Selection with recurrent backcrossing to develop congenic lines for quantitative trait loci analysis

SEWALL WRIGHT suggested that genes of large effect on a quantitative trait could be isolated by recurrent backcrossing with selection on the trait. Loci quantitative trait loci (QTL)] at which the recurrent and nonrecurrent lines have genes of different large effect on the trait would remain segregating, while other loci would become fixed for the gene carried by the recurrent parent. If the recurrent line is inbred and the backcrossing and selection is conducted in a series of replicate lines, in each of which only one backcross parent is selected for each generation, the lines will become congenic to the recurrent parent except for the QTL of large effect and closely linked regions of the genome, and these regions can be identified using a dense set of markers that differ between the parental lines. Such lines would be particularly valuable for subsequent fine-scale mapping and gene cloning; but by chance, even QTL of large effect will be lost from some lines. The probability that QTL of specified effect remain segregating is computed as a function of its effect on the trait, the intensity of selection, and the number of generations of backcrossing. Analytical formulas are given for one or two loci, and simulation is used for more. It is shown that the method could have substantial discriminating ability and thus potential practical value.