Mapping dominant markers using F2 matings |
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Authors: | S J Knapp J L Holloway W C Bridges B H Liu |
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Institution: | (1) Department of Crop and Soil Science, Oregon State University, 97331 Corvallis, OR, USA;(2) Department of Experimental Statistics, Clemson University, SC29634 Clemson, USA;(3) Department of Forestry, North Carolina State University, 27695 Raleigh, NC, USA |
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Abstract: | 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 ( ) estimates, is the bias of the maximum-likelihood estimator (MLE) of (
ML).
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 — . We used simulation to estimate the mean bias of
ML. Mean bias is a function of n and 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 increase as increases for coupling linkages and are equal to those for backcross matings when =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. |
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Keywords: | Bias Recombination frequency Genetic maps DNA markers |
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