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Rapid alterations of gene expression and cytosine methylation in newly synthesized Brassica napus allopolyploids

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Abstract

Allopolyploidy is an important speciation mechanism and is ubiquitous among plants. Brassica napus is a model system for studying the consequences of hybridization and polyploidization on allopolyploid genome. In this research, two sets of plant materials were used to investigate the transcriptomic and epigenetic changes in the early stages of allopolyploid formation. The first comparison was between a synthetic B. napus allotetraploid and its diploid progenitors, B. rapa (AA genome) and B. oleracea (CC genome). Using cDNA-amplified fragment length polymorphism (cDNA-AFLP) and methylation-sensitive amplification polymorphism (MSAP) approaches, ~4.09 and 6.84% of the sequences showed changes in gene expression and DNA methylation in synthesized B. napus compared to its diploid progenitors. The proportions of C-genome-specific gene silencing and DNA methylation alterations were significantly greater than those of A-genome-specific alterations. The second comparison was between amphihaploid and amphidiploid B. napus organs grown on synthesized dimorphic plants. About 0.73% of the cDNA-AFLP fragments and 1.94% of the MSAP fragments showed changes in gene expression and DNA methylation. We sequenced 103 fragments that differed in the synthetic/parental or the amphihaploid/amphidiploid cDNA-AFLP and MSAP comparisons. Sequence analysis revealed these fragments were involved in various biological pathways. Our results provided evidence for genome-wide changes in gene expression and DNA methylation occurring immediately after hybridization and polyploidization in synthetic B. napus. Moreover, this study contributed to the elucidation of genome doubling effects on responses of transcriptome and epigenetics in B. napus.

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Abbreviations

AFLP:

Amplified fragment length polymorphism

CTAB:

Cetyltrimethylammonium bromide

MSAP:

Methylation-sensitive amplification polymorphism

PCR:

Polymerase chain reaction

RFLP:

Restriction fragment length polymorphism

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Acknowledgments

We are grateful to the two anonymous reviewers for critical reading and constructive suggestions on improving the quality of this manuscript. This work was carried out with the financial support from the National Natural Science Foundation of China (No. 30570112, 30521004) and PCSIRT.

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Authors and Affiliations

  1. Key Laboratory of the MOE for Plant Developmental Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, China

    Yanhao Xu, Lan Zhong & Jianbo Wang

  2. Key Laboratory of Oil Crops Genetic Improvement of the Ministry of Agriculture, Oil Crops Research Institute, CAAS, Wuhan, 430062, China

    Xiaoming Wu & Xiaoping Fang

Authors
  1. Yanhao Xu
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  2. Lan Zhong
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  3. Xiaoming Wu
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  4. Xiaoping Fang
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  5. Jianbo Wang
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Correspondence to Jianbo Wang.

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Xu, Y., Zhong, L., Wu, X. et al. Rapid alterations of gene expression and cytosine methylation in newly synthesized Brassica napus allopolyploids. Planta 229, 471–483 (2009). https://doi.org/10.1007/s00425-008-0844-8

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