Missing markers when estimating quantitative trait loci using regression mapping

When using molecular markers to estimate the locations and sizes of effects of QTLs in plant populations a common problem is the loss of marker genotypes for many individuals. Here we present a method that uses the information from individuals with missing marker genotypes when fitting regression mapping models using two or three neighbouring markers. The approach uses other nearby markers to recover information from the individuals with missing markers. The method is presented in detail for the two markers regression mapping technique applied to backcross or double haploid populations. The method is exemplified with a simulated data set and with data on a quantitative character in double haploid lines of barley. Generalizations of the method to three markers regression mapping models and to F₂ populations are outlined.