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Open Access Methodology article

Bayesian shrinkage mapping of quantitative trait loci in variance component models

Ming Fang

Author Affiliations

Life Science College, Heilongjiang August First Land Reclamation University, Daqing, 163319, China

Department of Animal Genetics and breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China

BMC Genetics 2010, 11:30  doi:10.1186/1471-2156-11-30

Published: 29 April 2010

Abstract

Background

In this article, I propose a model-selection-free method to map multiple quantitative trait loci (QTL) in variance component model, which is useful in outbred populations. The new method can estimate the variance of zero-effect QTL infinitely to zero, but nearly unbiased for non-zero-effect QTL. It is analogous to Xu's Bayesian shrinkage estimation method, but his method is based on allelic substitution model, while the new method is based on the variance component models.

Results

Extensive simulation experiments were conducted to investigate the performance of the proposed method. The results showed that the proposed method was efficient in mapping multiple QTL simultaneously, and moreover it was more competitive than the reversible jump MCMC (RJMCMC) method and may even out-perform it.

Conclusions

The newly developed Bayesian shrinkage method is very efficient and powerful for mapping multiple QTL in outbred populations.