After 4 rounds of backcrosses with CJ06, the BC4F1 and BC4F2 generations were scanned with a set of 71 SSR markers, which were uniformly distributed on a previous linkage map (Additional file 1: Table S4).
A set of 71 SSR markers (Additional file 1: Table S4) uniformly distributed on a previous linkage map (Sogawa et al., 2005; Sogawa et al., 2004; Zeng et al., 2009) were used to select the individual plants containing the least TN1 DNA in BC4F1 lines.
A list of GO terms for which the genes annotated with them are found to be non-randomly distributed on the map.
The 175 markers distributed on the map were much fewer than the synthetic tetraploid map which consisted of 370 RFLP markers.
Table 3 lists the 59 GO terms for which this null hypothesis is rejected at P <0.01 (after multiple testing correction), that is, functions which are non-randomly distributed on the map.
Among these mapped BrGMS markers, 168 were only distributed on the A genome linkage groups (LGs), 18 distrubuted both on the A and C genome LGs, and 33 only distributed on the C genome LGs.
They were evenly distributed on the integrated map and showed a low number of missing data (<5%) and high minor allele frequencies (MAF > 10%) on the OSR panel.
The results in this report suggest that the integrated Solexa paired-end sequences that were produced with one forward primer and 384 reverse primers were quite evenly distributed on the genetic map of B. rapa and no clear clusters of SRAP markers on a genetic map were identified.
Among these mapped BrGMS loci, 186 were evenly distributed on the A genome LGs.
To evaluate whether the mapped markers were randomly distributed on the linkage map, the linkage groups were divided into 1, 2.5, 5, 10, 20, and 40 cM blocks, and the number of markers per block was counted.
