DNA Methylation in Genomes of Several Annual Herbaceous and Woody Perennial Plants of Varying Ploidy as Detected by MSAP

Plant Molecular Biology Reporter

Volumn 29, Issue 4, 2011, Pages 784-793

  Li, Ai ^a   Hu, Bao Quan ^a   Xue, Zhen Yi ^a   Chen, Li ^a   Wang, Wei Xing ^b   Song, Wen Qin ^a   Chen, Cheng Bin ^a   Wang, Chun Guo ^a  

^a NANKAI UNIVERSITY   (China)

^b Faculty of Food Science   (China)

Author keywords

Annual herbaceous plants; DNA methylation; MSAP; Polyploidization; Woody perennial

Indexed keywords

CITRULLUS LANATUS VAR. LANATUS; EMBRYOPHYTA; ERIOBOTRYA JAPONICA; PYRUS; SALVIA;

EID: 80255140514     PISSN: 07359640     EISSN: 15729818     Source Type: Journal    
DOI: 10.1007/s11105-010-0280-3     Document Type: Article

References (62)

1. Adams KL, Wendel JF (2005) Polyploidy and genome evolution in plants. Curr Opin Plant Biol 8: 135-141.
2. Adams KL, Cronn R, Percifield R, Wendel JF (2003) Genes duplicated by polyploidy show unequal contributions to the transcriptome and organspecific reciprocal silencing. Proc Natl Acad Sci 100: 4649-4654.
3. Adams KL, Percifield R, Wendel JF (2004) Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid. Genetics 168: 2217-2226.
4. Albertin W, Brabant P, Catrice O, Eber F, Jenczewski E, Chèvre AM, Thiellement H (2005) Autopolyploidy in cabbage (Brassica oleracea L.) does not alter significantly the proteomes of green tissues. Proteomics 5: 2131-2139.
5. Auger DL, Gray AD, Ream TS, Kato A, Jrcoe EH, Birchler JA (2005) Nonadditive gene expression in diploid and triploid hybrids of maize. Genetics 169: 389-397.
6. Bhojwani SS, Razdan MK (1996) Plant tissue culture: theory and practice, a revised edition. Elsevier: Amsterdam pp 1-766.
7. Blanc G, Barakat A, Guyot R, Cooke R, Delseny M (2000) Extensive duplication and reshuffling in the Arabidopsis genome. Plant Cell 12: 1093-1101.
8. Cao X, Jacobsen SE (2002) Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr Biol 12: 1138-1144.
9. Carvalho A, Polanco C, Lima-Brito J, Guedes-Pinto H (2010) Differential rRNA genes expression in hexaploid wheat related to NOR methylation. Plant Mol Biol Rep 28: 403-412.
10. Chen ZJ (2007) Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annu Rev Plant Biol 58: 377-406.
11. Chen L, Chen J (2008) Changes of cytosine methylation induced by wide hybridization and allopolyploidy in Cucumis. Genome 51: 789-799.
12. Cuozzo C, Porcellii A, Angrisano T et al (2007) DNA damage, homology directed repair, and DNA methylation. PLoS Genet 3: 110.
13. Demetriou K, Kapazoglou A, Bladenopoulos K, Tsaftaris AS (2010) Epigenetic chromatin modifiers in barley: II. Characterization and expression analysis of the HDA1 family of barley histone deacetylases during development and in response to jasmonic acid. Plant Mol Biol Rep 28: 9-21.
14. Diéguez MJ, Bellotto M, Afsar K, Mittelsten SO, Paszkowski J (1997) Methylation of cytosines in nonconventional methylation acceptor sites can contribute to reduced gene expression. Mol Gen Genet 253: 581-588.
15. Fiuk A, Bednarek PT, Rybczyński JJ (2010) Flow Cytometry, HPLC-RP, and metAFLP analyses to assess genetic variability in somatic embryo-derived plantlets of Gentiana pannonica Scop. Plant Mol Biol Rep 28: 413-420.
16. Fortune PM, Schierenbeck KA, Ainouche AK, Jacquemin J, Wendel JF, Ainouche ML (2007) Evolutionary dynamics of Waxy and the origin of hexaploid Spartina species (Poaceae). Mol Phylogenet Evol 43: 1040-1055.
17. 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: 3403-3417.
18. Gaut BS, Doebley JF (1997) DNA sequence evidence for the segmental allopolyploid origin of maize. Proc Natl Acad Sci 94: 6808-6814.
19. Guo M, Davis D, Birchler JA (1996) Dosage effects on gene expression in a maize ploidy series. Genetics 142: 1349-1355.
20. Hamada S (1963) Polyploid mulberry tree in practice. Indian J Ser 1: 3-4.
21. Han FP, Fedak G, Ouellet T, Liu B (2003) Rapid genomic changes in interspecific and intergenetic hybrids and allopolyploids of Triticeae. Genome 46: 716-723.
22. Hegarty MJ, Hiscock S (2007) Polyploidy: doubling up for evolutionary success. Curr Biol 17: 927-929.
23. Hilu KW (1993) Polyploidy and the evolution of domesticated plants. Am J Bot 80: 1494-1499.
24. Kashkush K, Feldman M, Levy AA (2002) Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics 160: 1651-1659.
25. Keyte AL, Percifield R, Liu B, Wendel JF (2006) Intraspecific DNA methylation polymorphism in cotton (Gossypium hirsutum L.). J Hered 97: 444-450.
26. Lagercrantz U, Lydiate D (1996) Comparative genome mapping in Brassica. Genetics 144: 1903-1910.
27. Lee HS, Chen ZJ (2001) Protein-coding genes are epigenetically regulated in Arabidopsis polyploids. Proc Natl Acad Sci 98: 6753-6758.
28. Levy AA, Feldman M (2004) Genetic and epigenetic reprogramming of the wheat genome upon allopolyploidization. Biol J Linn Soc Lond 82: 607-613.
