A two-phase procedure for QTL mapping with regression models.

It is typical in QTL mapping experiments that the number of markers under investigation is large. This poses a challenge to commonly used regression models since the number of feature variables is usually much larger than the sample size, especially, when epistasis effects are to be considered. The greedy nature of the conventional stepwise procedures is well known and is even more conspicuous in such cases. In this article, we propose a two-phase procedure based on penalized likelihood techniques and extended Bayes information criterion (EBIC) for QTL mapping. The procedure consists of a screening phase and a selection phase. In the screening phase, the main and interaction features are alternatively screened by a penalized likelihood mechanism. In the selection phase, a low-dimensional approach using EBIC is applied to the features retained in the screening phase to identify QTL. The two-phase procedure has the asymptotic property that its positive detection rate (PDR) and false discovery rate (FDR) converge to 1 and 0, respectively, as sample size goes to infinity. The two-phase procedure is compared with both traditional and recently developed approaches by simulation studies. A real data analysis is presented to demonstrate the application of the two-phase procedure.