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Originally published as Genetics Published Articles Ahead of Print on April 15, 2007.

Genetics, Vol. 176, 1169-1185, June 2007, Copyright © 2007
doi:10.1534/genetics.106.064279

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Bayesian Shrinkage Analysis of Quantitative Trait Loci for Dynamic Traits

Runqing Yang* and Shizhong Xu{dagger},1

* School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 201101, People's Republic of China and {dagger} Department of Botany and Plant Science, University of California, Riverside, California 92521

1 Corresponding author: Department of Botany and Plant Sciences, University of California, Riverside, CA 92521.
E-mail: xu{at}genetics.ucr.edu

Many quantitative traits are measured repeatedly during the life of an organism. Such traits are called dynamic traits. The pattern of the changes of a dynamic trait is called the growth trajectory. Studying the growth trajectory may enhance our understanding of the genetic architecture of the growth trajectory. Recently, we developed an interval-mapping procedure to map QTL for dynamic traits under the maximum-likelihood framework. We fit the growth trajectory by Legendre polynomials. The method intended to map one QTL at a time and the entire QTL analysis involved scanning the entire genome by fitting multiple single-QTL models. In this study, we propose a Bayesian shrinkage analysis for estimating and mapping multiple QTL in a single model. The method is a combination between the shrinkage mapping for individual quantitative traits and the Legendre polynomial analysis for dynamic traits. The multiple-QTL model is implemented in two ways: (1) a fixed-interval approach where a QTL is placed in each marker interval and (2) a moving-interval approach where the position of a QTL can be searched in a range that covers many marker intervals. Simulation study shows that the Bayesian shrinkage method generates much better signals for QTL than the interval-mapping approach. We propose several alternative methods to present the results of the Bayesian shrinkage analysis. In particular, we found that the Wald test-statistic profile can serve as a mechanism to test the significance of a putative QTL.




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S. Xu
Derivation of the Shrinkage Estimates of Quantitative Trait Locus Effects
Genetics, October 1, 2007; 177(2): 1255 - 1258.
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