Mapping dominant markers using F2 matings
1995
Knapp, S.J. | Holloway, J.L. | Bridges, W.C. | Liu, B.H.
The development of efficient methods for amplifying random DNA sequences by the polymerase chain reaction has created the basis for mapping virtually unlimited numbers of mixed-phase dominant DNA markers in one population. Although dominant markers can be efficiently mapped using many different kinds of matings, recombination frequencies and locus orders are often mis-estimated from repulsion F2 matings. The major problem with these matings, apart from excessive sampling errors of recombination frequency theta estimates, is the bias of the maximum-likelihood estimator (MLE) of theta (theta ML). Estimated theta ML = 0 when the observed frequency of double-recessive phenotypes is -theta and the observed frequency of double-dominant phenotypes is less than 2/3 - the bias for those samples is -theta. We used simulation to estimate the mean bias of theta ML. Mean bias is a function of n and theta and decreases as n increases. Valid maps of dominant markers can be built by using sub-sets of markers linked in coupling, thereby creating male and female coupling maps, as long as the maps are fairly dense (about 5 cM)--the sampling errors of theta increase as theta increases for coupling linkages and are equal to those for backcross matings when theta = 0. The use of F2 matings for mapping dominant markers is not necessarily proscribed because they yield twice as many useful markers as a backcross population, albeit in two maps, for the same number of DNA extractions and PCR assays; however, dominant markers can be more efficiently exploited by using double-haploid, recombinant-inbred, or other inbred populations.
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