A new Whole Genome Shotgun (WGS) assembly of the Chinese Spring (CS) reference wheat genome is now available (http://plants.ensembl.org/index.html; https://urgi.versailles.inra.fr/download/iwgsc/IWGSC-WGA_Sequences/). However, genetic and genomic studies in wheat continue to lag behind the research in other members of the grass family (Gramineae), such as rice and maize. The gradual enrichment of SNP markers and the sequences released for CS (https://urgi.versailles.inra.fr/download/iwgsc/IWGSC-WGA_Sequences/), Triticum urartu 2 and Aegilops tauschii 1 have facilitated comparative genomic analysis in wheat. Comparative genomic analysis with species whose genomes have been well characterized has been used as an effective method for the construction of high-resolution genetic linkage maps of target wheat genes and for the prediction of candidate genes in regions of interest. For instance, the construction of high-density genetic maps has facilitated the mapping of the gene grain protein content-B1 (Gpc-B1)19, the yellow rust resistance gene Yr36 20 and the powdery mildew resistance gene Pm41 21. Comparative genomics studies have also furthered the understanding of the basic processes of genome evolution and the transfer of information from model species to related organisms and facilitated the cross-referencing of various types of information, such as QTLs, mutants, and gene expression22, 23. These correlations and integrations will take full advantage of the collective intellectual contributions from scientists across many disciplines22.