Epigenetic changes and their relationship to somaclonal variation: a need to monitor the micropropagation of plantation crops
Parisa Azizi
A C , Mohamed M. Hanafi A B C F , Mahbod Sahebi C , Jennifer A. Harikrishna D , Sima Taheri D , Ali Yassoralipour E and Abbas Nasehi A
+ Author Affiliations
- Author Affiliations
A Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
B Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
C Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
D Centre of Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603, Kuala Lumpur, Malaysia.
E Department of Agricultural and Food Science, Faculty of Science (Kampar Campus), Universiti Tunku Abdul Rahman (UTAR), Jalan Universiti, Bandar Barat, 31900 Kampar, Perak, Malaysia.
F Corresponding author. Email: mmhanafi@upm.edu.my
Functional Plant Biology 47(6) 508-523 https://doi.org/10.1071/FP19077
Submitted: 22 March 2019 Accepted: 23 February 2020 Published: 30 April 2020
Abstract
Chromatin modulation plays important roles in gene expression regulation and genome activities. In plants, epigenetic changes, including variations in histone modification and DNA methylation, are linked to alterations in gene expression. Despite the significance and potential of in vitro cell and tissue culture systems in fundamental research and marketable applications, these systems threaten the genetic and epigenetic networks of intact plant organs and tissues. Cell and tissue culture applications can lead to DNA variations, methylation alterations, transposon activation, and finally, somaclonal variations. In this review, we discuss the status of the current understanding of epigenomic changes that occur under in vitro conditions in plantation crops, including coconut, oil palm, rubber, cotton, coffee and tea. It is hoped that comprehensive knowledge of the molecular basis of these epigenomic variations will help researchers develop strategies to enhance the totipotent and embryogenic capabilities of tissue culture systems for plantation crops.
Additional keywords: chromatin modulation, epigenetic changes, histone modification, DNA methylation, tissue culture system.
References
Adam H, Marguerettaz M, Qadri R, Adroher B, Richaud F, Collin M, Thuillet A-C, Vigouroux Y, Laufs P, Tregear JW (2011) Divergent expression patterns of miR164 and CUP-SHAPED COTYLEDON genes in palms and other monocots: implication for the evolution of meristem function in angiosperms. Molecular Biology and Evolution 28, 1439–1454.| Divergent expression patterns of miR164 and CUP-SHAPED COTYLEDON genes in palms and other monocots: implication for the evolution of meristem function in angiosperms.Crossref | GoogleScholarGoogle Scholar | 21135149PubMed |
Ahmad A, Zhang Y, Cao X-F (2010) Decoding the epigenetic language of plant development. Molecular Plant 3, 719–728.
| Decoding the epigenetic language of plant development.Crossref | GoogleScholarGoogle Scholar | 20663898PubMed |
Almeida R, Allshire RC (2005) RNA silencing and genome regulation. Trends in Cell Biology 15, 251–258.
| RNA silencing and genome regulation.Crossref | GoogleScholarGoogle Scholar | 15866029PubMed |
Alvarez-Venegas R, Casas-Mollano JA, De la Pea C (2014) ‘Epigenetics in plants of agronomic importance.’ (Springer: Berlin, Germany)
Alwee SS, Van der Linden C, Van der Schoot J, De Folter S, Angenent G, Cheah S, Smulders M (2006) Characterization of oil palm MADS box genes in relation to the mantled flower abnormality. Plant Cell, Tissue and Organ Culture 85, 331–344.
| Characterization of oil palm MADS box genes in relation to the mantled flower abnormality.Crossref | GoogleScholarGoogle Scholar |
Alzohairy AM, Sabir JS, Gyulai G, Younis RA, Jansen RK, Bahieldin A (2014) Environmental stress activation of plant long-terminal repeat retrotransposons. Functional Plant Biology 41, 557–567.
| Environmental stress activation of plant long-terminal repeat retrotransposons.Crossref | GoogleScholarGoogle Scholar |
Anzola JM, Sieberer T, Ortbauer M, Butt H, Korbei B, Weinhofer I, Müllner AE, Luschnig C (2010) Putative Arabidopsis transcriptional adaptor protein (PROPORZ1) is required to modulate histone acetylation in response to auxin. Proceedings of the National Academy of Sciences of the United States of America 107, 10308–10313.
| Putative Arabidopsis transcriptional adaptor protein (PROPORZ1) is required to modulate histone acetylation in response to auxin.Crossref | GoogleScholarGoogle Scholar | 20479223PubMed |
Avivi Y, Morad V, Ben‐Meir H, Zhao J, Kashkush K, Tzfira T, Citovsky V, Grafi G (2004) Reorganization of specific chromosomal domains and activation of silent genes in plant cells acquiring pluripotentiality. Developmental Dynamics 230, 12–22.
