Tissue culture-induced locus-specific alteration in DNA methylation and its correlation with genetic variation in Codonopsis lanceolata Benth. et Hook. f

Plant Cell Reports

Volumn 26, Issue 8, 2007, Pages 1297-1307

  Guo, W L ^a   Wu, R ^a   Zhang, Y F ^b   Liu, X M ^b   Wang, H Y ^a   Gong, L ^a   Zhang, Z H ^b   Liu, Bao ^a  

^a NORTHEAST NORMAL UNIVERSITY   (China)

^b QIQIHAR UNIVERSITY   (China)

Author keywords

Codonopsis lanceolata; Correlation; DNA methylation; Epigenetic polymorphism; Molecular marker; Sequence analysis; Somaclonal variation

Indexed keywords

METHYLATION; PLANTS (BOTANY); TISSUE CULTURE;

CODONOPSIS LANCEOLATA; DNA METHYLATION; EPIGENETIC POLYMORPHISM; MOLECULAR MARKER; SEQUENCE ANALYSIS; SOMACLONAL VARIATION;

DNA;

CYTOSINE; PLANT DNA;

ARTICLE; CODONOPSIS; DNA METHYLATION; GENE EXPRESSION REGULATION; GENETIC EPIGENESIS; GENETIC VARIABILITY; GENETICS; PHYLOGENY; REGENERATION; TISSUE CULTURE TECHNIQUE;

CODONOPSIS; CYTOSINE; DNA METHYLATION; DNA, PLANT; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION, PLANT; PHYLOGENY; REGENERATION; TISSUE CULTURE TECHNIQUES; VARIATION (GENETICS);

CODONOPSIS; CODONOPSIS LANCEOLATA;

EID: 34547208165     PISSN: 07217714     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00299-007-0320-0     Document Type: Article

References (54)

