Bayesian analysis of genetic architecture of quantitative trait using data of crosses of multiple inbred lines

Using the data of crosses of multiple of inbred lines for mapping QTL can increase QTL detecting power compared with only cross of two inbred lines. Although many fixed-effect model methods have been proposed to analyze such data, they are largely based on one-QTL model or main effect model, and the interaction effects between QTL are always neglected. However, effectively separating the interaction effects from the residual error can increase the statistical power. In this article, we both extended the novel Bayesian model selection method and Bayesian shrinkage estimation approaches to multiple inbred line crosses. With two extensions, interacting QTL are effectively detected with high solution; in addition, the posterior variances for both main effects and interaction effects are also subjected to full Bayesian estimate, which is more optimal than two step approach involved in maximum-likelihood. A series of simulation experiments have been conducted to demonstrate the performance of the methods. The computer program written in FORTRAN language is freely available on request.