For future food security it is important that wheat, one of the most widely consumed crops in the world, is able to survive the threat of abiotic and biotic stresses. New genetic variation is currently being introduced into wheat through introgressions from its wild relatives. Triticum timopheevii, a tetraploid wild relative of wheat (2n = 4x = 28, AtAtGG), is an important source of resistance to various diseases such as wheat rusts, powdery mildew and Fusarium head blight (FHB), as well as fertility restorer genes and tolerance for various abiotic stresses. Its practical utilisation in wheat improvement is being facilitated through the generation of genome-wide introgressions leading to a variety of different wheat-T. timopheevii introgression lines.

For trait discovery, the recombinant lines require stable homozygous introgressions. Breeding programs rely on efficient genotyping platforms for marker-assisted selection (MAS). Through whole genome sequencing of T. timopheevii and filtering for single-copy regions of the wheat genome, a large number of chromosome-specific single nucleotide polymorphisms (SNPs) between Chinese Spring wheat and T. timopheevii have been generated and converted into chromosome-specific Kompetitive allele-specific PCR (KASP™) assays. These markers 1) allow rapid detection of T. timopheevii segments in a hexaploid background 2) distinguish between segments originating from the At and G genomes of T. timopheevii 3) provide information on the segment’s homozygosity in bread wheat and 4) indicate the potential site of introgression of the segment in the wheat genome. Here, we report the generation of 99 wheat–T. timopheevii homozygous introgression lines which carried 309 homozygous segments from the At and G subgenomes of T. timopheevii. These introgressions contained 89 and 74 unique segments from the At and G subgenomes, respectively. These overlapping segments covered 98.9% of the T. timopheevii genome that has now been introgressed into bread wheat cv. Paragon including the entirety of all T. timopheevii chromosomes via varying sized segments except for chromosomes 3At, 4G, and 6G. These lines were characterized using 480 chromosome-specific KASP markers and multi-colour genomic in situ hybridization (mc-GISH).

Spray inoculation with Fusarium graminearum revealed very rare Type 1 FHB resistance in two introgression lines. Molecular analysis of these lines indicates the source of resistance to be on the distal end of chromosome 3GS of T. timopheevii. Phenotyping analysis of an F6 mapping population between two T. timopheevii accessions, showing resistance and susceptibility to FHB (genotyped using the Axiom Wheat Breeders Array), also indicated a potential QTL for FHB resistance corresponding to wheat homoeologous group 3. Further characterisation to find the novel source of this resistance and its incorporation in commercial breeding could save the worldwide wheat breeding industry billions of dollars in yield and quality losses due to this economically devastating disease.