Abstract
BackgroundMixed models are commonly used for the estimation of variance components and genetic evaluation of livestock populations. Some evaluation models include two types of additive genetic effects, direct and maternal. Estimates of variance components obtained with models that account for maternal effects have been the subject of a long-standing controversy about strong negative estimates of the covariance between direct and maternal effects. Genomic imprinting is known to be in some cases statistically confounded with maternal effects. In this study, we analysed the consequences of ignoring paternally inherited effects on the partitioning of genetic variance.ResultsWe showed that the existence of paternal parent-of-origin effects can bias the estimation of variance components when maternal effects are included in the evaluation model. Specifically, we demonstrated that adding a constraint on the genetic parameters of a maternal model resulted in correlations between relatives that were the same as those obtained with a model that fits only paternally inherited effects for most pairs of individuals, as in livestock pedigrees. The main consequence is an upward bias in the estimates of the direct and maternal additive genetic variances and a downward bias in the direct-maternal genetic covariance. This was confirmed by a simulation study that investigated five scenarios, with the trait affected by (1) only additive genetic effects, (2) only paternally inherited effects, (3) additive genetic and paternally inherited effects, (4) direct and maternal additive genetic effects and (5) direct and maternal additive genetic plus paternally inherited effects. For each scenario, the existence of a paternally inherited effect not accounted for by the estimation model resulted in a partitioning of the genetic variance according to the predicted pattern. In addition, a model comparison test confirmed that direct and maternal additive models and paternally inherited models provided an equivalent fit.ConclusionsIgnoring paternally inherited effects in the maternal models for genetic evaluation can lead to a specific pattern of bias in variance component estimates, which may account for the unexpectedly strong negative direct-maternal genetic correlations that are typically reported in the literature.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-015-0141-5) contains supplementary material, which is available to authorized users.
Highlights
Mixed models are commonly used for the estimation of variance components and genetic evaluation of livestock populations
Scenario 1: additive model of inheritance In Scenario 1, all genetic variation was generated as direct additive; there were no maternal genetic or paternally inherited effects
When the estimation model only included paternal gametic effects (Model S), a significant proportion of the variation was assigned to these effects and the remaining additive variation was incorporated into the residual variance
Summary
Mixed models are commonly used for the estimation of variance components and genetic evaluation of livestock populations. Some evaluation models include two types of additive genetic effects, direct and maternal. We analysed the consequences of ignoring paternally inherited effects on the partitioning of genetic variance. Some traits may be affected by maternal genetic effects that refer to the influence from the Genomic imprinting [7, 8] is the total or partial silencing of paternal or maternal alleles in the progeny. Studies on pig growth [16] and bovine fatness traits [17] have provided statistical evidence for the existence of genetic variation associated with paternal parent-oforigin inheritance that can account for over 10 % of the phenotypic variability in these traits. Neugenbauer et al [18, 19] and Tier and Meyer [20] confirmed this result on other cattle and pig traits
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
