The high-density SNP map developed in the present study first documented the genetic positions of 119 001 SNPs from the Wheat660K SNP array. Based on the SNP flanking sequences, we assigned 118 785 SNPs to 56 904 CSS-assembled contigs (Table S3). The physical positions of the corresponding CSS-assembled contigs could be used to validate genetic position (chromosome and chromosomal arms assignment). As shown in Fig. 2 and Table S3, the physical and genetic positions of these mapped markers were generally in agreement.