In previous studies, 7504 SNPs from the Wheat9K SNP array12, 46977 SNPs from the Wheat90K array16, and 56505 SNPs from the Wheat820K SNP array18 were genetically mapped to the hexaploid wheat genome. These SNPs have also been physically assigned to the corresponding CSS-assembled contigs. Based on the common CSS contigs, we analysed the synteny of the mapped SNPs (Wheat660K SNP array vs. Wheat90K array and Wheat660K SNP array vs. Wheat820K SNP array) across different mapping populations (Figs 5 and 6). These common contigs were generally aligned with the chromosomes in a consistent order across different mapping populations, verifying the accuracy and credibility of our high-density genetic map. Regarding the total map length, the Wheat90K/820 SNP consensus integrative genetic map is 2.4/1.9 times longer (data not shown) than that of the present map. The increased genetic map length is proportionate to the increased mapping population size16, 18. A relatively small mapping population size resulted in limited identification of recombination events and lower resolution of the genetic map, contributing to the short map length in this study24, 25. In addition, comparative analysis among these three SNP maps revealed that genetic maps of chromosomes 3 A, 4B, 5D, 6D, and 7B derived from the wheat 820 K SNP array were inverted, with long arms at the top and short arms at the bottom (data not shown)18. Chromosome 4 A, derived from the Wheat820K SNP array, might be involved in chromosomal rearrangement compared with the genetic maps derived from the Wheat90K SNP array and our Wheat660K SNP array. The genetic information from the common contigs and their genetic collinearity analysis across different mapping populations will lay the foundation for obtaining a consensus integrative genetic linkage map.Figure 5Synteny of the mapped SNPs from the Wheat660K SNP array (in blue) with that from the Wheat90K array (in red) based on their common CSS-assembled contigs. Figure 6Synteny of the mapped SNPs from the Wheat660K SNP array (in blue) with that from the Wheat820K array (in green) based on their common CSS-assembled contigs. Notes: The genetic maps of chromosomes 3A, 4B, 5D, 6D and 7B derived from the Wheat820K SNP array are shown in inverted form, with long arms at the top and short arms at the bottom18. In this figure, these inversions were corrected.