The role of small RNAs in wide hybridisation and allopolyploidisation between Brassica rapa and Brassica nigra

Abstract

BackgroundAn allopolyploid formation consists of the two processes of hybridisation and chromosome doubling. Hybridisation makes a different genome combined in the same cell, and genome “shock” and instability occur during this process, whereas chromosome doubling results in doubling and reconstructing the genome dosage. Recent studies have demonstrated that small RNAs, play an important role in maintaining the genome reconstruction and stability. However, to date, little is known regarding the role of small RNAs during the process of wide hybridisation and chromosome doubling, which is essential to elucidate the mechanism of polyploidisation. Therefore, the genetic and DNA methylation alterations and changes in the siRNA and miRNA were assessed during the formation of an allodiploid and its allotetraploid between Brassica rapa and Brassica nigra in the present study.ResultsThe phenotypic analysis exhibited that the allotetraploid had high heterosis compared with their parents and the allodiploid. The methylation-sensitive amplification polymorphism (MSAP) analysis indicated that the proportion of changes in the methylation pattern of the allodiploid was significantly higher than that found in the allotetraploid, while the DNA methylation ratio was higher in the parents than the allodiploid and allotetraploid. The small RNAs results showed that the expression levels of miRNAs increased in the allodiploid and allotetraploid compared with the parents, and the expression levels of siRNAs increased and decreased compared with the parents B. rapa and B. nigra, respectively. Moreover, the percentages of miRNAs increased with an increase in the polyploidy levels, but the percentages of siRNAs and DNA methylation alterations decreased with an increase in the polyploidy levels. Furthermore, qRT-PCR analysis showed that the expression levels of the target genes were negatively corrected with the expressed miRNAs.ConclusionsThe study showed that siRNAs and DNA methylation play an important role in maintaining the genome stability in the formation of an allotetraploid. The miRNAs regulate gene expression and induce the phenotype variation, which may play an important role in the occurrence of heterosis in the allotetraploid. The findings of this study may provide new information for elucidating that the allotetraploids have a growth advantage over the parents and the allodiploids.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0272-9) contains supplementary material, which is available to authorized users.

Asymmetrical changes of gene expression, small RNAs and chromatin in two resynthesized wheat allotetraploids

“…There is a burst of siRNAs from the A subgenome in both allotetraploids, with more changes in AADD than in S l S l AA. This suggests rapid changes in siRNA regulation in wheat allotetraploids as in Arabidopsis and Brassica allopolyploids (Ha et al ., ; Ghani et al ., ). Interestingly, disruption of siRNAs in the allotetraploids is associated with expression changes of some genes and activation of various TEs in AADD, while more TEs were suppressed than activated in the other allotetraploid S l S l AA.…”

“…In Arabidopsis seeds, a group of siRNAs is maternally expressed (Mosher et al ., ); their biogenesis depends on the maternal genome dosage in the interploidy crosses, which affects seed size and gene expression (Lu et al ., ), probably via siRNA‐directed DNA methylation (RdDM) (Wassenegger et al ., ; Law and Jacobsen, ). Consistent with this siRNA regulation in Arabidopsis allotetraploids and interploidy crosses, siRNAs in TEs change rapidly in resynthesized wheat hexaploids (Kenan‐Eichler et al ., ) and Brasicca allotetraploids (Ghani et al ., ). Moreover, siRNAs in hexaploid wheat might function to suppress TEs through transcriptional and post‐transcriptional silencing, as well as RdDM (Cantu et al ., ).…”

Molecular basis underlying the successful invasion of hexaploid cytotypes ofSolidago canadensisL.: Insights from integrated gene and miRNA expression profiling

“…Analogously, the number of miRNA or miRNA families in cultivated allotetraploid cotton G. hirsutum (AADD) was markedly greater than those in its two diploid ancestors, G. raimondii (DD), and G. arboreum (AA) (Xie & Zhang, ). Ghani et al () also reported that the percentages and expression levels of miRNAs increased in allodiploid (AB) and allotetraploid (AABB) relative to the parents Brassica rapa (AA) and Brassica nigra (BB). In the present work, the number and expression levels of miRNAs in hexaploid cytotypes were greater than those in their diploids, which was consistent with the findings of the above‐mentioned studies.…”

Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes

“…A number of studies have found that transposons can be activated in newly formed polyploids (Kashkush et al, 2002(Kashkush et al, , 2003Madlung et al, 2005). There is evidence for novel or reduced expression of small interfering RNAs (siRNA) in some of these newly formed polyploids as well (Ha et al, 2009;Kenan-Eichler et al, 2011;Ghani et al, 2014;Li et al, 2014;Shen et al, 2014). There are several possible explanations for the presence of novel small RNAs in polyploids (Figure 3).…”