Free Access
Genet. Sel. Evol.
Volume 37, Number 5, September-October 2005
Page(s) 501 - 522
Genet. Sel. Evol. 37 (2005) 501-522
DOI: 10.1051/gse:2005013

Correcting for bias in estimation of quantitative trait loci effects

Joel Ira Weller, Meital Shlezinger and Micha Ron

Institute of Animal Sciences, ARO, The Volcani Center, Bet Dagan 50250, Israel

(Received 28 February 2005; accepted 4 May 2005)

Abstract - Estimates of quantitative trait loci (QTL) effects derived from complete genome scans are biased, if no assumptions are made about the distribution of QTL effects. Bias should be reduced if estimates are derived by maximum likelihood, with the QTL effects sampled from a known distribution. The parameters of the distributions of QTL effects for nine economic traits in dairy cattle were estimated from a daughter design analysis of the Israeli Holstein population including 490 marker-by-sire contrasts. A separate gamma distribution was derived for each trait. Estimates for both the $\alpha $ and $\beta $ parameters and their SE decreased as a function of heritability. The maximum likelihood estimates derived for the individual QTL effects using the gamma distributions for each trait were regressed relative to the least squares estimates, but the regression factor decreased as a function of the least squares estimate. On simulated data, the mean of least squares estimates for effects with nominal 1% significance was more than twice the simulated values, while the mean of the maximum likelihood estimates was slightly lower than the mean of the simulated values. The coefficient of determination for the maximum likelihood estimates was five-fold the corresponding value for the least squares estimates.

Key words: genetic markers / quantitative trait loci / genome scans / maximum likelihood / dairy cattle

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© INRA, EDP Sciences 2005