Abstract
BackgroundIn classical pedigree-based analysis, additive genetic variance is estimated from between-family variation, which requires the existence of larger phenotyped and pedigreed populations involving numerous families (parents). However, estimation is often complicated by confounding of genetic and environmental family effects, with the latter typically occurring among full-sibs. For this reason, genetic variance is often inferred based on covariance among more distant relatives, which reduces the power of the analysis. This simulation study shows that genome-wide identity-by-descent sharing among close relatives can be used to quantify additive genetic variance solely from within-family variation using data on extremely small family samples.MethodsIdentity-by-descent relationships among full-sibs were simulated assuming a genome size similar to that of humans (effective number of loci ~80). Genetic variance was estimated from phenotypic data assuming that genomic identity-by-descent relationships could be accurately re-created using information from genome-wide markers. The results were compared with standard pedigree-based genetic analysis.ResultsFor a polygenic trait and a given number of phenotypes, the most accurate estimates of genetic variance were based on data from a single large full-sib family only. Compared with classical pedigree-based analysis, the proposed method is more robust to selection among parents and for confounding of environmental and genetic effects. Furthermore, in some cases, satisfactory results can be achieved even with less ideal data structures, i.e., for selectively genotyped data and for traits for which the genetic variance is largely under the control of a few major genes.ConclusionsEstimation of genetic variance using genomic identity-by-descent relationships is especially useful for studies aiming at estimating additive genetic variance of highly fecund species, using data from small populations with limited pedigree information and/or few available parents, i.e., parents originating from non-pedigreed or even wild populations.
Highlights
In classical pedigree-based analysis, additive genetic variance is estimated from between-family variation, which requires the existence of larger phenotyped and pedigreed populations involving numerous families
Estimation of genetic variance based on pedigree relationships is further complicated by the fact that common environmental effects may be important for some relatives, especially full-sibs, which means that the genetic variance must be estimated from covariances among phenotypes of more distant relatives
For the classical pedigree-based analyses, the data structure did not make it possible to separate permanent environmental effects common to full-sibs from genetic effects, since both factors are estimated from between-family variation only
Summary
In classical pedigree-based analysis, additive genetic variance is estimated from between-family variation, which requires the existence of larger phenotyped and pedigreed populations involving numerous families (parents). Estimation is often complicated by confounding of genetic and environmental family effects, with the latter typically occurring among full-sibs For this reason, genetic variance is often inferred based on covariance among more distant relatives, which reduces the power of the analysis. Genetic variance is often inferred based on covariance among more distant relatives, which reduces the power of the analysis This simulation study shows that genome-wide identity-by-descent sharing among close relatives can be used to quantify additive genetic variance solely from within-family variation using data on extremely small family samples. Additive genetic relationships can be defined as twice the identityby-descent (IBD) probability of two randomly drawn alleles, which can be estimated from pedigree data The advantages of these pedigree-based analyses are that they do not require any knowledge about the genetic architecture of the traits and that the additive relationships are inferred from a known pedigree. Estimation of genetic variance based on pedigree relationships is further complicated by the fact that common environmental effects may be important for some relatives, especially full-sibs (e.g., maternal environment, rearing environment, litter effects, etc.), which means that the genetic variance must be estimated from covariances among phenotypes of more distant relatives (e.g., half sibs, cousins, etc.)
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