Efficiencies of F2 and backcross generations for bulked segregant analysis using dominant markers

Bulked segregant analysis (BSA) is being used increasingly as a screen for quantitative trait loci (QTL), which have been suggested to be more easily detected in backcross (Bc) populations than in the F 2 . However, for dominant markers the number of loci segregating in the F 2 will be double that in the Bc, and the probability of false-positive results differs between F 2 and Bc generations. This study was conducted to re-examine the relative value of Bc and F 2 populations for use in BSA by using theoretical estimates of the genotypic composition of the selected bulks. It is shown that doubling the number of marker loci segregating in the F 2 roughly halves the expected distance from the QTL to the nearest marker, while the bulk size in the F 2 can be reduced to nearly one-half that of the Bc and still give the same probability of a false positive. The results show that for the same recombination frequency, the Bc is slightly superior to the F 2 in its ability to detect QTL. However, if the likely distance of the nearest marker to the QTL is taken into account, the F 2 is the more favorable generation. Overall, for dominant marker systems, the F 2 is therefore the best generation in which to conduct BSA.