| Reorganization of specific chromosomal domains and activation of silent genes in plant cells acquiring pluripotentiality.Crossref | GoogleScholarGoogle Scholar | 15108305PubMed |
Bairu MW, Aremu AO, Van Staden J (2011) Somaclonal variation in plants: causes and detection methods. Plant Growth Regulation 63, 147–173.
| Somaclonal variation in plants: causes and detection methods.Crossref | GoogleScholarGoogle Scholar |
Barret P, Brinkman M, Beckert M (2006) A sequence related to rice Pong transposable element displays transcriptional activation by in vitro culture and reveals somaclonal variations in maize. Genome 49, 1399–1407.
| A sequence related to rice Pong transposable element displays transcriptional activation by in vitro culture and reveals somaclonal variations in maize.Crossref | GoogleScholarGoogle Scholar | 17426755PubMed |
Bednarek PT, Orłowska R, Koebner RM, Zimny J (2007) Quantification of the tissue-culture induced variation in barley (Hordeum vulgare L.). BMC Plant Biology 7, 10
| Quantification of the tissue-culture induced variation in barley (Hordeum vulgare L.).Crossref | GoogleScholarGoogle Scholar | 17335560PubMed |
Berger SL (2007) The complex language of chromatin regulation during transcription. Nature 447, 407
| The complex language of chromatin regulation during transcription.Crossref | GoogleScholarGoogle Scholar | 17522673PubMed |
Bernatavichute YV, Zhang X, Cokus S, Pellegrini M, Jacobsen SE (2008) Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana. PLoS One 3, e3156
| Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana.Crossref | GoogleScholarGoogle Scholar | 18776934PubMed |
Bodi Z, Zhong S, Mehra S, Song J, Li H, Graham N, May S, Fray RG (2012) Adenosine methylation in Arabidopsis mRNA is associated with the 3′ end and reduced levels cause developmental defects. Frontiers of Plant Science 3, 48
| Adenosine methylation in Arabidopsis mRNA is associated with the 3′ end and reduced levels cause developmental defects.Crossref | GoogleScholarGoogle Scholar |
Bouchabke-Coussa O, Obellianne M, Linderme D, Montes E, Maia-Grondard A, Vilaine F, Pannetier C (2013) Wuschel overexpression promotes somatic embryogenesis and induces organogenesis in cotton (Gossypium hirsutum L.) tissues cultured in vitro. Plant Cell Reports 32, 675–686.
| Wuschel overexpression promotes somatic embryogenesis and induces organogenesis in cotton (Gossypium hirsutum L.) tissues cultured in vitro.Crossref | GoogleScholarGoogle Scholar | 23543366PubMed |
Bräutigam K, Cronk Q (2018) DNA methylation and the evolution of developmental complexity in plants. Frontiers of Plant Science 9, 1447
Braybrook SA, Stone SL, Park S, Bui AQ, Le BH, Fischer RL, Goldberg RB, Harada JJ (2006) Genes directly regulated by LEAFY COTYLEDON2 provide insight into the control of embryo maturation and somatic embryogenesis. Proceedings of the National Academy of Sciences of the United States of America 103, 3468–3473.
| Genes directly regulated by LEAFY COTYLEDON2 provide insight into the control of embryo maturation and somatic embryogenesis.Crossref | GoogleScholarGoogle Scholar | 16492731PubMed |
Brettell RI, Dennis ES (1991) Reactivation of a silent Ac following tissue culture is associated with heritable alterations in its methylation pattern. Molecular and General Genetics MGG 229, 365–372.
| Reactivation of a silent Ac following tissue culture is associated with heritable alterations in its methylation pattern.Crossref | GoogleScholarGoogle Scholar | 1658596PubMed |
Burggren W (2016) Epigenetic inheritance and its role in evolutionary biology: re-evaluation and new perspectives. Biology (Basel) 5, 24
| Epigenetic inheritance and its role in evolutionary biology: re-evaluation and new perspectives.Crossref | GoogleScholarGoogle Scholar |
Chakrabarty D, Yu K-W, Paek KY (2003) Detection of DNA methylation changes during somatic embryogenesis of Siberian ginseng (Eleuterococcus senticosus). Plant Science 165, 61–68.
