AUTHOR=King Julie , Grewal Surbhi , Othmeni Manel , Coombes Benedict , Yang Cai-yun , Walter Nicola , Ashling Stephen , Scholefield Duncan , Walker Jack , Hubbart-Edwards Stella , Hall Anthony , King Ian Phillip 

TITLE=Introgression of the Triticum timopheevii Genome Into Wheat Detected by Chromosome-Specific Kompetitive Allele Specific PCR Markers

JOURNAL=Frontiers in Plant Science

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.919519

DOI=10.3389/fpls.2022.919519

ISSN=1664-462X

ABSTRACT=<p><italic>Triticum timopheevii</italic> (2<italic>n</italic> = 28, A<italic><sup>t</sup></italic>A<italic><sup>t</sup></italic>GG) is a tetraploid wild relative species with great potential to increase the genetic diversity of hexaploid wheat <italic>Triticum aestivum</italic> (2<italic>n</italic> = 42, AABBDD) for various important agronomic traits. A breeding scheme that propagated advanced backcrossed populations of wheat-<italic>T. timopheevii</italic> introgression lines through further backcrossing and self-fertilisation resulted in the generation of 99 introgression lines (ILs) that carried 309 homozygous segments from the A<italic><sup>t</sup></italic> and G subgenomes of <italic>T. timopheevii</italic>. These introgressions contained 89 and 74 unique segments from the A<italic><sup>t</sup></italic> and G subgenomes, respectively. These overlapping segments covered 98.9% of the <italic>T. timopheevii</italic> genome that has now been introgressed into bread wheat cv. Paragon including the entirety of all <italic>T. timopheevii</italic> chromosomes <italic>via</italic> varying sized segments except for chromosomes 3A<italic><sup>t</sup></italic>, 4G, and 6G. Homozygous ILs contained between one and eight of these introgressions with an average of three per introgression line. These homozygous introgressions were detected through the development of a set of 480 chromosome-specific Kompetitive allele specific PCR (KASP) markers that are well-distributed across the wheat genome. Of these, 149 were developed in this study based on single nucleotide polymorphisms (SNPs) discovered through whole genome sequencing of <italic>T. timopheevii.</italic> A majority of these KASP markers were also found to be <italic>T. timopheevii</italic> subgenome specific with 182 detecting A<italic><sup>t</sup></italic> subgenome and 275 detecting G subgenome segments. These markers showed that 98% of the A<italic><sup>t</sup></italic> segments had recombined with the A genome of wheat and 74% of the G genome segments had recombined with the B genome of wheat with the rest recombining with the D genome of wheat. These results were validated through multi-colour <italic>in situ</italic> hybridisation analysis. Together these homozygous wheat-<italic>T. timopheevii</italic> ILs and chromosome-specific KASP markers provide an invaluable resource to wheat breeders for trait discovery to combat biotic and abiotic stress factors affecting wheat production due to climate change.</p>