Development of wheat D genome-specific molecular markers based on subgenome-specific repeats

Species from the tribe Triticeae can be used for wheat improvement by introgression of valuable genes through wide hybridization. More than 85% of Triticeae genomes consist of repetitive sequences with species-specific content and composition, which can be used to detect introgression chromatin. We developed repeat-based molecular markers specific for the D genome of allopolyploid wheat Triticum aestivum (2n = 6x = 42, AABBDD) and applied them to detect D-genome chromatin in tetraploid wheat T. turgidum (2n = 4x = 28, AABB). To identify wheat subgenome-specific repeats, comparative analysis of low-coverage sequence data was performed using the RepeatExplorer pipeline. Three types of repeats, suitable for the development of D-genome-specific markers were identified: the centromeric retrotransposons Quinta, Afa-family repeats associated with the CACTA DNA transposons and the Ty3/gypsy LTR retrotransposon from the Tekay lineage. Consensus sequences of these repeats were used to select D-genome-specific SNPs and design PCR allelic competitive extension (PACE) assays for detecting D-genome chromatin. The assays were applied to screen introgression populations derived from T. aestivum x T. turgidum crosses. The PACE results were confirmed by fluorescent in situ hybridization, which showed that the markers detected introgressions ranging from translocation segments to intact chromosomes. Given the increasing availability of whole-genome sequence data, the presented approach can be used to develop molecular markers for detection of any introgression regardless of its chromosomal homoeologous group.