Efficiencies of F-2 and backcross generations for bulked segregant analysis using dominant markers

Bulked segregant analysts (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 domina nt 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 val ue 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 doubli ng the number of marker loci segregating in the F-2 roughly halves the expe cted distance from the QTL to the nearest marker, while the bulk size in th e F-2 can be reduced to nearly one-half that of the Bc and still give the s ame probability of a false positive. The results show that for the same rec ombination 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 th e QTL is taken into account, the F-2 is the more favorable generation. Over all, for dominant marker systems, the F-2 is therefore the best generation in which to conduct BSA.