| Issue |
Genet. Sel. Evol.
Volume 36, Number 4, July-August 2004
|
|
|---|---|---|
| Page(s) | 455 - 479 | |
| DOI | https://doi.org/10.1051/gse:2004011 | |
DOI: 10.1051/gse:2004011
A simulation study on the accuracy of position and effect estimates of linked QTL and their asymptotic standard deviations using multiple interval mapping in an F2 scheme
Manfred Mayera, Yuefu Liub and Gertraude Freyeraa Research Unit Genetics and Biometry, Research Institute for the Biology of Farm Animals, Dummerstorf, Germany
b Centre of the Genetic Improvement of Livestock, University of Guelph, Ontario, Canada
(Received 4 August 2003; accepted 22 March 2004)
Abstract
Approaches like multiple interval mapping using a
multiple-QTL model for simultaneously mapping QTL can aid the identification
of multiple QTL, improve the precision of estimating QTL positions and
effects, and are able to identify patterns and individual elements of QTL
epistasis. Because of the statistical problems in analytically deriving the standard
errors and the distributional form of the estimates and because the
use of resampling techniques is not feasible for several linked QTL, there is
the need to perform large-scale simulation studies in order to evaluate the accuracy
of multiple interval mapping for linked QTL and to assess confidence
intervals based on the standard statistical theory. From our simulation
study it can be concluded that in comparison with a monogenetic background a
reliable and accurate estimation of QTL positions and QTL effects of
multiple QTL in a linkage group requires much more information from the
data. The reduction of the marker interval size from 10 cM to 5 cM led to a
higher power in QTL detection and to a remarkable improvement of the QTL
position as well as the QTL effect estimates. This is different from the
findings for (single) interval mapping. The empirical standard deviations of
the genetic effect estimates were generally large and they were the largest for the
epistatic effects. These of the dominance effects were larger than those of the additive
effects. The asymptotic standard deviation of the position estimates was not
a good criterion for the accuracy of the position estimates and confidence
intervals based on the standard statistical theory had a clearly smaller
empirical coverage probability as compared to the nominal probability.
Furthermore the asymptotic standard deviation of the additive, dominance and
epistatic effects did not reflect the empirical standard deviations of the
estimates very well, when the relative QTL variance was smaller/equal to 0.5.
The implications of the above findings are discussed.
Key words: mapping / QTL / simulation / asymptotic standard error / confidence interval
Correspondence and reprints: mmayer@fbn-dummerstorf.de
© INRA, EDP Sciences 2004