Progressive erosion of genetic and epigenetic variation in callus-derived cocoa (Theobroma cacao) plants

New Phytologist

Volumn 186, Issue 4, 2010, Pages 856-868

  Rodríguez López, Carlos M ^a   Wetten, Andrew C ^b   Wilkinson, Michael J ^a  

^a ABERYSTWYTH UNIVERSITY   (United Kingdom)

^b UNIVERSITY OF READING   (United Kingdom)

Author keywords

Methylation sensitive amplified fragment length polymorphisms; Methylation sensitive amplified polymorphism; Microsatellites; Single sequence repeat; Somaclonal variation; Somatic embryogenesis; Theobroma cacao

Indexed keywords

COCOA; DEVELOPMENTAL BIOLOGY; EMBRYONIC DEVELOPMENT; GENETIC MARKER; GENETIC VARIATION; METHYLATION; MULTIVARIATE ANALYSIS; MUTATION;

ANTIBODY SPECIFICITY; ARTICLE; CACAO; DNA METHYLATION; EMBRYO DEVELOPMENT; GENETIC EPIGENESIS; GENETIC MARKER; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENETICS; GENOMIC INSTABILITY; METHODOLOGY; PLANT CHROMOSOME; PRENATAL DEVELOPMENT; TIME; TISSUE CULTURE TECHNIQUE; VARIABLE NUMBER OF TANDEM REPEAT; EMBRYOLOGY; PROCEDURES;

CACAO; CHROMOSOMES, PLANT; DNA METHYLATION; EMBRYONIC DEVELOPMENT; EPIGENESIS, GENETIC; GENETIC MARKERS; GENETIC VARIATION; GENOMIC INSTABILITY; MINISATELLITE REPEATS; ORGAN SPECIFICITY; POLYMORPHISM, GENETIC; TIME FACTORS; TISSUE CULTURE TECHNIQUES;

THEOBROMA CACAO;

GENETIC MARKER;

EID: 77953925873     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/j.1469-8137.2010.03242.x     Document Type: Article

References (69)

