Advertisement

Planta

, Volume 229, Issue 3, pp 471–483 | Cite as

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

  • Yanhao Xu
  • Lan Zhong
  • Xiaoming Wu
  • Xiaoping Fang
  • Jianbo Wang
Original Article

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.

Keywords

Allopolyploid Brassica DNA methylation Genome doubling Gene silencing Hybridization 

Abbreviations

AFLP

Amplified fragment length polymorphism

CTAB

Cetyltrimethylammonium bromide

MSAP

Methylation-sensitive amplification polymorphism

PCR

Polymerase chain reaction

RFLP

Restriction fragment length polymorphism

Notes

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.

Supplementary material

425_2008_844_MOESM1_ESM.doc (170 kb)
Electronic supplementary material (DOC 170 kb)

References

  1. Adams KL, Cronn R, Percifield R, Wendel JF (2003) Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proc Natl Acad Sci USA 100:4649–4654PubMedCrossRefGoogle Scholar
  2. Adams KL, Percifield R, Wendel JF (2004) Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid. Genetics 168:2217–2226PubMedCrossRefGoogle Scholar
  3. Albertin W, Balliau T, Brabant P, Chevre AM, Eber F, Malosse C, Thiellement H (2006) Numerous and rapid nonstochastic modifications of gene products in newly synthesized Brassica napus allotetraploids. Genetics 173:1101–1113PubMedCrossRefGoogle Scholar
  4. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402PubMedCrossRefGoogle Scholar
  5. Bachem CWB, van der Hoeven RS, de Bruijn SM, Vreugdenhil D, Zabeau M, Visser RGF (1996) Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP: analysis of gene expression during potato tuber development. Plant J 9:745–753PubMedCrossRefGoogle Scholar
  6. Blanc G, Wolfe KH (2004) Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16:1667–1678PubMedCrossRefGoogle Scholar
  7. Chen ZJ (2007) Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annu Rev Plant Biol 58:377–406PubMedCrossRefGoogle Scholar
  8. Chen L, Lou Q, Zhuang Y, Chen J, Zhang X, Wolukau JN (2007) Cytological diploidization and rapid genome changes of the newly synthesized allotetraploids Cucumis × hytivus. Planta 225:603–614PubMedCrossRefGoogle Scholar
  9. Comai L, Tyagi AP, Winter K, Holmes-Davis R, Reynolds SH, Stevens Y, Byers B (2000) Phenotypic instability and rapid gene silencing in newly formed Arabidopsis allotetraploids. Plant Cell 12:1551–1568PubMedCrossRefGoogle Scholar
  10. Gaeta RT, Pires JC, Iniguez-Luy F, Leon E, Osborn TC (2007) Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. Plant Cell 19:3403–3417PubMedCrossRefGoogle Scholar
  11. He P, Friebe BR, Gill BS, Zhou JM (2003) Allopolyploidy alters gene expression in the highly stable hexaploid wheat. Plant Mol Biol 52:401–414PubMedCrossRefGoogle Scholar
  12. Hegarty MJ, Hiscock S (2007) Polyploidy: doubling up for evolutionary success. Curr Biol 17:R927–R929PubMedCrossRefGoogle Scholar
  13. Hegarty MJ, Jones JM, Wilson ID, Barker GL, Coghill JA, Sanchez-Baracaldo P, Liu G, Buggs RJA, Abbott RJ, Edwards KJ (2005) Development of anonymous cDNA microarrays to study changes to the Senecio floral transcriptome during hybrid speciation. Mol Ecol 14:2493–2510PubMedCrossRefGoogle Scholar
  14. Hegarty MJ, Barker GL, Wilson ID, Abbott RJ, Edwards KJ, Hiscock SJ (2006) Transcriptome shock after interspecific hybridization in Senecio is ameliorated by genome duplication. Curr Biol 16:1652–1659PubMedCrossRefGoogle Scholar
  15. Kashkush K, Feldman M, Levy AA (2002) Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics 160:1651–1659PubMedGoogle Scholar
  16. Kashkush K, Feldman M, Levy AA (2003) Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nat Genet 33:102–106PubMedCrossRefGoogle Scholar
  17. Lee HS, Chen ZJ (2001) Protein-coding genes are epigenetically regulated in Arabidopsis polyploids. Proc Natl Acad Sci USA 98:6753–6758PubMedCrossRefGoogle Scholar
  18. Leitch IJ, Bennett MD (1997) Polyploidy in angiosperms. Trends Plant Sci 2:470–476CrossRefGoogle Scholar
  19. Liu HT, Guan PC (1998) Studies on the taxonomy of Chinese kale (B. alboglabra). J South China Agric Univ 19:82–86Google Scholar
  20. Liu B, Wendel JF (2003) Epigenetic phenomena and the evolution of plant allopolyploids. Mol Phylogenet Evol 29:365–379PubMedCrossRefGoogle Scholar
  21. Liu B, Brubaker CL, Mergeai G, Cronn RC, Wendel JF (2001) Polyploid formation in cotton is not accompanied by rapid genomic changes. Genome 44:321–330PubMedCrossRefGoogle Scholar
