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.sub.2], rather than an expanded map basis) among markers, which correlate relatively well with the estimates obtained from the Monsanto composite map (r = 0.71, p < 0.01); however, the total map distances differ.
More generally, for given initial allele frequency, number of loci, and recombination fraction
, and when the results are evaluated for identical t/N, equal values of Nih lead to the same mean divergence scores for both selected and correlated traits regardless of the pleiotropic system (Table 1).
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.sub.2] population is used.
No morphological markers have been found to be linked to either of the Rf genes (Kohel et al., 1984; Zhang, 1999) except for the cracked root trait that is linked to [Rf.sub.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.sub.2] segregating population (see Tables A1-A3 in Appendix), similar to the equations derived by De Winton and Haldane (1931) for dominant characters.
A LOD score of 4.0 and recombination fraction
of 0.30 was set as the linkage threshold.
However, the probability of the gamete with all markers being m except T generated by two individuals is 1/2(1 - [r.sub.1+2+3])[r.sub.4][r.sub.5] for Individual 1 (since [m.sub.2] and [m.sub.3] are fixed already, only [r.sub.1+2+3] is relevant here), and 1/2(1 - [r.sub.3])[r.sub.4][r.sub.5] for Individual 2, where r is the recombination fraction
in the corresponding interval and [r.sub.1+2+3] represents the recombination between Marker 1 and Marker 4.
Let c be the coincidence (actual double recombinations)/ (number expected with no interference), and assume that it approximates to [(2r).sup.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.
A logarithm of odds (LOD) score of 4.0 was used as a linkage threshold to construct the linkage map, with maximum recombination fraction