Integration of the D-genome, following introgression,  reshapes gene transcription, chromatin architecture and metabolome in allohexaploid wheat
The integration of the DD genome into tetraploid lead to the birth of allohexaploid wheat which has subsequently been grown under global environments. However, the impact of the DD genome integration on genome structure, chromatin organization, gene transcription and more importantly on wheat adaptability remains largely unknown. Here, we investigated the change of genomic sequence, transcriptome and epigenome profiles (including chromatin-chromatin interactions) and metabolome in three independent polyploidization events which featured a DD genome integration. Polyploidizations activate defense-related genes and suppress translation related genes by reorganizing both the wheat genome and chromatin architecture. Meanwhile, stress response related secondary metabolic pathways are boosted upon polyploidization, particularly the alkaloid and flavonoid pathways which have been demonstrated to be of importance in plant adaptation to the environment. DD integration not only brings one additional copy of genes into these pathways but also activates the genes originally existing in the A and B sub-genomes. As such these results highlight the integration of the DD genome as an indispensable element in allohexaploid wheat adaptability during evolution of the crop and thereby provide new perspectives for polyploidy crop improvement.