Analysis of co-linearity between the two maps was performed by connecting the BAC markers in common between the RH map and FISH data.
The syntenic relationship between these two maps was highly collinear, except for a few small parts of the genomes.
Marker order between the two maps was generally consistent when taking into account the regions covered by homologous markers.
Although the number of markers shared between this study and that of Timusk et al. (2011) was relatively modest, comparison between the two maps was possible.
The average correlation coefficient between the two maps was 0.95 on a scale of 10 cM, indicating a high degree of similarity.
When comparing the maps from different populations, the number of markers in common between any two maps was approximately 43% of the number of markers on the smaller map.
We were able to verify long-range colinearity as the median number of markers shared between any two maps was 793 (quartiles Q1 = 656 and Q3 = 983), or approximately 44 per LG.
Besides the high degree of synteny between the two maps, genetic distance between markers on the two maps was also highly correlated (r = 0.98, p≤0.0001).
Although the azimuth and the elevation stimulus lines were exactly perpendicular to each other, the angle between the colour codings of the two maps was obviously different from 90°.
There were a total of 16 discrepancies between the two maps that were 2 to 10 cM with all other discrepancies between the two maps being less than 2 cM in genetic distances between the SoyOPA-4 SNP markers.