1. 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 25:3389-3402
2. Bardini M, Labra M, Winfield M, Sala F (2003) Antibiotic-induced DNA methylation changes in calluses of Arabidopsis thaliana. Plant Cell Tissue Org 72:157-162
3. Baurens F-C, Bonnot F, Bienvenu D, Causse S, Legavre T (2003) Using SD-AFLP and MSAP to Assess CCGG Methylation in the Banana Genome. Plant Mol Biol Rep 21:339-348
4. Bourc'his D, Bestor TH (2004) Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature 431:96-99
5. Cervera MT, Ruiz-Garcia L, Martinez-Zapater JM (2002) Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers. Mol Genet Genomics 268:543-552
6. Chakrabarty D, Yu KW, Paek KY (2003) Detection of DNA methylation changes during somatic embryogenesis of Siberian ginseng (Eleuterococcus senticosus). Plant Sci 165:61-68
7. Chan SW, Henderson IR, Jacobsen SE (2005) Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat Rev Genet 6:351-360
8. Dong ZY, Wang YM, Zhang ZJ, Shen Y, Lin XY, Ou XF, Han FP, Liu B (2006) Extent and pattern of DNA methylation alteration in rice lines derived from introgressive hybridization of rice and Zizania latifolia Griseb. Theor Appl Genet 113:196-205
9. Feschotte C, Jiang N, Wessler SR (2002) Plant transposable elements: where genetics meets genomics. Nat Rev Genet 3:329-341
10. Golyasnaya N, Tsvetkova N (2006) Mismatch repair. Mol Biol 40:183-193
11. Gonzalgo ML, Jones PA (1997) Mutagenic and epigenetic effects of DNA methylation. Mutat Res/Rev Mutat Res 386:107-118
12. Guo WL, Gong L, Ding ZF, Li YD, Li FX, Zhao SP, Liu B (2006) Genomic instability in phenotypically normal regenerants of medicinal plant Codonopsis lanceolata Benth. et Hook. f., as revealed by ISSR and RAPD markers. Plant Cell Rep 25:896-906
13. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95-98
14. Han EG, Cho SY (1997) Effect of Codonopsis lanceolata water extract on the activities of antionxidative enzymes in carbon tetrachloride treated rats. J Koreon Soc Food Sci Nutr 26:1181-1186
15. Hao YJ, You CX, Deng XX (2002) Analysis of ploidy and the patterns of amplified fragment length polymorphism and methylation-sensitive amplified polymorphism in strawberry plants recovered from cryopreservation. Cryo Lett 23:37-46
16. Jaccard P (1908) Nouvelles rescherches sur la distribution florale. Bull Soc Vaud Sci Nat 44:223-270
17. Joyce SM, Cassells AC (2002) Variation in potato microplant morphology in vitro and DNA methylation. Plant Cell Tissue Org 70:125-137
18. Kaeppler SM, Kaeppler HF, Rhee Y (2000) Epigenetic aspects of somaclonal variation in plants. Plant Mol Biol 43:179-188
19. Kaup S, Grandjean V, Mukherjee R, Kapoor A, Keyes E, Seymour CB, Mothersill CE, Schofield PN (2006) Radiation-induced genomic instability is associated with DNA methylation changes in cultured human keratinocytes. Mutat Res/Fundam Mol Mech Mutagen 597:87-97
20. Kidwell KK, Osborn TC (1992) Simple plant DNA isolation procedures. In: Beckman JS, Osborn TC (eds) Plant genomes: methods for genetic and physical mapping. Kluwer, Amsterdam, pp 1-13
21. Knox MR, Ellis THN (2001) Stability and inheritance of methylation states at PstI sites in Pisum. Mol Genet Genomics 265:497-507
22. Kosman E, Leonard KJ (2005) Similarity coefficients for molecular markers in studies of genetic relationships between individuals for haploid, diploid, and polyploid species. Mol Ecol 14:415-424
23. Kunkel G (1984) Plants for human consumption. Koeltz Scientific Books, Koenigsten
24. Larkin PJ, Scowcroft WR (1981) Somaclonal variation: a novel source of variability from cell cultures for plant improvement. Theor Appl Genet 60:197-214
25. Law RD, Suttle JC (2002) Transient decreases in methylation at 5́-CCGG-3́ sequences in potato (Solanum tuberosum L.) meristem DNA during progression of tubers through dormancy precede the resumption of sprout growth. Plant Mol Biol 51:437-447
26. Li XQ, Xu ML, Korban SS (2002) DNA methylation profiles differ between field- and in vitro-grown leaves of apple. J Plant Physiol 159:1229-1234
27. Li YS, Li HL, An JH, Li LH, Shu YM (2003) Morphology and germination of C. lanceolata. J Agric Sci Yanbian Univ 25:155-158
28. Mantel NA (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209-220
29. Martienssen RA, Colot V (2001) DNA methylation and epigenetic inheritance in plants and filamentous fungi. Science 293:1070-1074
30. Matthes M, Singh R, Cheah SC, Karp A (2001) Variation in oil palm (Elaeis guineensis Jacq.) tissue culture-derived regenerants revealed by AFLPs with methylation-sensitive enzymes. Theor Appl Genet 102:971-979
31. McClelland M, Nelson M, Raschke E (1994) Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases. Nucleic Acid Res 22:3640-3659
32. Mohan JS (2001) Tissue culture-derived variation in crop improvement. Euphytica 118:153-166
33. Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76:5269-5273
34. Nybom H (2004) Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Mol Ecol 13:1143-1155
35. Peraza-Echeverria S, Herrera-Valencia V, Andrew James K (2001) Detection of DNA methylation changes in micropropagated banana plants using methylation-sensitive amplification polymorphism (MSAP). Plant Sci 161:359-367
36. Phillips RL, Kaeppler SM, Olhoft P (1994) Genetic instability of plant tissue cultures: Breakdown of normal controls. Proc Nati Acad Sci USA 91:5222-5226
37. Piao S (1991) The function and utilization of Korean traditional vegetables. The Encyclopedia Press, Seoul, p 56
38. Popescu CF, Falk A, Glimelius K (2002) Application of AFLPs to characterize somaclonal variation in anther-derived grapevines. Vitis 41:177-182
39. Rangwala SH, Richards EJ (2004) The value-added genome: building and maintaining genomic cytosine methylation landscapes. Curr Opin Genet Dev 14:686-691
40. Renau-Morata B, Nebauer SG, Arrillaga I, Segura J (2005) Assessments of somaclonal variation in micropropagated shoots of Cedrus: consequences of axillary bud breaking. Tree Genet Genomes 1:3-10
41. Reyna-López GE, Simpson J, Ruiz-Herrera J (1997) Differences in DNA methylation patterns are detectable during the dimorphic transition of fungi by amplification of restriction polymorphisms. Mol Gen Genet 253:703-710
42. Richards EJ (1997) DNA methylation and plant development. Trends Genet 13:319-323
43. Richards EJ (2006) Inherited epigenetic variation-revisiting soft inheritance. Nat Rev Genet 7:395-401
44. Rohlf FJ (1993) NTSYS-pc: numerical taxonomy and multivariate analysis system. Exeter Publishing Ltd, New York
45. Rohlf FJ (2000) NTSYS-pc: numerical taxonomy and multivariate analysis system, ver. 2.1. Exeter software, Setauket
46. Stegemann S, Hartmann S, Ruf S, Bock R (2003) High-frequency gene transfer from the chloroplast genome to the nucleus. Proc Natl Acad Sci USA 100:8828-8833
47. Suzuki K, Suzuki I, Leodolter A, Alonso S, Horiuchi S, Yamashita K, Perucho M (2006) Global DNA demethylation in gastrointestinal cancer is age dependent and precedes genomic damage. Cancer Cell 9:199-207
48. Tariq M, Paszkowski J (2004) DNA and histone methylation in plants. Trends Genet 20:244-251
49. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876-4882
50. Vos P, Hogers R, Bleeker M, Reijans M, Lee TVD, Hornes M, Friters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: A new technique for DNA fingerprinting. Nucleic Acids Res 23:4407-4414
51. 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 261:439-446
52. Xu M, Li X, Korban SS (2004) DNA-methylation alterations and exchanges during in vitro cellular differentiation in rose (Rosa hybrida L.). Theor Appl Genet 109:899-910
53. Zhang JY (1982) The medicinal flora of Changbai Mountains. Jilin Peoples' Press, Changchun, pp 1093-1095
54. Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S (2007) Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 39:61-69