Extensive homoeologous genome exchanges in allopolyploid crops revealed by mRNAseq-based visualization

Zhesi He, Lihong Wang, Andrea Louise Harper, Lenka Havlickova, AK Pradhan, IAP Parkin, Ian Bancroft

Research output: Contribution to journalArticlepeer-review


Polyploidy, the possession of multiple sets of chromosomes, has been a predominant factor in the evolution and success of the angiosperms. Although artificially formed allopolyploids show a high rate of genome rearrangement, the genomes of cultivars and germplasm used for crop breeding were assumed stable and genome structural variation under the artificial selection process of commercial breeding has remained little studied. Here, we show, using a repurposed visualization method based on transcriptome sequence data, that genome structural rearrangement occurs frequently in varieties of three polyploid crops (oilseed rape, mustard rape and bread wheat), meaning that the extent of genome structural variation present in commercial crops is much higher than expected. Exchanges were found to occur most frequently where homoeologous chromosome segments are collinear to telomeres and in material produced as doubled haploids. The new insights into genome structural evolution enable us to reinterpret the results of recent studies and implicate homoeologous exchanges, not deletions, as being responsible for variation controlling important seed quality traits in rapeseed. Having begun to identify the extent of genome structural variation in polyploid crops, we can envisage new strategies for the global challenge of broadening crop genetic diversity and accelerating adaptation, such as the molecular identification and selection of genome deletions or duplications encompassing genes with trait-controlling dosage effects.

Original languageEnglish
Pages (from-to)594-604
Number of pages11
JournalPlant biotechnology journal
Issue number5
Early online date3 Nov 2016
Publication statusPublished - 1 May 2017

Bibliographical note

© 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.


  • crop genomes
  • genome structural evolution
  • mRNAseq
  • Brassica napus/genetics
  • Polyploidy
  • Crops, Agricultural/genetics
  • Triticum/genetics
  • Genome, Plant
  • Computational Biology/methods
  • RNA, Messenger
  • Brassica rapa/genetics
  • Sequence Analysis, RNA/methods

Cite this