Mapping dominant markers using F2 matings

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 (θ) estimates, is the bias of the maximum-likelihood estimator (MLE) of θ (θ _ML). \(\hat \theta _{ML} = 0\) when the observed frequency of double-recessive phenotypes is 0 and the observed frequency of double-dominant phenotypes is less than 2/3 — the bias for those samples is — θ. We used simulation to estimate the mean bias of θ _ML. Mean bias is a function of n and θ 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 feamle coupling maps, as long as the maps are fairly dense (about 5 cM) — the sampling errors of θ increase as θ increases for coupling linkages and are equal to those for backcross matings when θ=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 effeciently exploited by using doubled-haploid, recombinant-inbred, or other inbred populations.