Mapping quantitative trait loci incorporating the markers of entire genome in populations derived from inbred line crosses

A linear mixed model method for mapping quantitative trait loci (QTL) in inbred crosses was developed which treats the QTL (marker) effects as random. The method has two steps. First, significance of the variance associated with markers (genome variance) is tested using the Residual maximum likelihood ratio test (REMLRT). A significant genome variance component indicates the presence of at least one QTL in the genome. In the second step, the best linear unbiased predictions (BLUPs) of the markers are used to locate the QTL position (marker selection). The selected marker; having the highest BLUP's rank; is then fitted as fixed covariate and the above two steps are repeated until that there is no significant genome variance. The power of the suggested method was studied using simulated data. The results showed that the method is robust in detecting QTL in medium and relatively large populations derived from crosses between inbred lines. Although the power of the method is low in detecting QTL in small populations (as other available methods), the main advantages of the method are the ability to incorporate all of the markers in the analysis simultaneously and to overcome the multiple testing problem.