Understanding the use of Bayes factor for testing candidate genes.

After quantitative trait loci (QTL) detection, one of the main objectives of research is to identify the causal mutation explaining phenotypic differences. Candidate genes are usually selected according to the physiological mechanism of the trait and their location within the same region of the QTL. After detection of any polymorphism at the candidate gene sequence, it is important to determine whether the detected mutation is the one that causes the phenotypic variation. This is not, however, an easy task, because of the linkage disequilibrium between the genes located in the same region. Several methods have been proposed that consider the neutral marker information in validating the involvement of candidate genes. However, some statistical information may be lost because of the presence of both the QTL and candidate gene effects in the model of analysis. Here, the Bayes factor is suggested as an alternative and a procedure for its calculation between candidate gene and QTL models is presented. The procedure is illustrated with a simulation study and with an example consisting of three SNPs detected at the leptin receptor (LEPR) in an experimental intercross between Iberian and Landrace pigs. The results indicate that the Bayes factor procedure is more powerful than the classical approach.