Of the 339757 functional SNPs, 136973 (40.3%) were polymorphic between KN9204 and J411. Of these, 8407 had more than 10% missing data in the 188 KJ-RILs, and were removed from the linkage analysis. Among the remaining 128566 SNPs, 90567 (70.4%) were transitions, and 37999 (29.6%) were transversions. The 128566 functional SNPs and the previously reported 591 loci3 were used for linkage analysis and map construction. The 129157 markers fell into 5175 bins, and to create a chromosome frame, only one marker was selected as a representative from each bin.