29. Liu B, Wendel JF (2002) Non-mendelian phenomena in allopolyploid genome evolution. Curr Genomics 3: 489-505.
30. Liu B, Wendel JF (2003) Epigenetic phenomena and the evolution of plant allopolyploids. Mol Phylogenet Evol 29: 365-379.
31. Liu B, Brubaker CL, Mergeai G, Cronn RC, Wendel JF (2001) Polyploid formation in cotton is not accompanied by rapid genomic changes. Genome 44: 321-330.
32. Lu BB, Pan XZ, Zhang L, Huang BB (2006) A genome-wide comparison of genes responsive to autopolyploidy in Isatis indigotica using Arabidopsis thaliana Affymetrix Genechips. Plant Mol Biol Rep 24: 197-204.
33. 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: 336-348.
34. 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: 733-746.
35. Martienssen RA, Colot V (2001) DNA methylation and epigenetic inheritance in plants and filamentous fungi. Science 293: 1070-1073.
36. Masterson J (1994) Stomatal size in fossil plants: evidence for polyploid in majority of angiosperms. Science 264: 421-424.
37. McClintock B (1984) The significance of responses of the genome to challenge. Science 226: 792-801.
38. Murray MG, Thompson WF (1980) Rapid isolation of high-weight plant DNA. Nucleic Acids Res 8: 4231-4235.
39. 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: 141-147.
40. Pires JC, Zhao JW, Schranz ME, Quijada PA, Lukens LN, Osborn TC (2004) Flowering time divergence and genomic rearrangements in resynthesized polyploids (Brassica). Biol J Linn Soc Lond 82: 675-688.
41. Pontes O, Neves N, Silva M, Lewis MS, Madlung A, Comai L, Viegas W, Pikaard CS (2004) Chromosomal locus rearrangements are a rapid response to formation of the allotetraploid Arabidopsis suecica genome. Proc Natl Acad Sci 101: 18240-18245.
42. Portis E, Acquadro A, Comino C et al (2004) Analysis of DNA methylation during germination of peper (Capsicum annuum L.) seeds using methylation-sensitive amplification polymorphism (MSAP). Plant Sci 166: 169-178.
43. Rayburn AL, Crawford J, Rayburn CM, Juvik JA (2009) Genome size of three Miscanthus species. Plant Mol Biol Rep 27: 184-188.
44. Salmon A, Ainouche ML, Wendel JF (2005) Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae). Mol Ecol 14: 1163-1175.
45. 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: 1749-1759.
46. Shoemaker RC, Polzin K, Labate J, Specht J, Brummer EC, Olson T, Young N, Concibido V, Wilcox J, Tamulonis JP, Kochert G, Boerma HR (1996) Gemome duplication in soybean (Glycine subgenus soja). Genetics 144: 329-338.
47. Soltis DE, Soltis PS, Tate JA (2004) Advances in the study of polyploidy since plant speciation. New Phytol 161: 173-191.
48. 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 92: 7719-7723.
49. Spring J (1997) Vertebrate evolution by interspecific hybridization: are we polyploid? FEBS Lett 400: 2-8.
50. Sreekumari MT, Jos JS, Nair SG (1999) 'Sree Harsha': a superior triploid hybrid in cassava. Euphytica 106: 1-6.
51. Stupar RM, Bhaskar PB, Yandell BS, Rensink WA, Hart AL, Ouyang S, Veilleux RE, Busse JS, Erhardt RJ, Buell CR, Jiang J (2007) Phenotypic and transcriptomic changes associated with potato autopolyploidization. Genetics 176: 2055-2067.
52. Swapna M, Sivaraju K, Sharma RK, Singh NK, Mohapatra T (2010) Single-strand conformational polymorphism of EST-SSRs: a potential tool for diversity analysis and varietal identification in sugarcane. Plant Mol Biol Rep. doi: 10. 1007/s11105-010-0254-5.
53. Thomas TD, Bhatnagar AK, Bhojwani SS (2000) Production of triploid plants of mulberry (Morus alba L.) by endosperm culture. Plant Cell Rep 19: 395-399.
54. 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: 967-979.
55. Urdampilleta JD, Ferrucci MS, Torezan JMD, Vanzela ALL (2006) Karyotype relationships among four South American species of Urvillea (Sapindaceae: Paullinieae). Pl Syst Evol 258: 85-95.
56. Wada Y, Miyamoto K, Kusano T, Sano H (2004) Association between up-regulation of stress-responsive genes and hypomethylation of genomic DNA in tobacco plants. Mol Gen Genomics 271: 658-666.
57. 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 expession in Arabidopsis polyploids. Genetics 167: 1961-1973.
58. 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: 507-517.
59. Wolfe KH, Shields DC (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387: 708-713.
60. Xiong LZ, Xu CG (1999) Patterns of cytosine methylation in an elite rice hybrid and its parentallines, detected by a methylation-sensitive amplication polymorphism technique. Mol Gen Genet 261: 439-446.
61. Zhang HY, Peng H, Li Y, Xu PZ, Wang XD, Wu XJ (2006) Analysis of DNA cytosine methylation between haploid and its corresponding diploid rice. Chin Sci Bull 51: 1529-1535.
62. Zhao XX, Chai Y, Liu B (2007) Epigenetic inheritance and variation of DNA methylation level and pattern in maize intra-specific hybrids. Plant Sci 172: 930-938.