Finally, the mapping order is fine-tuned by using a sliding window of five markers (ripple command).
The map order was refined using the annealing and flips procedures of CarthaGene.
Map order was verified visually by examining the raw genotypes and the linkage map was generated using MapChart [ 55].
The map order was further confirmed using Regression mapping (default parameters, recombination frequency < 0.4, LOD > 1 and jump = 5).
Once a stable map order was obtained after 3 4 cycles, we turned to the next map building round.
Remaining markers were located using the 'try' command, and the map order was re-tested using the 'ripple' command.
The IT 2 gene lies between these two loci, along with eight markers whose map order was not determined.
Map order was improved by maintaining markers exhibiting a nearest neighbor stress value less than 2 cM.
A consensus map order was then produced by assigning to all markers an observed or implied map position on all four component maps.
Second, many of the anchored scaffolds contained just one mapped marker, or contained multiple tightly linked markers whose map order was questionable due to insufficient recombination.
