The SNP flanking sequences mapped in the KJ-RIL map were kindly provided by Professor Jia JZ. We used the Basic Local Alignment Search Tool (BLAST) (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/) to align the SNP probes to the IWGSC survey sequences (contigs). All IWGSC survey sequences were downloaded from http://www.wheatgenome.org/. In addition, contig sequences to which the SNPs were best hits were screened in a BLASTN search against the coding sequences (CDSs) of B. distachyon, rice (O. sativa L.), maize (Z. mays L.), and sorghum (S. vulgare L.). All CDSs were downloaded from http://plants.ensembl.org/index.html. An expectation value (E) of 1E−10 was used as the significance threshold. Synteny analyses with common wheat, Brachypodium, rice, maize and sorghum genomes were performed based on the SNP orders in the KJ genetic map and on the corresponding CDSs in the genome sequences of Brachypodium, rice, maize and sorghum genomes.