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Bayesian functional mapping of dynamic quantitative traits

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Abstract

Without consideration of other linked QTLs responsible for dynamic trait, original functional mapping based on a single QTL model is not optimal for analyzing multiple dynamic trait loci. Despite that composite functional mapping incorporates the effects of genetic background outside the tested QTL in mapping model, the arbitrary choice of background markers also impact on the power of QTL detection. In this study, we proposed Bayesian functional mapping strategy that can simultaneously identify multiple QTL controlling developmental patterns of dynamic traits over the genome. Our proposed method fits the change of each QTL effect with the time by Legendre polynomial and takes the residual covariance structure into account using the first autoregressive equation. Also, Bayesian shrinkage estimation was employed to estimate the model parameters. Especially, we specify the gamma distribution as the prior for the first-order auto-regressive coefficient, which will guarantee the convergence of Bayesian sampling. Simulations showed that the proposed method could accurately estimate the QTL parameters and had a greater statistical power of QTL detection than the composite functional mapping. A real data analysis of leaf age growth in rice is used for the demonstration of our method. It shows that our Bayesian functional mapping can detect more QTLs as compared to composite functional mapping.

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Acknowledgments

This work was partially supported by the National Natural Science Foundation of China (30972077).

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Authors and Affiliations

  1. College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, 163319, Daqing, People’s Republic of China

    Runqing Yang

  2. School of Agriculture and Biology, Shanghai Jiaotong University, 200240, Shanghai, People’s Republic of China

    Runqing Yang, Jiahan Li & Xin Wang

  3. Department of Mathematics, Heilongjiang Bayi Agricultural University, 163319, Daqing, People’s Republic of China

    Xiaojing Zhou

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  1. Runqing Yang
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  2. Jiahan Li
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  3. Xin Wang
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  4. Xiaojing Zhou
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Correspondence to Runqing Yang.

Additional information

Communicated by F. van Eeuwijk.

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Yang, R., Li, J., Wang, X. et al. Bayesian functional mapping of dynamic quantitative traits. Theor Appl Genet 123, 483–492 (2011). https://doi.org/10.1007/s00122-011-1601-0

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  • DOI: https://doi.org/10.1007/s00122-011-1601-0

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