Tracing the genetic diversity of the bread wheat D genome

Bread wheat ( Triticum aestivum ) became a globally dominant crop after incorporating the D genome from donor species Aegilops tauschii , while evolutionary history shaping the D genome during this process remains elusive. Here, we proposed a renewed evolutionary model linking Ae. tauschii and hexaploid wheat D genome, based on an ancestral haplotype map covering a total of 762 Ae. tauschii and hexaploid wheat accessions. We dissected the evolutionary process of Ae. tauschii lineages and clarified L3 as the most ancient lineage. A few independent intermediate accessions were reported, demonstrating the low-frequent inter-sublineage geneflow enriched the diversity of Ae. tauschii . We discovered that the D genome of hexaploid wheat inherited from a unified ancestral template, but with a mosaic composition that is highly mixed by three Ae. tauschii L2 sublineages located in the Caspian coastal region, suggesting the early agricultural activities facilitate the innovation of D genome compositions that finalized the success of hexaploidization. We further found that the majority (65.6%) of polymorphisms were attributed to novel mutations absent during the spreading of bread wheat, and also identified large Ae. tauschii introgressions from wild Aegilops lineages, expanding the diversity of wheat D genome and introducing beneficial alleles. This work decoded the mystery of the wheat hexaploidization process and the evolutionary significance of the multi-layered origins of the genetic diversity of the bread wheat D genome.