Homoeologous exchanges cause extensive dosage-dependent gene expression changes in an allopolyploid crop

Andrew Lloyd, Aurélien Blary, Delphine Charif, Catherine Charpentier, Joseph Tran, Sandrine Balzergue, Etienne Delannoy, Guillem Rigaill, Eric Jenczewski

Research output: Contribution to journalArticlepeer-review

51 Citations (SciVal)


Structural variation is a major source of genetic diversity and an important substrate for selection. In allopolyploids, homoeologous exchanges (i.e. between the constituent subgenomes) are a very frequent type of structural variant. However, their direct impact on gene content and gene expression had not been determined. Here, we used a tissue-specific mRNA-Seq dataset to measure the consequences of homoeologous exchanges (HE) on gene expression in Brassica napus, a representative allotetraploid crop. We demonstrate that expression changes are proportional to the change in gene copy number triggered by the HEs. Thus, when homoeologous gene pairs have unbalanced transcriptional contributions before the HE, duplication of one copy does not accurately compensate for loss of the other and combined homoeologue expression also changes. These effects are, however, mitigated over time. This study sheds light on the origins, timing and functional consequences of homeologous exchanges in allopolyploids. It demonstrates that the interplay between new structural variation and the resulting impacts on gene expression, influences allopolyploid genome evolution.
Original languageEnglish
Pages (from-to)367-377
Number of pages11
JournalNew Phytologist
Issue number1
Early online date16 Oct 2017
Publication statusPublished - 31 Jan 2018
Externally publishedYes


  • Brassica napus (Rapeseed)
  • copy number variation
  • gene expression
  • homoeologous exchanges
  • meiotic recombination
  • polyploidy


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