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

Abstract

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.

The legacy of diploid progenitors in allopolyploid gene expression patterns

“…Both of these methods can distinguish between homoeologues, but are gel-based and therefore not fully quantitative in the measurement of expression levels. At the same time, anonymous surveys of many genes were carried out using cDNA amplified fragment length polymorphism gels in, for example, Brassica [30,31], Tragopogon [29], Triticum [32,33] and Arabidopsis [34].…”

Transgene Expression and Transgene-Induced Silencing in Diploid and Autotetraploid Arabidopsis

“…Recent studies using newly formed synthetic auto-or allopolyploid plants have shown that polyploidization is associated with genome-wide changes in gene expression, and these changes appear to be controlled primarily by epigenetic mechanisms such as cytosine methylation and small RNAs (Comai et al 2000;Kashkush et al 2002;Wang et al 2004;Xu et al 2009;Yu et al 2010).…”

Genetic and epigenetic status of triple exotic consanguinity cotton introgression lines

“…Further sequencing results of the methylation polymorphism fragments confirmed that most of the DNA methylation alteration happened at the repetitive sequences or non-coding sequences. However, the movement of transposable elements induced by DNA methylation alteration played an important role in the regulation of gene expression (Jin et al, 2008;Xu et al, 2009). The potential impacts, especially methylation alternation of transposable elements should be investigated on PD0111 and PD0113.…”