Polyploidy, or whole genome duplication (WGD), has played an important role in the evolution of all eukaryotes. If WGD occurs concomitantly with interspecific hybridization, that is, allopolyploidy, it may cause rapid karyotypic reconfiguration and dramatic changes in gene expression. Previously, we have reported transgenerationally propagated karyotypic heterogeneity in a relatively older (several generations away from formation) artificially constructed allotetraploid with a AADD genome combination wherein the A and D subgenomes were from Triticum urartu and Aegilops tauschii, respectively. We observed dramatic differences in whole-chromosome gain and/or loss and structural variations between A and D subgenomes and among chromosomes, the causes for these differences, however, remained unexplored. To address this issue, we resynthesized a pair of reciprocal allotetraploid wheats with genomes AADD and DDAA using identical parental accessions of T. urartu (TMU38) and Ae. tauschii (TQ27), and performed karyotypic analysis. We detected extensive karyotypic variations already in the first selfed generation (S1) in both AADD and DDAA allotetraploids. More retention of chromosomes of subgenome A than D was found in both allotetraploids, indicating differential chromosome retention was not due to maternal or cytoplasmic influence but a chromosome-specific property. We analyzed meiotic chromosome behavior of euploid S0 plants and found that chromosomes that showed the highest frequencies of irregularity were not those that showed more gain or loss in somatic cells of the resulting S1 plants. This suggests that it was differential retention rather than occurrence that was responsible for the observed chromosomal variations in number and structure. We next performed transcriptome analyses of young inflorescence at four stages (5, 10, 15 and 20 mm in length, respectively) together with seedling leaves taken from euploid individuals of the reciprocal allotetraploids, reciprocal F1 hybrids (AD and DA), and both diploid parents. We analyzed effects of hybridization itself and hybridization coupled with WGD (allopolyploidy) by comparing the expression differences in subgenomes of hybrids and allotetraploids relative to the corresponding diploid parents. We found that, during young inflorescence development, gene expression was temporally up-regulated in all plant lines. In both hybrids and allotetraploids in relation with parents, the numbers of up-regulated genes in subgenomes A and D were similar, but the numbers of down-regulated genes were greater in subgenome D than in subgenome A at each of the sampled stages. This observation indicates that, in young inflorescence, downregulated expression of more genes occurred in the D- than in the A-subgenome in both F1 hybrids and allotetraploids, and this trend was increasingly stronger with development. This is consistent with the higher phenotypic resemblance of the hybrids and allotetraploids to T. urartu than to Ae. tauschii. We further found that the numbers of downregulated genes were variable across the chromosomes, and significantly more genes mapped to 2D and 3D were suppressed than those mapped to the rest chromosomes. This is consistent with the greater loss of these two chromosomes in the S1 plants. Together, our results indicate that biased subgenome expression suppression likely plays an important role in differential retention of chromosomes following allopolyploidization.