1. Abe T, Ii N, Togashi A, Sasahara T. Large deletions in chloroplast DNA of rice calli after long-term culture. Journal of Plant Physiology 2002, 159:917-923.
2. Bardini M, Labra M, Winfield M, Sala F. Antibiotic-induced DNA methylation changes in calluses of Arabidopsis thaliana. Plant Cell Tissue and Organ Culture 2003, 72:157-162.
3. Barret P, Brinkman M, Beckert M. A sequence related to rice Pong transposable element displays transcriptional activation by in vitro culture and reveals somaclonal variations in maize. Genome 2006, 49:1399-1407.
4. Bossdorf O, Richards CL, Pigliucci M. Epigenetics for ecologists. Ecology Letters 2008, 11:106-115.
5. Bouman H, De Klerk GJ. Measurement of the extent of somaclonal variation in begonia plants regenerated under various conditions. Comparison of three assays. Theoretical and Applied Genetics 2001, 102:111-117.
6. Brar DS, Jain SM. Somaclonal variation: mechanisms and applications in crop improvement. Somaclonal variation and induced mutations in crop improvement 1998, 15-38. Jain SM, Brar DSAhloowalia BS. eds, Dordrecht, the Netherlands, Kluwer Academic Publisher
7. Burg K, Helmersson A, Bozhkov P, von Arnold S. Developmental and genetic variation in nuclear microsatellite stability during somatic embryogenesis in pine. Journal of Experimental Botany 2007, 58:687-698.
8. Chang CL, Marra G, Chauhan DP, Ha HT, Chang DK, Ricciardiello L, Randolph A, Carethers JM, Boland CR. Oxidative stress inactivates the human mismatch repair system. American Journal of Physiology-Cell Physiology 2002, 283:C148-C154.
9. Cheng X, Roberts RJ. AdoMet-dependent methylation, DNA methyltransferases and base flipping. Nucleic Acids Research 2001, 29:3784-3795.
10. Cote FX, Teisson C, Perrier X. Somaclonal variation rate evolution in plant tissue culture: contribution to understanding through a statistical approach. In vitro Cellular and Developmental Biology-Plant 2001, 37:539-542.
11. Cotton RGH. Mutation Detection 1997, Oxford, UK, Oxford University Press
12. Cuatrecasas J. Cacao and its allies. A taxonomic review of the genus Theobroma. Contributions from the United States National Herbarium 1964, 35:379-614.
13. De Schepper S, Debergh P, Van Bockstaele E, De Loose M, Gerats A, Depicker A. Genetic and epigenetic aspects of somaclonal variation: flower colour bud sports in azalea, a case study. South African Journal of Botany 2003, 69:117-128.
14. De Schepper S, Leus L, Mertens M, Debergh P, Van Bockstaele E, De Loose M. Somatic polyploidy and its consequences for flower coloration and flower morphology in azalea. Plant Cell Reports 2001, 20:583-590.
15. DeVerno LL, Charest PJ, Bonen L. Mitochondrial DNAvariation in somatic embryogenic cultures of Larix. Theoretical and Applied Genetics 1994, 88:727-732.
16. DeVerno LL, Park YS, Bonga JM, Barrett JD. Somaclonal variation in cryopreserved embryogenic clones of white spruce (Picea glauca (Moench) Voss.). Plant Cell Reports 1999, 18:948-953.
17. Duchesne P, Bernatchez L. AFLPOP: a computer program for simulated and real population allocation based on AFLP data. Molecular Ecology Notes 2002, 3:380-383.
18. Fang J-Y, Wetten A, Adu-Gyamfi R, Wilkinson M, Rodriguez-Lopez C. Use of secondary somatic embryos promotes genetic fidelity in cryopreservation of cocoa (Theobroma cacao L.). Agricultural and Food Science 2009, 18:152-159.
19. Fras A, Maluszynska J. The correlation between the chromosome variation in callus and genotype of explants of Arabidopsis thaliana. Genetica 2004, 121:145-154.
20. Goldstein DB, Schlötterer C. Microsatellites: evolution and applications 1999, Suffolk, UK, Oxford University Press
21. Gower JC. Some distance properties of latent root and vectors methods used in multivariate analysis. Biometrika 1966, 53:325-338.
22. Gupta PK. Chromosomal basis of somaclonal variation in plants. Somaclonal variation and induced mutations in crop improvement 1998, 149-168. Jain SMBrar DSAhloowalia BS. eds, Dordrecht, the Netherlands, Kluwer Academic Publisher
23. Hao YJ, You CX, Deng XX. Analysis of ploidy and the patterns of amplified length polymorphism and methylation sensitive amplification polymorphism in strawberry plants recovered from cryopreservation. Cryoletters 2002, 23:37-46.
24. Henry RJ. Molecular and biochemical characterization of somaclonal variation. Somaclonal variation and induced mutations in crop improvement 1998, 485-499. Jain SMBrar DSAhloowalia BS. eds, Dordrecht, the Netherlands, Kluwer Academic Publisher
