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Originally published as Genetics Published Articles Ahead of Print on January 31, 2005.

Genetics, Vol. 169, 2371-2382, April 2005, Copyright © 2005
doi:10.1534/genetics.104.035410

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A Model Selection-Based Interval-Mapping Method for Autopolyploids

Dachuang Cao*, Bruce A. Craig* and R. W. Doerge*,{dagger},1

* Department of Statistics, Purdue University, West Lafayette, Indiana 47907
{dagger} Department of Agronomy, Purdue University, West Lafayette, Indiana 47907

1 Corresponding author: Department of Statistics, Purdue University, 1399 Math Bldg., West Lafayette, IN 47907.
E-mail: doerge{at}purdue.edu

While extensive progress has been made in quantitative trait locus (QTL) mapping for diploid species, similar progress in QTL mapping for polyploids has been limited due to the complex genetic architecture of polyploids. To date, QTL mapping in polyploids has focused mainly on tetraploids with dominant and/or codominant markers. Here, we extend this view to include any even ploidy level under a dominant marker system. Our approach first selects the most likely chromosomal marker configurations using a Bayesian selection criterion and then fits an interval-mapping model to each candidate. Profiles of the likelihood-ratio test statistic and the maximum-likelihood estimates (MLEs) of parameters including QTL effects are obtained via the EM algorithm. Putative QTL are then detected using a resampling-based significance threshold, and the corresponding parental configuration is identified to be the underlying parental configuration from which the data are observed. Although presented via pseudo-doubled backcross experiments, this approach can be readily extended to other breeding systems. Our method is applied to single-dose restriction fragment autotetraploid alfalfa data, and the performance is investigated through simulation studies.




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