Analysis of allopolyploidy-induced rapid genetic and epigenetic changes and their relationship in wheat

We used the conventional and methylation-sensitive randomly amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) analyses to assess genome-wide changes and explore the relationships between genetic and epigenetic variations among individuals of a newly synthesized allohexaploid wheat line whose genomic constitution is identical to that of the natural common wheat, compared with its parent plants and a natural counterpart named Chinese Spring. We found rapid, extensive, and predominantly consistent non-Mendelian changes in the form of genetic and DNA methylation variations in the allohexaploid individuals. Specifically, at least 30-40% of the epigenetic component was truly independent of genetic changes, which answered a critical question, i.e. its autonomy in relation to the genetic context. Striking correlations were detected between genetic and epigenetic changes. Interestingly, as previously reported, the paternally donated nuclear genomes showed more genetic changes than the maternally donated ones; the loss of paternal bands was significantly correlated with the hypomethylation of CG or CHG sequences, suggesting an unknown link between genetic instability and hypomethylation. Sequence analysis indicated that most variations occurred in the cellular genes and sequences related to transposable elements. Based on these findings, the possible mechanisms and effects of the genomic changes in allopolyploid speciation and evolution were discussed.