In that study, RH mapping was tested as a mean to provide good quality scaffolding for physical mapping.
In the analysis with CLC genomics workbench, the influence of three combinations of parameters on mapping was tested: mismatch cost, insertion cost, deletion cost, matching length and similarity.
The difference between direct observations and distribution maps was tested and shown to give similar results.
Quality of the RH map was tested by comparison with two previously published genetic maps [ 36, 41].
The framework map was tested using a flips algorithm, which checks all local permutations in a window of 6 markers, and a greedy algorithm, which tries to improve the map by inversion of parts of the reference map.
The framework status of the map was tested by calculation of likelihood of maps produced after all local permutations in a slipping window of 6 markers, and by global local inversions.
The accuracy of the AL8/78-RH maps was tested for both chromosome assignment and marker order by comparing with previously published genetic and RH maps [ 5, 14, 21, 23].
Starting from the existing order of a linkage group, each marker assigned to that linkage group by two-point analysis, but not present on the multi-point map, was tested in every possible location.
The robustness of the map was tested by comparison of the likelihood of the reference map to the likelihood of maps derived from the reference map by all possible permutations in a window of 6 markers and by inversion of parts of the map using the simulated annealing algorithm.
So, the marker order of AL8/78-RH maps was tested by comparison with: 1) a DArT consensus genetic map [ 23]; 2) a SNP based genetic map with anchored D-genome BAC contigs [ 5]; 3) a SNP genetic map anchoring sequence scaffolds of D-genome (referred as Y2280 × AL8/78 map hereafter [ 21]); and 4) a RH map of D-genome of Chinese Spring (referred as CS RH map hereafter [ 14]).
The quality of the physical map was tested using two types of checks: first, an estimate was obtained for the percentage of chimerical contigs, that is BAC clones from different genomic regions spuriously assembled in the same contig, and second, an assay on the reliability of BAC clone order within physical contigs was performed.
