Simulation analysis to test the influence of model adequacy and data structure on the estimation of genetic parameters for traits with direct and maternal effects

Abstract

-Simulations were used to study the influence of model adequacy and data structure on the estimation of genetic parameters for traits governed by direct and maternal effects. To test model adequacy, several data sets were simulated according to different underlying genetic assumptions and analysed by comparing the correct and incorrect models. Results showed that omission of one of the random effects leads to an incorrect decomposition of the other components. If maternal genetic effects exist but are neglected, direct heritability is overestimated, and sometimes more than double. The bias depends on the value of the genetic correlation between direct and maternal effects. To study the influence of data structure on the estimation of genetic parameters, several populations were simulated, with different degrees of known paternity and different levels of genetic connectedness between flocks. Results showed that the lack of connectedness affects estimates when flocks have different genetic means because no distinction can be made between genetic and environmental differences between flocks. In this case, direct and maternal heritabilities are under-estimated, whereas maternal environmental effects are overestimated. The insufficiency of pedigree leads to biased estimates of genetic parameters.genetic parameters / animal model / maternal effects / simulations / connectedness

The quantitative genetics of sexual dimorphism: assessing the importance of sex-linkage

“…However, a citation search revealed no citations to this work and, to the best of our knowledge, the animal model has not yet been used to estimate sex-linked variance (personal communication: Loeske Kruuk, University of Edinburgh; William Hill, University of Edinburgh; Denis Reale, Université du Québec à Montréal). Given the proposed wide occurrence of sexlinked effects in SD traits and the bias introduced by use of an incomplete genetic model (Clément et al, 2001), we recommend inclusion of sex-linked effects whenever the traits examined are sexually dimorphic.…”

“…In the simplest extension of the animal model, maternal effects are fitted by making dam identity a random effect (e.g., Kruuk et al, 2000;Milner et al, 2000). Parameter estimation in domestic breeds has frequently included the maternal additive genetic variance, direct maternal additive genetic covariance and maternal environmental variance (e.g., see Clément et al, 2001) and this model was fitted to the feral population of Soay sheep (Wilson et al, 2005). Additionally, non-additive variances have been estimated for domestic breeds (e.g., Rodriguez-Almeida et al, 1995).…”

Simultaneous Estimation of Additive and Mutational Genetic Variance in an Outbred Population of Drosophila serrata

“…In general, and ignoring biases introduced by maternal and environmental effects (Clément et al 2001;Kruuk and Hadfield 2007), in an animal model analysis of genetic variation, statistical power is determined by the size of the base population, accuracy is determined by the number of pedigree links between levels of the fixed effects (i.e., generations in our case) (Kennedy and Trus 1993;Hanocq et al 1996;Clément et al 2001;Quinn et al 2006), and precision is determined by the number of phenotypes per family (Quinn et al 2006). All these properties of the experimental design are captured by the T-matrix and hence should apply to both additive genetic [Equation (2)] and mutational [Equation (4)] effects.…”

Genetic Parameter Estimates for Growth and Reproductive Trait of Sheep for Genetic Improvement and Designing Breeding Program in Ethiopia: A Review

“…However, despite the theoretical advantages of this model, some data and model conditions can affect the validity and precision of the estimation of variance components [12]. According to [13], Animal models resulted in slightly greater estimates of heritability for fertility than did sire models but ovulation rate heritability estimates from sire models were much greater than estimates form animal models.…”