Rapid alterations of gene expression and cytosine methylation in newly synthesized Brassica napus allopolyploids

Allopolyploidy is an important speciation mechanism and is ubiquitous among plants. Brassica napus is a model system for studying the consequences of hybridization and polyploidization on allopolyploid genome. In this research, two sets of plant materials were used to investigate the transcriptomic and epigenetic changes in the early stages of allopolyploid formation. The first comparison was between a synthetic B. napus allotetraploid and its diploid progenitors, B. rapa (AA genome) and B. oleracea (CC genome). Using cDNA-amplified fragment length polymorphism (cDNA-AFLP) and methylation-sensitive amplification polymorphism (MSAP) approaches, 4.09 and 6.84% of the sequences showed changes in gene expression and DNA methylation in synthesized B. napus compared to its diploid progenitors. The proportions of C-genome-specific gene silencing and DNA methylation alterations were significantly greater than those of A-genome-specific alterations. The second comparison was between amphihaploid and amphidiploid B. napus organs grown on synthesized dimorphic plants. About 0.73% of the cDNA-AFLP fragments and 1.94% of the MSAP fragments showed changes in gene expression and DNA methylation. We sequenced 103 fragments that differed in the synthetic/parental or the amphihaploid/amphidiploid cDNA-AFLP and MSAP comparisons. Sequence analysis revealed these fragments were involved in various biological pathways. Our results provided evidence for genome-wide changes in gene expression and DNA methylation occurring immediately after hybridization and polyploidization in synthetic B. napus. Moreover, this study contributed to the elucidation of genome doubling effects on responses of transcriptome and epigenetics in B. napus.