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

Planta

Volumn 229, Issue 3, 2009, Pages 471-483

  Xu, Yanhao ^a   Zhong, Lan ^a   Wu, Xiaoming ^b   Fang, Xiaoping ^b   Wang, Jianbo ^a  

^a WUHAN UNIVERSITY   (China)

^b AGRO ENVIRONMENTAL PROTECTION INSTITUTE   (China)

Author keywords

Allopolyploid; Brassica; DNA methylation; Gene silencing; Genome doubling; Hybridization

Indexed keywords

CYTOSINE;

ARTICLE; COMPARATIVE STUDY; DNA METHYLATION; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; HYBRIDIZATION; METABOLISM; METHYLATION; PLANT GENOME; POLYPLOIDY; RAPESEED;

BRASSICA NAPUS; CYTOSINE; DNA METHYLATION; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; HYBRIDIZATION, GENETIC; METHYLATION; POLYPLOIDY;

BRASSICA; BRASSICA NAPUS; BRASSICA OLERACEA; BRASSICA RAPA;

EID: 59449095429     PISSN: 00320935     EISSN: 14322048     Source Type: Journal    
DOI: 10.1007/s00425-008-0844-8     Document Type: Article

References (42)

1. KL Adams R Cronn R Percifield JF Wendel 2003 Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing Proc Natl Acad Sci USA 100 4649 4654
2. KL Adams R Percifield JF Wendel 2004 Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid Genetics 168 2217 2226
3. W Albertin T Balliau P Brabant AM Chevre F Eber C Malosse H Thiellement 2006 Numerous and rapid nonstochastic modifications of gene products in newly synthesized Brassica napus allotetraploids Genetics 173 1101 1113
4. SF Altschul TL Madden AA Schaffer J Zhang Z Zhang W Miller DJ Lipman 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res 25 3389 3402
5. CWB Bachem RS van der Hoeven SM de Bruijn D Vreugdenhil M Zabeau RGF Visser 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 9 745 753
6. G Blanc KH Wolfe 2004 Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes Plant Cell 16 1667 1678
7. ZJ Chen 2007 Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids Annu Rev Plant Biol 58 377 406
8. L Chen Q Lou Y Zhuang J Chen X Zhang JN Wolukau 2007 Cytological diploidization and rapid genome changes of the newly synthesized allotetraploids Cucumis × hytivus Planta 225 603 614
9. L Comai AP Tyagi K Winter R Holmes-Davis SH Reynolds Y Stevens B Byers 2000 Phenotypic instability and rapid gene silencing in newly formed Arabidopsis allotetraploids Plant Cell 12 1551 1568
10. RT Gaeta JC Pires F Iniguez-Luy E Leon TC Osborn 2007 Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype Plant Cell 19 3403 3417
11. P He BR Friebe BS Gill JM Zhou 2003 Allopolyploidy alters gene expression in the highly stable hexaploid wheat Plant Mol Biol 52 401 414
12. MJ Hegarty S Hiscock 2007 Polyploidy: doubling up for evolutionary success Curr Biol 17 R927 R929
13. MJ Hegarty JM Jones ID Wilson GL Barker JA Coghill P Sanchez-Baracaldo G Liu RJA Buggs RJ Abbott KJ Edwards 2005 Development of anonymous cDNA microarrays to study changes to the Senecio floral transcriptome during hybrid speciation Mol Ecol 14 2493 2510
14. MJ Hegarty GL Barker ID Wilson RJ Abbott KJ Edwards SJ Hiscock 2006 Transcriptome shock after interspecific hybridization in Senecio is ameliorated by genome duplication Curr Biol 16 1652 1659
15. K Kashkush M Feldman AA Levy 2002 Gene loss, silencing and activation in a newly synthesized wheat allotetraploid Genetics 160 1651 1659
16. K Kashkush M Feldman AA Levy 2003 Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat Nat Genet 33 102 106
17. HS Lee ZJ Chen 2001 Protein-coding genes are epigenetically regulated in Arabidopsis polyploids Proc Natl Acad Sci USA 98 6753 6758
18. IJ Leitch MD Bennett 1997 Polyploidy in angiosperms Trends Plant Sci 2 470 476