| Detection of DNA methylation changes during somatic embryogenesis of Siberian ginseng (Eleuterococcus senticosus).Crossref | GoogleScholarGoogle Scholar |
Chen ZJ, Tian L (2007) Roles of dynamic and reversible histone acetylation in plant development and polyploidy. Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 1769, 295–307.
| Roles of dynamic and reversible histone acetylation in plant development and polyploidy.Crossref | GoogleScholarGoogle Scholar |
Choudhuri S (2008) Epigenetic regulation of gene and genome expression. In ‘Genomics. Fundamentals and Applications’. (Eds S Choudhuri, DB Carlson) pp. 98–126. (CRC Press: Boca Raton, FL, USA)
Chuck G, Meeley R, Irish E, Sakai H, Hake S (2007) The maize tasselseed4 microRNA controls sex determination and meristem cell fate by targeting Tasselseed6/indeterminate spikelet1. Nature Genetics 39, 1517
| The maize tasselseed4 microRNA controls sex determination and meristem cell fate by targeting Tasselseed6/indeterminate spikelet1.Crossref | GoogleScholarGoogle Scholar | 18026103PubMed |
Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452, 215
| Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning.Crossref | GoogleScholarGoogle Scholar | 18278030PubMed |
Corley R, Lee C, Law I, Wong C (1986) Abnormal flower development in oil palm clones. Planter 62, 233–240.
Cristofolini C, do Nascimento Vieira L, de Freitas Fraga HP, da Costa IR, Guerra MP, Pescador R (2014) DNA methylation patterns and karyotype analysis of off-type and normal phenotype somatic embryos of feijoa. Theoretical and Experimental Plant Physiology 26, 217–224.
| DNA methylation patterns and karyotype analysis of off-type and normal phenotype somatic embryos of feijoa.Crossref | GoogleScholarGoogle Scholar |
Cullis CA, Cullis MA, Abdullah MO (2007) Development of markers for the mantled phenotype (and somaclonal variants in general) in oil palm. In Proceedings of the PIPOC 2007 international palm oil congress. Palm oil: empowering change, Kuala Lumpur’. (Malaysian Palm Oil Board: Bandar Baru Bangi, Malaysia)
De-la-Peña C, Nic-Can G, Ojeda G, Herrera-Herrera JL, López-Torres A, Wrobel K, Robert-Díaz ML (2012) KNOX1 is expressed and epigenetically regulated during in vitro conditions in Agave spp. BMC Plant Biology 12, 203
| KNOX1 is expressed and epigenetically regulated during in vitro conditions in Agave spp.Crossref | GoogleScholarGoogle Scholar | 23126409PubMed |
De-la-Peña C, Nic-Can GI, Galaz-Ávalos RM, Avilez-Montalvo R, Loyola-Vargas VM (2015) The role of chromatin modifications in somatic embryogenesis in plants. Frontiers of Plant Science 6, 635
| The role of chromatin modifications in somatic embryogenesis in plants.Crossref | GoogleScholarGoogle Scholar |
de Mendoza A, Bonnet A, Vargas-Landin DB, Ji N, Hong F, Yang F, Li L, Hori K, Pflueger J, Buckberry S (2018) Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons. Nature Communications 9, 1341
| Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons.Crossref | GoogleScholarGoogle Scholar | 29632298PubMed |
Delcuve GP, Khan DH, Davie JR (2012) Roles of histone deacetylases in epigenetic regulation: emerging paradigms from studies with inhibitors. Clinical Epigenetics 4, 5
| Roles of histone deacetylases in epigenetic regulation: emerging paradigms from studies with inhibitors.Crossref | GoogleScholarGoogle Scholar | 22414492PubMed |
Duncan R (1996) Tissue culture-induced variation and crop improvement. In ‘Advances in agronomy’. (Elsevier: Amsterdam, Netherlands)
Etienne H, Bertrand B, Dechamp E, Maurel P, Georget F, Guyot R, Breitler J-C (2016) Are genetics and epigenetic instabilities of plant embryogenic cells a fatality? The experience of coffee somatic embryogenesis. Human Genetics & Embryology : Current Research 6, 1000136
Fahlgren N, Montgomery TA, Howell MD, Allen E, Dvorak SK, Alexander AL, Carrington JC (2006) Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA affects developmental timing and patterning in Arabidopsis. Current Biology 16, 939–944.
| Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA affects developmental timing and patterning in Arabidopsis.Crossref | GoogleScholarGoogle Scholar | 16682356PubMed |
Fang L, Liang Y, Li D, Cao X, Zheng Y (2013) Dynamic expression analysis of miRNAs during the development process of oil palm mesocarp. Zhiwu Kexue Xuebao 31, 304–312.
