Estimation of heritability from limited family data using genome-wide identity-by-descent sharing

Identity-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.For 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.Estimation 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.Estimates of additive genetic variance are commonly based on data from large pedigreed populations incorporating all known relationship information. Additive genetic relationships can be defined as twice the identity-by-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 easily inferred from a known pedigree. However, these methods also have some major limitations. First, such analyses ignore relationships beyond those included in the known pedigre