  22. Lukens LN, Pires JC, Leon E, Vogelzang R, Oslach L, Osborn T (2006) Patterns of sequence loss and cytosine methylation within a population of newly resynthesized Brassica napus allopolyploids. Plant Physiol 140:336–348PubMedCrossRefGoogle Scholar
  23. Madlung A, Masuelli RW, Watson B, Reynolds SH, Davison J, Comai L (2002) Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiol 129:733–746PubMedCrossRefGoogle Scholar
  24. Madlung A, Tyagi AP, Watson B, Jiang H, Kagochi T, Doerge RW, Martienssen R, Comai L (2005) Genomic changes in synthetic Arabidopsis polyploids. Plant J 41:221–230PubMedCrossRefGoogle Scholar
  25. Masterson J (1994) Stomatal size in fossil plants: evidence for polyploidy in majority of angiosperms. Science 264:421–424PubMedCrossRefGoogle Scholar
  26. Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4325PubMedCrossRefGoogle Scholar
  27. Osborn TC, Pires JC, Birchler JA, Auger DL, Chen ZJ, Lee HS, Comai L, Madlung A, Doerge RW, Colot V, Martienssen RA (2003) Understanding mechanisms of novel gene expression in polyploids. Trends Genet 19:141–147PubMedCrossRefGoogle Scholar
  28. Pires JC, Zhao J, Schranz ME, Leon EJ, Quijada PA, Lukens LN, Osborn TC (2004) Flowering time divergence and genomic rearrangements in resynthesized Brassica polyploids (Brassicaceae). Biol J Linn Soc Lond 82:675–688CrossRefGoogle Scholar
  29. Portis E, Acquadro A, Comino C, Lanteri S (2004) Analysis of DNA methylation during germination of pepper (Capsicum annuum L.) seeds using methylation-sensitive amplification polymorphism (MSAP). Plant Sci 166:169–178CrossRefGoogle Scholar
  30. Roberts RJ, Vincze T, Posfai J, Macelis D (2007) REBASE—enzymes and genes for DNA restriction and modification. Nucleic Acids Res 35:D269–D270PubMedCrossRefGoogle Scholar
  31. Salmon A, Ainouche ML, Wendel JF (2005) Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae). Mol Ecol 14:1163–1175PubMedCrossRefGoogle Scholar
  32. Sambrook J, Fritsch EF, Maniatis T (2001) Molecular cloning: a laboratory manual, 3rd edn edn. Cold Spring Harbor Laboratory Press, Cold Spring HarborGoogle Scholar
  33. Semon M, Wolfe KH (2007) Consequences of genome duplication. Curr Opin Genet Dev 17:505–512PubMedCrossRefGoogle Scholar
  34. Shaked H, Kashkush K, Ozkan H, Feldman M, Levy AA (2001) Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell 13:1749–1759PubMedCrossRefGoogle Scholar
  35. Soltis DE, Soltis PS (2000) The role of genetic and genomic attributes in the success of polyploids. Proc Natl Acad Sci USA 97:7051–7057PubMedCrossRefGoogle Scholar
  36. Song K, Lu P, Tang K, Osborn TC (1995) Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. Proc Natl Acad Sci USA 92:7719–7723PubMedCrossRefGoogle Scholar
  37. Tate JA, Ni Z, Scheen AC, Koh J, Gilbert CA, Lefkowitz D, Chen ZJ, Soltis PS, Soltis DE (2006) Evolution and expression of homeologous loci in Tragopogon miscellus (Asteraceae), a recent and reciprocally formed allopolyploid. Genetics 173:1599–1611PubMedCrossRefGoogle Scholar
  38. Udall JA, Quijada PA, Osborn TC (2005) Detection of chromosomal rearrangements derived from homeologous recombination in four mapping populations of Brassica napus L. Genetics 169:967–979PubMedCrossRefGoogle Scholar
  39. Wang J, Tian L, Madlung A, Lee HS, Chen M, Lee JJ, Watson B, Kagochi T, Comai L, Chen ZJ (2004) Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids. Genetics 167:1961–1973PubMedCrossRefGoogle Scholar
  40. Wang J, Tian L, Lee HS, Wei NE, Jiang H, Watson B, Madlung A, Osborn TC, Doerge RW, Comai L, Chen ZJ (2006) Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics 172:507–517PubMedCrossRefGoogle Scholar
  41. Wendel JF (2000) Genome evolution in polyploids. Plant Mol Biol 42:225–249PubMedCrossRefGoogle Scholar
  42. Xiong LZ, Xu CG, Saghai Maroof MA, Zhang Q (1999) Patterns of cytosine methylation in an elite rice hybrid and its parental lines, detected by a methylation-sensitive amplification polymorphism technique. Mol Gen Genet 261:439–446PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Yanhao Xu
    • 1
  • Lan Zhong
    • 1
  • Xiaoming Wu
    • 2
  • Xiaoping Fang
    • 2
  • Jianbo Wang
    • 1
  1. 1.Key Laboratory of the MOE for Plant Developmental Biology, College of Life SciencesWuhan UniversityWuhanChina
  2. 2.Key Laboratory of Oil Crops Genetic Improvement of the Ministry of Agriculture, Oil Crops Research InstituteCAASWuhanChina

Personalised recommendations