Bayesian mixture structural equation modelling in multiple-trait QTL mapping

Xiaojuan Mi, Kent Eskridge, Dong Wang, P. Stephen Baenziger, B. Todd Campbell, Kulvinder S. Gill, Ismail Dweikat

Research output: Contribution to journalArticlepeer-review

7 Scopus citations

Abstract

Quantitative trait loci (QTLs) mapping often results in data on a number of traits that have well-established causal relationships. Many multi-trait QTL mapping methods that account for correlation among the multiple traits have been developed to improve the statistical power and the precision of QTL parameter estimation. However, none of these methods are capable of incorporating the causal structure among the traits. Consequently, genetic functions of the QTL may not be fully understood. In this paper, we developed a Bayesian multiple QTL mapping method for causally related traits using a mixture structural equation model (SEM), which allows researchers to decompose QTL effects into direct, indirect and total effects. Parameters are estimated based on their marginal posterior distribution. The posterior distributions of parameters are estimated using Markov Chain Monte Carlo methods such as the Gibbs sampler and the Metropolis-Hasting algorithm. The number of QTLs affecting traits is determined by the Bayes factor. The performance of the proposed method is evaluated by simulation study and applied to data from a wheat experiment. Compared with single trait Bayesian analysis, our proposed method not only improved the statistical power of QTL detection, accuracy and precision of parameter estimates but also provided important insight into how genes regulate traits directly and indirectly by fitting a more biologically sensible model.

Original languageEnglish (US)
Pages (from-to)239-250
Number of pages12
JournalGenetics Research
Volume92
Issue number3
DOIs
StatePublished - Jun 2010

ASJC Scopus subject areas

  • Genetics

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