Assessing the Significance of Quantitative Trait Loci in Replicable Mapping Populations

¹ University of North Carolina at Chapel Hill
² NIEHS

^* To whom correspondence should be addressed. E-mail: fzou{at}bios.unc.edu.

Submitted on April 14, 2006
Revised on July 1, 2006
Accepted on 31 July 2006

	Abstract

Replicable populations, such as panels of recombinant inbred or doubled haploid lines, are convenient resources for the mapping of QTL. To increase mapping power, replications are often collected within each RI line and a common way to analyze such data is to include in the QTL model only a single measurement from each line that represents the average among the replicates (a line means model). An obvious, but seldom explored, alternative, is to include every replicate in the model (a full data model). Here, we use simulations to compare these two approaches. Further, for the full data model, we show that the standard permutation procedure of Churchill and Doerge (1994) does not control the type I error at the targeted level while our proposed nested permutation procedure does.

Key Words: Permutation, Power, QTL, RIL, Type I error

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