25. Ingelbrecht IL, Irvine JE, Mirkov TE. Posttranscriptional gene silencing in transgenic sugarcane. Dissection of homology-dependent virus resistance in a monocot that has a complex polyploid genome. Plant Physiology 1999, 119:1187-1198.
26. Jaligot E, Beulé T, Baurens FC, Billote N, Rival A. Search for methylation-sensitive amplification polymorphisms associated with the " mantled" variant phenotype in oil palm (Elaeis guineensis Jacq.). Genome 2004, 47:224-228.
27. Jin SX, Mushke R, Zhu HG, Tu LL, Lin ZX, Zhang YX, Zhang XL. Detection of somaclonal variation of cotton (Gossypium hirsutum) using cytogenetics, flow cytometry and molecular markers. Plant Cell Reports 2008, 27:1303-1316.
28. Joyce SM, Cassells AC. Variation in potato microplant morphology in vitro and DNA methylation. Plant Cell Tissue and Organ Culture 2002, 70:125-137.
29. Joyce SM, Cassells AC, Jain SM. Stress and aberrant phenotypes in in vitro culture. Plant Cell Tissue and Organ Culture 2003, 74:103-121.
30. Kaeppler SM, Phillips RL. Tissue culture induced DNA methylation in maize. Proceedings of the National Academy of Sciences, USA 1993, 90:8773-8776.
31. Kato F, Suetake T, Murata A, Mukai T, Ueki H. Restriction endonuclease MroI useful for genetic engineering - obtained by culturing Micrococcus roseus S. 1988, JP 63098383
32. Kenedy AJ, Mooleedhar V. Conservation of cocoa in field genebanks - the international cocoa genebank, Trinidad. Proceedings of the international workshop on conservation, characterization and utilization of cocoa genetic resources in 21st century 1992, 21-26. In, 13-17 Sep. 1992, Port-of-Spain, Trinidad and Tobago
33. Kharabian A, Darabi A. Characterization of some chromosomal aberrations in regenerated rice plants (Oryza sativa). Plant Cell Tissue and Organ Culture 2005, 83:161-168.
34. Krizova K, Fojtova M, Depicker A, Kovarik A. Cell culture-induced gradual and frequent epigenetic reprogramming of invertedly repeated tobacco transgene epialleles. Plant Physiology 2009, 149:1493-1504.
35. Kunkel TA, Erie DA. DNA mismatch repair. Annual Review Biochemistry 2005, 74:681-710.
36. Lam E. Controlled cell death, plant survival and development. Nature Reviews Molecular Cell Biology 2004, 5:305-315.
37. Lanaud C. Origin of haploids and semigamy in Theobroma cacao L. Euphytica 1998, 38:221-228.
38. Lanaud C, Risterucci AM, Pieretti I, Falque M, Bouet A, Lagoda PJL. Isolation and characterization of microsatellites in Theobroma cacao L. Molecular Ecology 1999, 8:2141-2152.
39. Li YC, Korol A, Fahima T, Beiles A, Nevo E. Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Molecular Ecology 2002, 11:2453-2465.
40. Li Z, Traore A, Maximova S, Guiltinan MJ. Somatic embryogenesis and plant regeneration from floral explants of cacao (Theobroma cacao L.) using thidiazuron. In Vitro Cellular and Developmental Biology-Plant 1998, 34:293-299.
41. Lin CS, Lin HL, Jane WN, Hsiao HW, Lin CC, Jheng FY, Chang WC. Changes in the morphology and cation content of a Bambusa edulis xylem mutant, vse, derived from somaclonal. Journal of the American Society for Horticultural Science 2006, 131:445-451.
42. Lopez-Baez O, Bollon H, Eskes A, Petiard V. Somatic embryogenesis and plant regeneration from flower parts of cocoa Theobroma cacao L. Comptes rendus de l'Académie des sciences 1993, 316:579-584.
43. Marum L, Rocheta M, Maroco J, Oliveira MM, Miguel C. Analysis of genetic stability at SSR loci during somatic embryogenesis in maritime pine (Pinus pinaster). Plant Cell Reports 2009, 28:673-682.
44. Messeguer R, Ganal MW, Steffens JC, Tanksley SD. Characterization of the level, target sites and inheritance off cytosine methylation in tomato nuclear DNA. Plant Molecular Biology 1991, 16:753-770.
45. Park DS, Park SK, Lee BC, Song SY, Jun NS, Manigbas NL, Cho JH, Nam MH, Jeon JS, Han CD. Molecular characterization and physico-chemical analysis of a new giant embryo mutant allele (ge(t)) in rice (Oryza sativa L.). Genes & Genomics 2009, 31:277-282.
46. Patwary MU, Mackay RM, Vander MJP. Revealing genetic markers in Geledium vagum (Rhodophyta) through the random amplified polymorphic DNA (RAPD) technique. Journal of Phycology 1993, 29:216-222.
