Mapping dominant markers using F2 matings

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 (θ) estimates, is the bias of the maximum-likelihood estimator (MLE) of θ (θ ML). [Formula: see text] 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.

Domestication quantitative trait loci inTriticum dicoccoides, the progenitor of wheat

“…Genotyping was conducted by using standard molecular markers, i.e., microsatellite, or short sequence repeat, amplified fragment length polymorphism, random amplified polymorphic DNA, and restriction fragment length polymorphism (15). Two versions of genetic maps were constructed for each chromosome by MAPMAKER 3.0b (16) due to the paucity of linkage information from repulsively linked dominant markers (17) and verified by our own algorithm (18). These two maps consist mostly of dominant markers linked in the coupling phase and of codominant markers.…”

A New Strategy for Estimating Recombination Fractions Between Dominant Markers From an F2 Population

“…One is known as the repulsion phase, which corresponds to the situation in which these two dominant alleles reside on different chromosomes; otherwise, it is known as the coupling phase. In a twopoint analysis that considers two markers at a time, the repulsion phase provides much less information about linkage than the coupling phase (Allard 1956;Knapp et al 1995;Liu 1998;Mester et al 2003a). This is especially true for double heterozygotes from the F 2 population (Liu 1998).…”

Ordering dominant markers in F2 populations

“…With dominant markers, construction of linkage maps using data from F 2 populations is considered problematic (Knapp et al 1994;Liu 1997). In this paper, an F 2 population is considered to originate from the selfing of an individual, which itself is obtained by crossing two pure lines (Allard 1960).…”

“…The problem lies in integrating the linkage maps of the two types into one linkage map for the F 2 population. Knapp et al (1994) state that it is not possible to obtain reliable maximum likelihood estimates of the recombination frequency between two markers that are in repulsion phase. The maximum likelihood estimate will practically always be zero, if the number of individuals in the F 2 population, which do not carry the observable allele for both markers, is zero.…”