Theoretical and Applied Genetics

, Volume 125, Issue 7, pp 1575–1587 | Cite as

Swift block-updating EM and pseudo-EM procedures for Bayesian shrinkage analysis of quantitative trait loci

  • Crispin M. Mutshinda
  • Mikko J. Sillanpää
Original Paper



Virtually all existing expectation-maximization (EM) algorithms for quantitative trait locus (QTL) mapping overlook the covariance structure of genetic effects, even though this information can help enhance the robustness of model-based inferences.


Here, we propose fast EM and pseudo-EM-based procedures for Bayesian shrinkage analysis of QTLs, designed to accommodate the posterior covariance structure of genetic effects through a block-updating scheme. That is, updating all genetic effects simultaneously through many cycles of iterations.


Simulation results based on computer-generated and real-world marker data demonstrated the ability of our method to swiftly produce sensible results regarding the phenotype-to-genotype association. Our new method provides a robust and remarkably fast alternative to full Bayesian estimation in high-dimensional models where the computational burden associated with Markov chain Monte Carlo simulation is often unwieldy. The R code used to fit the model to the data is provided in the online supplementary material.


Quantitative Trait Locus Genetic Effect Quantitative Trait Locus Mapping Genomic Breeding Value Estimation Posterior Covariance 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



The authors wish to thank Hanni Kärkkäinen, Zitong Li and two anonymous referees for their pertinent comments and suggestions. This work was supported by a research grants from the Academy of Finland and University of Helsinki’s research funds.

Supplementary material

122_2012_1936_MOESM1_ESM.pdf (177 kb)
Supplementary material 1 (PDF 177 kb)
122_2012_1936_MOESM2_ESM.pdf (18 kb)
Supplementary material 2 (PDF 17 kb)


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Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Crispin M. Mutshinda
    • 1
    • 5
  • Mikko J. Sillanpää
    • 1
    • 2
    • 3
    • 4
  1. 1.Department of Mathematics and StatisticsUniversity of HelsinkiHelsinkiFinland
  2. 2.Department of Agricultural SciencesUniversity of HelsinkiHelsinkiFinland
  3. 3.Department of Mathematical SciencesUniversity of OuluOuluFinland
  4. 4.Department of BiologyUniversity of OuluOuluFinland
  5. 5.Department of Mathematics and Computer ScienceMount Allison UniversitySackvilleCanada

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