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Robust Bayesian mapping of quantitative trait loci using Student-t distribution for residual

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Abstract

In most quantitative trait loci (QTL) mapping studies, phenotypes are assumed to follow normal distributions. Deviations from this assumption may affect the accuracy of QTL detection, leading to detection of false positive QTL. To improve the robustness of QTL mapping methods, we replace the normal distribution assumption for residuals in a multiple QTL model with a Student-t distribution that is able to accommodate residual outliers. A Robust Bayesian mapping strategy is proposed on the basis of the Bayesian shrinkage analysis for QTL effects. The simulations show that Robust Bayesian mapping approach can substantially increase the power of QTL detection when the normality assumption does not hold and applying it to data already normally distributed does not influence the result. The proposed QTL mapping method is applied to mapping QTL for the traits associated with physics–chemical characters and quality in rice. Similarly to the simulation study in the real data case the robust approach was able to detect additional QTLs when compared to the traditional approach. The program to implement the method is available on request from the first or the corresponding author.

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Acknowledgments

The research was supported by the Chinese National Natural Science Foundation Grant 30471236 to RY.

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Authors and Affiliations

  1. School of Agriculture and Biology, Shanghai Jiaotong University, 200240, Shanghai, China

    Xin Wang, Biye Wang & Runqing Yang

  2. Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China

    Zhongze Piao

  3. Rice Research Institute, Anhui Academy of Agricultural Sciences, 230036, Hefei, China

    Zhixiang Luo

Authors
  1. Xin Wang
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  2. Zhongze Piao
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  3. Biye Wang
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  4. Runqing Yang
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  5. Zhixiang Luo
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Corresponding author

Correspondence to Runqing Yang.

Additional information

Communicated by M. Sillanpää.

Xin Wang and Zhongze Piao contributed equally to this study.

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Wang, X., Piao, Z., Wang, B. et al. Robust Bayesian mapping of quantitative trait loci using Student-t distribution for residual. Theor Appl Genet 118, 609–617 (2009). https://doi.org/10.1007/s00122-008-0924-y

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  • DOI: https://doi.org/10.1007/s00122-008-0924-y

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