A St-derived genome contributes to the formation of the wheat BB genome

Although substantial efforts have been made to identify the progenitor of the wheat BB genome, the precise donor remains elusive. In this study, we first investigated the origin of the BB genome using a BB-specific atp6 gene harboring unique 5'-end sequences, which is present in multiple copies and partially pseudogenized in the BB genome. BLAST searches revealed that multi-copied atp6 (pseudo)genes occur exclusively in polyploid St-genome species. An ultrametric phylogeny constructed from genome-wide single-copy genes resolved the divergence of Aegilops speltoides (SS genome) and the St genome c. 4 million years ago, coinciding with the estimated origin of the BB genome. Furthermore, genome-wide single-nucleotide polymorphism (SNP)-based allele matching showed that the St genome best explains BB alleles after SS, with an SS : St SNP ratio of 3 : 1, suggesting that the St genome likely contributed to the BB formation via two independent hybridization events with the SS ancestor. Finally, we identified 52 BB-specific genes to facilitate the search for the true BB donor or the transitional hybrid. This study provides compelling evidence for the St genome's critical contribution to the BB genome and advances our understanding of how the complex hexaploid genome of bread wheat was formed and reshaped over evolutionary time.