Selective phenotyping to accurately map quantitative trait loci

Recombination events are necessary to map QTL accurately and some progeny result from gametes with a greater number of recombination events than others. This observation suggests that some progeny should be more useful for QTL mapping than others. The marker genotypes of the progeny should allow the number of recombination events they carry to be determined such that the most useful progeny could be phenotyped, in a procedure termed selective phenotyping. Two methods to select genotypes for their usefulness in mapping are described, one that maximizes the overall mapping information content in the selected progeny, and one that seeks to maximize both overall mapping information and the uniformity of its distribution across the genome. Simulations showed that both methods successfully decreased the mean squared error (MSE) for QTL position. Average MSEs were similar for the two methods and variability of MSE was slightly lower for the latter relative to the former method. Simulations indicated that a large fraction of the decrease in the MSE achievable by selective phenotyping could be obtained by genotyping twice the number of progeny than were ultimately phenotyped, though further decreases in the MSE were observed when up to 16 times more progeny were genotyped than phenotyped. The procedure appears to most improve the accuracy of QTL mapping for QTL of small effect or when available markers do not allow marker spacing below 10 cM.