An overview (from the wheat genetic map perspective) of the relationships between the five grass family genomes at the resolution of the genetic map in centimorgans is provided in Figures S3 and S4. There were 113288 markers that corresponded to the CDS of Brachypodium (65357 markers) (Table S4; Figure S3a, S4a), rice (58825 markers) (Table S4; Figures S3b, S4b), maize (53745 markers) (Table S4; Figures S3c, S4c), and sorghum (59994 markers) (Table S4; Figures S3d, S4d). In general, chromosomes belonging to the same homoeologous groups showed correspondence with the same grass chromosomes, but some differences were observed. Large and especially small synteny blocks across wheat and grass family chromosomes were observed, indicating the complexity of the wheat genome among the grass family genomes. The structural relationships among the genomes indicate that for some individual wheat chromosomes, there is a preponderance of corresponding grass genes from one or two certain linkage groups. For example, wheat chromosomes 2 A/2B/2D corresponded to Bd5, wheat chromosomes 3 A/3D corresponded to Bd2 and Bd3, wheat chromosomes 4 A/4B/4D corresponded to Os3, and wheat chromosomes 7 A/7B/7D corresponded to Sb10. However, for most synteny blocks, the chromosomes were more fragmented and scattered, with a high frequency of breakdown.