Modern wheat cultivars can benefit from useful variability introduced from non-progenitor Aegilops species by using synthetic partial amphiploids. Cytological analysis of advanced generation wheat-Aegilops amphiploids (AABBDDU(k)U(k)S(k)S(k)) had 54-58 chromosomes in general with a higher frequency of bivalents (24.0-27.97). The average number of univalents in pollen mother cells (PMCs) varied from 1.32-5.28 with an average of 2.29 per cell. After the reductional division of paired chromosomes, the majority of univalents reached the metaphase-I plate and underwent equational division, eventually being eliminated via laggards and micronuclei. The D genome was the most vulnerable to deletion, followed by the S-k and U-k genomes, but the 1D chromosome was preferentially eliminated in almost all amphiploids investigated, as confirmed by SDS-PAGE. The partial amphiploids with white glumes, bold seeds, and robust rachis could be employed for wheat biofortification and resistance to powdery mildew. The presence of various important metal homeostasis genes (FRO2, FRO6, FRO7, ZIP2, ZIP4, ZIP5, ZIP7, NAS2, NAS4, YSL15, IRT2, NRAMP5, NAM, and HMA3) from Aegilops species suggests that these partial amphiploids could be used as pre-bred material to introgress the metal homeostasis genes from Aegilops to wheat in wheat biofortification program.