The SNP order in the present KJ-RIL genetic map was also in good agreement with that in the physical position, with the exception of chromosome 7DL, in which a segment inversion was identified (Fig. 3; Figure S2; Table S3). A previous report showed that wheat chromosome 7 was likely to involve a complex interchange26. These findings prompted us to search for candidate genes of targeted major QTLs. In wheat, a majority of recombination events occurred on the most distal portions of the chromosomal arms, whereas the recombination events tend to be suppressed around the centromere3, 27, 28. These characteristics result in a low resolution of the genetic map in the centromeric region, which was evident in the small genetic distance in the KJ-RIL genetic map corresponding to a large physical region around the centromere compared with the most distal portions of the chromosomal arms (Fig. 3; Figure S2; Table S3). These findings also indicate the difficulty of high-resolution mapping and map-based cloning of a QTL around the centromere because of the low coverage of genetic markers and the suppression of recombination events.