In summary, this paper reports a high-density wheat genetic map based on an individual mapping population. In total, 119 001 SNP markers derived from the Wheat660K SNP array were mapped onto the KJ-RIL genetic map. We observed good good collinearity of our high-density genetic map with the Wheat90K and Wheat820K consensus genetic maps, increasing the possibility of obtaining a consensus integrative higher-density wheat genetic map in the future. This high-density genetic map is also in good accordance with the recently released wheat genome assembly. Our high-density wheat genetic map provides a major resource for future wheat genetic and genomic research. Moreover, this paper provides an overview of the structural relationships between wheat and other gramineous plant genomes based on comparative genomics analysis. Finally, a major stable QTL for kernel number was thoroughly characterized based on this high-density genetic map and comparative genomics analysis.