Genomic shock induced genetic and epigenetic changes in homoeologs of class ABCDE MADS-box genes in hexaploid wheat

Polyploidy, the duplication of a single genome (autopolyploid) or the combination of two or more divergent genomes (allopolyploid), has occurred frequently during the evolutionary history of flowering plants . It is known that the polyploid genome displays dynamic changes in DNA sequences and gene expression patterns, which are caused by “genomic shock” . Bread wheat (Triticum aestivum) is a hexaploid species with a genomic constitution AABBDD that originated from three diploid ancestral species: the A genome came from T. urartu, the B genome from Aegilops speltoides or another species classified in the Sitopsis section, and the D genome from Ae. tauschii. In synthetic allopolyploid wheats, non-random and reproducible elimination of non-coding and low-copy DNA sequences was found in early generations after allopolyploidization . Furthermore, genome-wide alteration of the DNA methylation pattern was also identified . These observations indicate that genomic shock induces genetic and epigenetic changes in the polyploid wheat genome. Allopolyploidization leads to the generation of duplicated homoeologous genes (homoeologs) rather than of paralogous genes (paralogs). Consequently, the hexaploid wheat genome contains triplicated homoeologs derived from the ancestral diploid species. There are three possible evolutionary fates for homoeologs: functional diversification; gene silencing; or, retention of the original or similar function . How does genomic shock affect homoeologs? Is there any general rule regarding which homoeologs of which ancestral genome are changeable? Moreover, what is the mechanism of homoeolog-specific regulation? To answer these questions, we are studying gene structures and expression profiles of three homoeologs of MADS-box genes, as they provide a good model system of genes associated with a particular biological program, in this case floral organ formation.