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Background  During the bread wheat speciation by polyploidization, a series of genome rearrangement and sequence recombination occurred. Simple sequence repeat (SSR) sequences, predominately located in heterochromatic regions of chromosomes, are the effective marker for tracing the genomic DNA sequence variations. However, to date the distribution dynamics of SSRs on chromosomes of bread wheat and its donors, including diploid and tetraploid  Triticum urartu ,  Aegilops speltoides ,  Aegilops tauschii ,  Triticum turgidum  ssp.  dicocoides , reflecting the genome evolution events during bread wheat formation had not been comprehensively investigated.    Results  The genome evolution was studied by comprehensively comparing the distribution patterns of (AAC) n , (AAG) n , (AGC) n  and (AG) n  in bread wheat  Triticum aestivum  var. Chinese Spring and its progenitors  T. urartu ,  A. speltoides ,  Ae. tauschii , wild tetroploid emmer wheat  T. dicocoides , and cultivated emmer wheat  T. dicoccum . Results indicated that there are specific distribution patterns in different chromosomes from different species for each SSRs. They provided efficient visible markers for identification of some individual chromosomes and SSR sequence evolution tracing from the diploid progenitors to hexaploid wheat. During wheat speciation, the SSR sequence expansion occurred predominately in the centromeric and pericentromeric regions of B genome chromosomes accompanied by little expansion and elimination on other chromosomes. This result indicated that the B genome might be more sensitive to the “genome shock” and more changeable during wheat polyplodization.    Conclusions  During the bread wheat evolution, SSRs including (AAC) n , (AAG) n , (AGC) n  and (AG) n  in B genome displayed the greatest changes (sequence expansion) especially in centromeric and pericentromeric regions during the polyploidization from  Ae. speltoides  S genome, the most likely donor of B genome. This work would enable a better understanding of the wheat genome formation and evolution and reinforce the viewpoint that B genome was originated from S genome.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-020-07364-6.

Genome evolution during bread wheat formation unveiled by the distribution dynamics of SSR sequences on chromosomes using FISH