Of the 119566 loci, 118998 (99.5%) were best hits to 57036 CSS contigs, with 2.1 polymorphic markers per contig. In total, 93.0% contigs had coincident physical and genetic positions, 4.6% were mapped to homoeologous chromosomes such as 1 A in physical position and 1B in the KJ-RIL genetic map, and 2.4% were disordered (Fig. 2; Figure S1; Table S3). Based on the SNP flanking sequences, we assigned 116 261 SNPs to the recently released wheat genome assembly. SNP order in the present genetic map was in good agreement with that in the wheat genome assembly, with the exception of chromosome 7DL, in which a segment inversion was identified (Fig. 3; Figure S2; Table S3).Figure 3Schematic representation of the syntenic relationships between any one marker in wheat genetic and physical maps. Gen-1A to Gen-7D represent the 21 wheat chromosomal genetic maps released in this paper; Phy-1A to Phy-7D represent the 21 wheat chromosomal physical maps, which were constructed by assigning 116 261 SNPs to the wheat genome assembly using SNP flanking sequences as the query. For the redundant loci that showed co-segregation in the 188 KJ-RILs, only one unique informative marker is shown in this figure.