Using the SSR markers a genetic map can be established, the available sequence extensions by the underlying ESTs will greatly facilitate the implementation of the SSR marker loci during the pending iterative assembly process of the Physcomitrella genome sequence data.
The orientation of the SSR markers was based on the SSR maps (McCouch et al. [2002]).
Prior to construction of an integrated map, the orientation of each linkage group in the linkage map of Shirasawa et al. was adjusted in accordance with the linkage map using the consensus SSR markers.
However, using the RFLP/SSR map, kgw5 was located to a 4.6 Mb interval.
Using the SNP bin map, another two QTLs with small effects were identified on chromosomes 6 and 8, respectively, which were not detectable using the RFLP/SSR map.
When the mapping results above were compared with those obtained using the RFLP/SSR map, it was shown that the distance between the markers flanking GS3 was more than 10 cM in that map corresponding to about 6 Mb [27].
For grain length, two QTLs were identified on each of chromosomes 1 and 3 using the SNP bin map, compared to one QTL identified on each of these two chromosomes using the RFLP/SSR map.
While using the RFLP/SSR map, only 3 QTLs for grain length and 2 QTLs for grain width were detected above the LOD thresholds (Table S5), of which only one QTL for grain length (gl3a) was identified in both years.
It can also be seen from Table S6 that with LOD threshold 3.0, the number of QTLs detected in each of the trails was also larger using the SNP bin map than using the RFLP/SSR map, although the number of QTLs that were repeatedly detected were similar using the two maps.
Thus some small effect QTLs could be detected only with relative low stringency using the RFLP/SSR map, but could be detected with higher stringency using the SNP bin map, indicating that the high-density SNP bin map improved the QTL detection power.
