Assessing the Response of Small RNA Populations to Allopolyploidy Using Resynthesized Brassica napus Allotetraploids

Paulina Martinez Palacios, Marie-Pierre Jacquemot, Marion Tapie, Agnès Rousselet, Mamoudou Diop, Carine Remoué, Matthieu Falque, Andrew H Lloyd, Eric Jenczewski, Gilles Lassalle, Anne-Marie Chévre, Christine Lelandais, Martin Crespi, Philippe Brabant, Johann Joets, Karine Alix

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Allopolyploidy, combining interspecific hybridization with whole genome duplication, has had significant impact on plant evolution. Its evolutionary success is related to the rapid and profound genome reorganizations that allow neoallopolyploids to form and adapt. Nevertheless, how neoallopolyploid genomes adapt to regulate their expression remains poorly understood. The hypothesis of a major role for small noncoding RNAs (sRNAs) in mediating the transcriptional response of neoallopolyploid genomes has progressively emerged. Generally, 21-nt sRNAs mediate posttranscriptional gene silencing by mRNA cleavage, whereas 24-nt sRNAs repress transcription (transcriptional gene silencing) through epigenetic modifications. Here, we characterize the global response of sRNAs to allopolyploidy in Brassica, using three independently resynthesized Brassica napus allotetraploids originating from crosses between diploid Brassica oleracea and Brassica rapa accessions, surveyed at two different generations in comparison with their diploid progenitors. Our results suggest an immediate but transient response of specific sRNA populations to allopolyploidy. These sRNA populations mainly target noncoding components of the genome but also target the transcriptional regulation of genes involved in response to stresses and in metabolism; this suggests a broad role in adapting to allopolyploidy. We finally identify the early accumulation of both 21- and 24-nt sRNAs involved in regulating the same targets, supporting a posttranscriptional gene silencing to transcriptional gene silencing shift at the first stages of the neoallopolyploid formation. We propose that reorganization of sRNA production is an early response to allopolyploidy in order to control the transcriptional reactivation of various noncoding elements and stress-related genes, thus ensuring genome stability during the first steps of neoallopolyploid formation.

Original languageEnglish
Pages (from-to)709-726
Number of pages18
JournalMolecular Biology and Evolution
Issue number4
Early online date17 Jan 2019
Publication statusPublished - 01 Apr 2019
Externally publishedYes


  • Brassica napus/genetics
  • DNA Transposable Elements
  • Genetic Speciation
  • RNA, Small Untranslated/metabolism
  • Tetraploidy
  • allopolyploidy
  • small noncoding RNAs
  • transposable elements
  • Brassica
  • resynthesized oilseed rapes
  • regulation of gene expression
  • Small noncoding RNAs
  • Resynthesized oilseed rapes
  • Regulation of gene expression
  • Allopolyploidy
  • Transposable elements


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