High-density genetic linkage maps are essential for genetic and genomic research in crops1–4. Molecular breeding is more effective if the molecular map is dense to provide more choices in the quality and type of markers and to increase the probability of detecting polymorphic markers in important chromosomal intervals. In wheat, the large genome size (17 gigabases), hexaploid nature (AABBDD), high percentage of repetitive regions and low level of polymorphism have complicated the acquisition of high-resolution genetic maps by molecular markers1–4. To date, several kinds of molecular markers, including restriction fragment length polymorphism (RFLP)5, 6, amplified fragment length polymorphism (AFLP)7, simple sequence repeats (SSRs)8, 9, and diversity array technology (DArT)3, 4, 10, 11 have been used to construct genetic linkage maps in wheat. Information regarding wheat molecular markers and genetic maps is available in some datasets such as GrainGenes 2.0 (https://wheat.pw.usda.gov/GG3/), URGI (https://urgi.versailles.inra.fr/), etc. Most of these markers are mapped on the telomeric regions, and there is very limited map resolution in proximal part of the chromosomes3. Therefore, the density and coverage of the current genetic maps are less than satisfactory.