Estimation of variance components of quantitative traits in inbred populations

Use of variance-component estimation for mapping of quantitative-trait loci in humans is a subject of great current interest. When only trait values, not genotypic information, are considered, variance-component estimation ca n also be used to estimate heritability of a quantitative trait. Inbred ped igrees present special challenges for variance-component estimation. First, there are more variance components to be estimated in the inbred case, eve n for a relatively simple model including additive, dominance, and environm ental effects. Second, more identity coefficients need to be calculated fro m an inbred pedigree in order to perform the estimation, and these are comp utationally more difficult to obtain in the inbred than in the outbred case . As a result, inbreeding effects have generally been ignored in practice. We describe here the calculation of identity coefficients and estimation of variance components of quantitative traits in large inbred pedigrees, usin g the example of HDL in the Hutterites. We use a multivariate normal model for the genetic effects, extending the central-limit theorem of Lange to al low for both inbreeding and dominance under the assumptions of our variance -component model. We use simulated examples to give an indication of under what conditions one has the power to detect the additional variance compone nts and to examine their impact on variance-component estimation. We discus s the implications for mapping and heritability estimation by use of varian ce components in inbred populations.