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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 α and β 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.
Highlights
Many studies have shown that individual quantitative trait loci (QTL) can be detected and mapped in commercial animal populations with the aid of genetic markers
The estimation of the QTL distributions was based on several assumptions that will be addressed in detail
A more reasonable assumption would be to assume a finite number of segregating QTL, with most contrasts representing only random variation, as proposed by Meuwissen et al [15]
Summary
Many studies have shown that individual quantitative trait loci (QTL) can be detected and mapped in commercial animal populations with the aid of genetic markers. The daughter and granddaughter designs are most appropriate for analysis of dairy cattle populations [24]. With the advent of DNA microsatellites it became possible to scan the entire genome for QTL for all traits of economic interest. At least three complete genome QTL scans by the granddaughter design have been completed for the US Holstein population.
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