Improvement of quantitative traits in elite wheat breeding germplasm through introgression from Triticum dicoccoides via a wheat-Aegilops tauschii synthetic octoploid bridge

Abstract

Wild relatives of wheat provide an important reservoir of allelic diversity for crop improvement, but their use in elite breeding germplasm is constrained by reduced agronomic adaptation, persistent yield disadvantages, and the difficulty of recovering favorable recombinant deviates for quantitative traits. Wild emmer (Triticum dicoccoides), the progenitor of domesticated tetraploid and hexaploid wheats, carries extensive diversity for disease resistance, abiotic stress response, functional quality, phenology, and yield component traits. However, systematic introgression of wild emmer diversity into adapted hexaploid wheat backgrounds remains challenging, particularly when the breeding objective is improvement of complex quantitative traits rather than transfer of major effect loci. This project evaluated the use of a wheat-Aegilops tauschii synthetic octoploid amphiploid bridge as a strategy for introducing allelic diversity from wild emmer into elite winter wheat germplasm while retaining regional adaptation to Kansas production environments. Seven BC2-derived Triticum dicoccoides germplasm development (TdGD) populations were generated using two adapted hexaploid recurrent parents, two Aegilops tauschii accessions, and seven wild emmer accessions representing geographically diverse sources of A and B genome variation. High-density sequencing data from population founders were used to perform pedigree-based imputation into progeny with low-density SNP data to characterize genome-wide introgression architecture and detect donor segments. Across populations, donor introgression was successfully recovered on all three wheat subgenomes, with introgressions enriched in distal, high recombination regions and reduced in pericentromeric intervals. Chromosome-specific patterns were influenced by founder divergence, marker density, and recombination landscape. Population structure was driven primarily by recurrent parent background and variation in donor allele retention. These results demonstrate that the amphiploid bridge strategy can generate wild introgression germplasm and allow for quick recovery of an adapted hexaploid wheat background. To evaluate the breeding potential of this germplasm, one population, TdGD Pop80, was phenotyped across six Kansas field environments for agronomic, yield component, functional quality, and ionomic traits. Mixed model analyses were used to estimate within- and across- environment performance, trait relationships, and repeatability. Despite the observation that wild introgression broadly reduced agronomic performance, Pop80 exhibited substantial quantitative variation and included lines with favorable combinations of grain yield, kernel traits, protein quality, and elemental composition. Trait relationships reflected both expected physiological tradeoffs and opportunities for selection, including relationships among phenology, vegetative and reproductive performance under drought, grain yield, kernel size, grain protein, functional quality, and ionomic traits. Genome-wide association analyses identified marker-trait associations across trait groups, including loci corresponding to known developmental, quality, kernel size, and ionomic regions, as well as additional regions requiring validation. Overlaying association signals with donor introgression profiles provided a framework for distinguishing candidate wild-derived regions and for prioritizing loci for future breeding and genetic studies. A yield-weighted multi-trait selection index was constructed to identify competitive germplasm. Two Pop80 wild introgression lines, KSTdGD80-55 and KSTdGD80-175, were selected for germplasm release based on their favorable agronomic performance, yield potential, quality traits, and characterized introgression profiles. These lines represent adapted winter wheat germplasm carrying defined introgressions from wild emmer and Aegilops tauschii, and they provide useful material for continued evaluation of wild-derived alleles in breeding-relevant backgrounds. Together, this research demonstrates that bridge-mediated introgression can broaden the allelic base of elite wheat germplasm while maintaining sufficient agronomic performance for selection. The resulting genomic resources, phenotypic datasets, marker-trait associations, and released germplasm provide a foundation for future efforts to refine wild introgressions, validate candidate loci, and deploy favorable wild alleles for quantitative trait improvement in wheat breeding programs.