Significance testing for QTL mapping by marker difference regression

Marker difference regression, also known as joint mapping or simple marker regression, regresses differences of means for marker classes ('marker diff erences') on their expected value, which is a function of the QTL effect an d position. The genome is scanned by a likelihood ratio statistic, which co nditionally on the QTL position follows a chi-squared distribution. The unc onditional distribution is a chi-squared process. This paper proposes a qui ck method for controlling the genome wise Type-I error rate. The method is shown by simulation to work satisfactorily for a number of settings.