47. Peredo EL, Revilla MA, Arroyo-García R. Assessment of genetic and epigenetic variation in hop plants regenerated from sequential subcultures of organogenic calli. Journal of Plant Physiology 2006, 163:1071-1079.
48. Phillips RL, Kaeppler SM, Olhoft P. Genetic instability of plant tissue cultures: breakdown of normal controls. Proceedings of the National Academy of Sciences, USA 1994, 91:5222-5226.
49. Potter R, Jones MGK. An assessment of genetic stability of potato in vitro by molecular and phenotypic analysis. Plant Science 1991, 76:239-248.
50. Raimondi JP, Masuelli RW, Camadro EL. Assessment of somaclonal variation in asparagus by RAPD fingerprinting and cytogenetic analyses. Scientia Horticulturae 2001, 90:19-29.
51. Reyna-López GE, Simpson J, Ruiz-Herrera J. Differences in DNA methylation patterns are detectable during the dimorphic transition of fungi by amplification of restriction polymorphisms. Molecular and General Genetics 1997, 253:703-710.
52. Rodríguez López CM, Wetten AC, Wilkinson MJ. Detection and quantification of in vitro-culture induced chimerism using simple sequence repeat (SSR) analysis in Theobroma cacao (L.). Theoretical and Applied Genetics 2004, 110:157-166.
53. Rolf B, Wiegand P, Brinkmann B. Somatic mutations at STR loci-a reason for three-allele pattern and mosaicism. Forensic Science International 2002, 126:200-202.
54. Schmitt F, Oakeley EJ, Jost JP. Antibiotics induce genome-wide hypermethylation in cultured Nicotiana Tabacum plants. Journal of Biological Chemistry 1997, 272:1534-1540.
55. Sheidai M, Hamta A. Cytogenetic analysis of somaclonal variation in regenerated plants of Berseem clover (Trifolium alexandrium L.). Caryologia 2008, 61:392-396.
56. Sibly RM, Meade A, Boxall N, Wilkinson MJ, Corne DW, Whittaker JC. The structure of interrupted human AC microsatellites. Molecular Ecology and Evolution 2003, 20:453-459.
57. Takeda S, Tadele Z, Hofmann I, Probst AV, Angelis KJ, Kaya H, Araki T, Mengiste T, Scheid OM, Shibahara K. BRU1, a novel link between responses to DNA damage and epigenetic gene silencing in Arabidopsis. Genes & Development 2004, 18:782-793.
58. Thanos D, Scarpelis G, Papamatheakis J, Bouriotis V. Isolation and identification of restriction endonuclease BseAI. Nucleic Acids Research 1989, 17:8881.
59. Traore A, Maximova S, Guiltinan MJ. Micropropagation of Theobroma cacao L. using somatic embryo-derived plants. In Vitro Cellular and Developmental Biology-Plant 2003, 39:332-337.
60. Tremblay L, Levasseur C, Tremblay FM. Frequency of somaclonal variation in plants of black spruce (Picea maritima, Pinaceae) and white spruce (P. glauca, Pinaceae) derived from somatic embryogenesis and identification of some factors involved in genetic instability. American Journal of Botany 1999, 86:1373-1381.
61. Tsuro M, Inoue M, Kameoka H. Variation in essential oil components in regenerated lavender (Lavandula vera DC) plants. Scientia Horticulturae 2001, 88:309-317.
62. Vigouroux Y, Jaqueth JS, Matsuoka Y, Smith OS, Doebley J. Rate and pattern of mutation at microsatellite loci in maize. Molecular Biology and Evolution 2002, 19:1251-1260.
63. Von Aderkas P, Pattanavibool R, Hristoforoglu K, Ma Y. Embryogenesis and genetic stability in long term megagametophyte-derived cultures of larch. Plant Cell Tissue and Organ Culture 2003, 75:27-34.
64. Wang C, Liu Z. Arabidopsis ribonucleotide reductases are critical for cell cycle progression, DNA damage repair, and plant development. Plant Cell 2006, 18:350-365.
65. Wassenegger M, Heimes S, Riedel L, Sanger HL. RNA-directed de novo methylation of genomic sequences in plants. Cell 1994, 76:567-576.
66. Whittle CA, Beardmore T, Johnston MO. Is G1 arrest in plant seeds induced by a p53-related pathway? Trends in Plant Sciences 2001, 6:248-251.
67. Wu P, Qiu C, Sohail A, Zhang X, Bhagwat AS, Cheng X. Mismatch Repair in methylated DNA structure and activity of the mismatch-specific thymine glycosylase domain of methyl-cpg-binding protein MBD4. The Journal of Biological Chemistry 2003, 278:5285-5291.
68. Xiong LZ, Xu CG, Maroof MAS, Zhang QF. Patterns of cytosine methylation in an elite rice hybrid and its parental lines, detected by a methylation sensitive amplification polymorphism technique. Molecular General Genetics 1999, 261:439-446.
69. Zhao YP, Zhou Y, Grout BWW. Variation in leaf structures of micropropagated rhubarb (Rheum rhaponticum L.) PC49. Plant Cell Tissue and Organ Culture 2006, 85:115-121.