Model selection in binary trait locus mapping.

Published

Journal Article

Quantitative trait locus (QTL) mapping methodology for continuous normally distributed traits is the subject of much attention in the literature. Binary trait locus (BTL) mapping in experimental populations has received much less attention. A binary trait by definition has only two possible values, and the penetrance parameter is restricted to values between zero and one. Due to this restriction, the infinitesimal model appears to come into play even when only a few loci are involved, making selection of an appropriate genetic model in BTL mapping challenging. We present a probability model for an arbitrary number of BTL and demonstrate that, given adequate sample sizes, the power for detecting loci is high under a wide range of genetic models, including most epistatic models. A novel model selection strategy based upon the underlying genetic map is employed for choosing the genetic model. We propose selecting the "best" marker from each linkage group, regardless of significance. This reduces the model space so that an efficient search for epistatic loci can be conducted without invoking stepwise model selection. This procedure can identify unlinked epistatic BTL, demonstrated by our simulations and the reanalysis of Oncorhynchus mykiss experimental data.

Full Text

Duke Authors

Cited Authors

  • Coffman, CJ; Doerge, RW; Simonsen, KL; Nichols, KM; Duarte, CK; Wolfinger, RD; McIntyre, LM

Published Date

  • July 2005

Published In

Volume / Issue

  • 170 / 3

Start / End Page

  • 1281 - 1297

PubMed ID

  • 15834149

Pubmed Central ID

  • 15834149

International Standard Serial Number (ISSN)

  • 0016-6731

Digital Object Identifier (DOI)

  • 10.1534/genetics.104.033910

Language

  • eng

Conference Location

  • United States