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CROP BREEDING, GENETICS & CYTOLOGY

Efficiencies of F₂ and Backcross Generations for Bulked Segregant Analysis Using Dominant Markers

^a Oxagen Limited, Milton Park, Abingdon, Oxon 14 4RY UK
^b Dep. of Agric. Botany, School of Plant Sciences, The Univ. of Reading, Reading RG6 6AS, UK

p.d.s.caligari{at}reading.ac.uk

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.

Abbreviations: a, average effect of an allele • AFLP, amplified fragment length polymorphism • Bc Backcross • BSA, bulked segregant analysis • cM, centimorgan • ISSR, inter-simple sequence repeat • PCR, polymerase chain reaction • QTL, quantitative trait locus • RAPD, random amplified polymorphic DNA