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 F2. However, for dominant markers the number of loci segregating in the F2 will be double that in the Bc, and the probability of false-positive results differs between F2 and Bc generations. This study was conducted to re-examine the relative value of Bc and F2 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 F2 roughly halves the expected distance from the QTL to the nearest marker, while the bulk size in the F2 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 F2 in its ability to detect QTL. However, if the likely distance of the nearest marker to the QTL is taken into account, the F2 is the more favorable generation. Overall, for dominant marker systems, the F2 is therefore the best generation in which to conduct BSA.
Mackay, I. J., & Caligari, P. D. S. (2000). Efficiencies of F2 and backcross generations for bulked segregant analysis using dominant markers. Crop Science, 40(3), 626–630. https://doi.org/10.2135/cropsci2000.403626x