In general, locus order was well maintained between the consensus linkage map and the component maps.
Locus order was generally well conserved; however, the robustness of the locus order differed slightly depending on the linkage group and the accession-specific linkage map.
Locus order was well conserved across all of the linkage groups, except for LG3, which exhibited conflicting marker positions for 4 loci.
The recombination threshold was set to 0.3 and the logarithmic odds (LOD) score was set to 5. The locus order was calculated by the regression module of JoinMap4.
In addition, for these common markers, complete conservation of locus order was observed along the individual LGs between the two maps.
Because this step introduced additional segregation data, which in some cases resolved the order of hitherto (almost) unresolved loci, a final round of manual improvement of the locus order was required.
The locus order was calculated using a regression mapping module of JoinMap and the following parameters: Kosambi's mapping function, LOD ≥ 2.0, REC frequency ≤ 0.4, goodness-of-fit Jump threshold for removal loci = 5.0, number of added loci after which to perform a ripple = 1, and third round = Yes.
The integrated linkage analysis, including estimation of recombination fraction and locus order was performed using the windows-based package OUTMAP [ 68] specifically developed to map codominant loci in outcrossed trees with higher efficiency when compared to other existing programs, Map figures were constructed using the computer program QGene [ 69].
Locus order was well conserved between the consensus map and accession-specific maps for all linkage groups (Fig. 1), with the exception of loci in LG1 of the WF1680 map, which did not correlate significantly (P < 0.05) with the consensus map (Table 5).
We observed that despite the fact that approximately 17% of the two-point estimates of recombination frequency observed for the same pairs of microsatellite markers differed considerably (on average by 25%), conservation of locus order was observed between the two parental maps, with 82% of the markers mapping with the same linear order along the individual linkage groups.
