The detection of linkage among AFLP markers were based on pair-wise recombination estimates with a threshold recombination fraction
The LOD score (Z) was calculated at recombination fraction
of = 0.
The optimization procedure provided recombination fraction
estimates (on an [F.
We then have r = 1/211 - exp(-2L/n - 1)] or equivalently L = -1/2(n - 1)ln(1 - 2r), where L is the map length in Morgans on which the loci are evenly distributed, n is the number of loci, and r is the recombination fraction
between adjacent loci.
The two loci involved in these descent measures are allowed to recombine in all individuals at a recombination fraction
This situation has not been taken into consideration in most statistical packages for linkage analysis, and no methods are available for estimating recombination fraction
(r) between a gametophytic Rf gene and its linked genetic markers when a fertile [F.
1] with a recombination fraction
of 14% (Weaver and Weaver, 1979).
Equations were first derived for calculating the expected proportion of progeny (m) displaying a particular combination of marker genotypes (for codominant markers) or phenotypes (for dominant markers) at two linked markers as a function of the recombination fraction
(p) between markers in an [F.
5] for Individual 2, where r is the recombination fraction
in the corresponding interval and [r.
k], where r is the recombination fraction
in an interval between two markers, and k is a constant that depends on the mapping function to be used.
0 was used as a linkage threshold to construct the linkage map, with maximum recombination fraction
However, estimation of maximum likelihood estimators of the recombination fraction
(Wu et al.