He, Zhesi orcid.org/0000-0001-8335-9876, Wang, Lihong, Harper, Andrea Louise orcid.org/0000-0003-3859-1152 et al. (4 more authors) (2017) Extensive homoeologous genome exchanges in allopolyploid crops revealed by mRNAseq-based visualization. Plant biotechnology journal. pp. 594-604. ISSN 1467-7644
Abstract
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.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd. |
Keywords: | 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 |
Dates: |
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Institution: | The University of York |
Academic Units: | The University of York > Faculty of Sciences (York) > Biology (York) The University of York > Faculty of Sciences (York) > Biology (York) > Centre for Novel Agricultural Products (CNAP) (York) |
Funding Information: | Funder Grant number BBSRC (BIOTECHNOLOGY AND BIOLOGICAL SCIENCES RESEARCH COUNCIL) BB/L011751/1 BBSRC (BIOTECHNOLOGY AND BIOLOGICAL SCIENCES RESEARCH COUNCIL) BB/L027844/1 BBSRC (BIOTECHNOLOGY AND BIOLOGICAL SCIENCES RESEARCH COUNCIL) BB/L002124/1 |
Depositing User: | Pure (York) |
Date Deposited: | 01 Nov 2016 12:01 |
Last Modified: | 10 Mar 2025 00:05 |
Published Version: | https://doi.org/10.1111/pbi.12657 |
Status: | Published |
Refereed: | Yes |
Identification Number: | 10.1111/pbi.12657 |
Related URLs: | |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:106762 |
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