MAPPING DOMINANT MARKERS USING F2 MATINGS

The development of efficient methods for amplifying random DNA sequenc es 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 F-2 matings. The major p roblem with these matings, apart from excessive sampling errors of rec ombination frequency (theta) estimates, is the bias of the maximum-lik elihood estimator (MLE) of theta (theta(ML)). theta(ML) = 0 when the o bserved frequency of double-recessive phenotypes is 0 and the observed frequency of double-dominant phenotypes is less than 2/3 - the bias f or those samples is - theta. We used simulation to estimate the mean b ias 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 feam le coupling maps, as long as the maps are fairly dense (about 5 cM)- t he sampling errors of theta increase as theta increases for coupling l inkages and are equal to those for backcross matings when theta = 0. T he use of F-2 matings for mapping dominant markers is not necessarily proscribed because they yield twice as many useful markers as a backcr oss population, albeit in two maps, for the same number of DNA extract ions and PCR assays; however, dominant markers can be more effeciently exploited by using doubled-haploid, recombinant-inbred, or other inbr ed populations.