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GrainGenes Reference Report: GEN-142-285

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Reference	GEN-142-285
Title	Permutation tests for multiple loci affecting a quantitative character
Journal	Genetics
Year	1996
Volume	142
Pages	285-294
Author	Doerge R Churchill G
Abstract	The problem of detecting minor quantitative trait loci (QTL) responsible for genetic variation not explained by major QTL is of importance in the complete dissection of quantitative characters Two extensions of the permutation-based method for estimating empirical threshold values are presented These methods, the conditional empirical threshold (CET) and the residual empirical threshold (RET), yield critical values that can be used to construct tests for the presence of minor QTL effects while accounting for effects of known major QTL The CET provides a completely nonparametric test through conditioning on markers linked to major QTL It allows for general nonadditive interactions among QTL but its practical application is restricted to regions of the genome that are unlinked to the major QTL. The RET assumes a structural model for the effect of major QTL, and a threshold is constructed using residuals from this structural model. The search space for minor QTL is unrestricted, and RET-based tests may be more powerful than the CET-based test when the structural model is approximately true.
Keyword	conditional-empirical-threshold [ Show all 11 ]

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