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Background   Triticum timopheevii  (2n = 4x = 28; A t A t GG), is an important source for new genetic variation for wheat improvement with genes for potential disease resistance and salt tolerance. By generating a range of interspecific hybrid lines,  T. timopheevii  can contribute to wheat’s narrow gene-pool and be practically utilised in wheat breeding programmes. Previous studies that have generated such introgression lines between wheat and its wild relatives have been unable to use high-throughput methods to detect the presence of wild relative segments in such lines.    Results  A whole genome introgression approach, exploiting homoeologous recombination in the absence of the  Ph1  locus, has resulted in the transfer of different chromosome segments from both the A t  and G genomes of  T. timopheevii  into wheat. These introgressions have been detected and characterised using single nucleotide polymorphism (SNP) markers present on a high-throughput Axiom® Genotyping Array. The analysis of these interspecific hybrid lines has resulted in the detection of 276 putative unique introgressions from  T. timopheevii , thereby allowing the generation of a genetic map of  T. timopheevii  containing 1582 SNP markers, spread across 14 linkage groups representing each of the seven chromosomes of the A t  and G genomes of  T. timopheevii . The genotyping of the hybrid lines was validated through fluorescence in situ hybridisation (FISH). Comparative analysis of the genetic map of  T. timopheevii  and the physical map of the hexaploid wheat genome showed that synteny between the two species is highly conserved at the macro-level and confirmed the presence of inter- and intra-genomic translocations within the A t  and G genomes of  T. timopheevii  that have been previously only detected through cytological techniques.    Conclusions  In this work, we report a set of SNP markers present on a high-throughput genotyping array, able to detect the presence of  T. timopheevii  in a hexaploid wheat background making it a potentially valuable tool for marker assisted selection (MAS) in wheat pre-breeding programs. These valuable resources of high-density molecular markers and wheat- T. timopheevii  hybrid lines will greatly enhance the work being undertaken for wheat improvement through wild relative introgressions.    Electronic supplementary material  The online version of this article (10.1186/s12870-019-1785-z) contains supplementary material, which is available to authorized users.

bmc plant biology

Development and characterisation of interspecific hybrid lines with genome-wide introgressions from Triticum timopheevii in a hexaploid wheat background