeding values for calf mortality traits should take into account both polygenic and recessive lethal components
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