19. HT Liu PC Guan 1998 Studies on the taxonomy of Chinese kale (B. alboglabra) J South China Agric Univ 19 82 86
20. B Liu JF Wendel 2003 Epigenetic phenomena and the evolution of plant allopolyploids Mol Phylogenet Evol 29 365 379
21. B Liu CL Brubaker G Mergeai RC Cronn JF Wendel 2001 Polyploid formation in cotton is not accompanied by rapid genomic changes Genome 44 321 330
22. LN Lukens JC Pires E Leon R Vogelzang L Oslach T Osborn 2006 Patterns of sequence loss and cytosine methylation within a population of newly resynthesized Brassica napus allopolyploids Plant Physiol 140 336 348
23. A Madlung RW Masuelli B Watson SH Reynolds J Davison L Comai 2002 Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids Plant Physiol 129 733 746
24. A Madlung AP Tyagi B Watson H Jiang T Kagochi RW Doerge R Martienssen L Comai 2005 Genomic changes in synthetic Arabidopsis polyploids Plant J 41 221 230
25. J Masterson 1994 Stomatal size in fossil plants: evidence for polyploidy in majority of angiosperms Science 264 421 424
26. MG Murray WF Thompson 1980 Rapid isolation of high molecular weight plant DNA Nucleic Acids Res 8 4321 4325
27. TC Osborn JC Pires JA Birchler DL Auger ZJ Chen HS Lee L Comai A Madlung RW Doerge V Colot RA Martienssen 2003 Understanding mechanisms of novel gene expression in polyploids Trends Genet 19 141 147
28. JC Pires J Zhao ME Schranz EJ Leon PA Quijada LN Lukens TC Osborn 2004 Flowering time divergence and genomic rearrangements in resynthesized Brassica polyploids (Brassicaceae) Biol J Linn Soc Lond 82 675 688
29. E Portis A Acquadro C Comino S Lanteri 2004 Analysis of DNA methylation during germination of pepper (Capsicum annuum L.) seeds using methylation-sensitive amplification polymorphism (MSAP) Plant Sci 166 169 178
30. RJ Roberts T Vincze J Posfai D Macelis 2007 REBASE-enzymes and genes for DNA restriction and modification Nucleic Acids Res 35 D269 D270
31. A Salmon ML Ainouche JF Wendel 2005 Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae) Mol Ecol 14 1163 1175
32. Sambrook J, Fritsch EF, Maniatis T (2001) Molecular cloning: a laboratory manual, 3rd edn edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor
33. M Semon KH Wolfe 2007 Consequences of genome duplication Curr Opin Genet Dev 17 505 512
34. H Shaked K Kashkush H Ozkan M Feldman AA Levy 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 1759
35. DE Soltis PS Soltis 2000 The role of genetic and genomic attributes in the success of polyploids Proc Natl Acad Sci USA 97 7051 7057
36. K Song P Lu K Tang TC Osborn 1995 Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution Proc Natl Acad Sci USA 92 7719 7723
37. JA Tate Z Ni AC Scheen J Koh CA Gilbert D Lefkowitz ZJ Chen PS Soltis DE Soltis 2006 Evolution and expression of homeologous loci in Tragopogon miscellus (Asteraceae), a recent and reciprocally formed allopolyploid Genetics 173 1599 1611
38. JA Udall PA Quijada TC Osborn 2005 Detection of chromosomal rearrangements derived from homeologous recombination in four mapping populations of Brassica napus L Genetics 169 967 979
39. J Wang L Tian A Madlung HS Lee M Chen JJ Lee B Watson T Kagochi L Comai ZJ Chen 2004 Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids Genetics 167 1961 1973
40. J Wang L Tian HS Lee NE Wei H Jiang B Watson A Madlung TC Osborn RW Doerge L Comai ZJ Chen 2006 Genomewide nonadditive gene regulation in Arabidopsis allotetraploids Genetics 172 507 517
41. JF Wendel 2000 Genome evolution in polyploids Plant Mol Biol 42 225 249
42. LZ Xiong CG Xu MA Saghai Maroof Q Zhang 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 261 439 446