| Dynamic expression analysis of miRNAs during the development process of oil palm mesocarp.Crossref | GoogleScholarGoogle Scholar |
Fedoroff NV (2012) Transposable elements, epigenetics, and genome evolution. Science 338, 758–767.
| Transposable elements, epigenetics, and genome evolution.Crossref | GoogleScholarGoogle Scholar | 23145453PubMed |
Fehér A (2019) Callus, dedifferentiation, totipotency, somatic embryogenesis: what these terms mean in the era of molecular plant biology? Frontiers of Plant Science 10, 536
| Callus, dedifferentiation, totipotency, somatic embryogenesis: what these terms mean in the era of molecular plant biology?Crossref | GoogleScholarGoogle Scholar |
Feschotte C, Zhang X, Wessler SR (2002) Miniature inverted-repeat transposable elements and their relationship to established DNA transposons. In ‘Mobile DNA II’. (American Society for Microbiology Press: Washington, DC, USA)
Fukai E, Dobrowolska AD, Madsen LH, Madsen EB, Umehara Y, Kouchi H, Hirochika H, Stougaard J (2008) Transposition of a 600 thousand-year-old LTR retrotransposon in the model legume Lotus japonicus. Plant Molecular Biology 68, 653–663.
| Transposition of a 600 thousand-year-old LTR retrotransposon in the model legume Lotus japonicus.Crossref | GoogleScholarGoogle Scholar | 18802778PubMed |
Fukai E, Umehara Y, Sato S, Endo M, Kouchi H, Hayashi M, Stougaard J, Hirochika H (2010) Derepression of the plant chromovirus LORE1 induces germline transposition in regenerated plants. PLOS Genetics 6, e1000868
| Derepression of the plant chromovirus LORE1 induces germline transposition in regenerated plants.Crossref | GoogleScholarGoogle Scholar | 20221264PubMed |
Furner IJ, Matzke M (2011) Methylation and demethylation of the Arabidopsis genome. Current Opinion in Plant Biology 14, 137–141.
| Methylation and demethylation of the Arabidopsis genome.Crossref | GoogleScholarGoogle Scholar | 21159546PubMed |
Furuta K, Kubo M, Sano K, Demura T, Fukuda H, Liu Y-G, Shibata D, Kakimoto T (2011) The CKH2/PKL chromatin remodeling factor negatively regulates cytokinin responses in Arabidopsis calli. Plant & Cell Physiology 52, 618–628.
| The CKH2/PKL chromatin remodeling factor negatively regulates cytokinin responses in Arabidopsis calli.Crossref | GoogleScholarGoogle Scholar |
Galindo-González L, Sarmiento F, Quimbaya M (2018) Shaping plant adaptability, genome structure and gene expression through transposable element epigenetic control: focus on methylation. Agronomy (Basel) 8, 180
| Shaping plant adaptability, genome structure and gene expression through transposable element epigenetic control: focus on methylation.Crossref | GoogleScholarGoogle Scholar |
Gallois J-L, Woodward C, Reddy GV, Sablowski R (2002) Combined SHOOT MERISTEMLESS and WUSCHEL trigger ectopic organogenesis in Arabidopsis. Development 129, 3207–3217.
George EF, Hall MA, De Klerk G-J (2007) ‘Plant propagation by tissue culture. Vol. 1. The background.’ (Springer Science & Business Media: Berlin, German)
Grafi G, Ben-Meir H, Avivi Y, Moshe M, Dahan Y, Zemach A (2007) Histone methylation controls telomerase-independent telomere lengthening in cells undergoing dedifferentiation. Developmental Biology 306, 838–846.
| Histone methylation controls telomerase-independent telomere lengthening in cells undergoing dedifferentiation.Crossref | GoogleScholarGoogle Scholar | 17448460PubMed |
Grandbastien M-A (1998) Activation of plant retrotransposons under stress conditions. Trends in Plant Science 3, 181–187.
| Activation of plant retrotransposons under stress conditions.Crossref | GoogleScholarGoogle Scholar |
Greenwood M (1987) Rejuvenation of forest trees. In ‘Hormonal control of tree growth. Forestry sciences. Vol. 28’. (Eds SV Kossuth, SD Ross) pp. 1–12. (Springer: Berlin, Germany)
Guan X, Song Q, Chen ZJ (2014) Polyploidy and small RNA regulation of cotton fiber development. Trends in Plant Science 19, 516–528.
| Polyploidy and small RNA regulation of cotton fiber development.Crossref | GoogleScholarGoogle Scholar | 24866591PubMed |
Guan Y, Li S-G, Fan X-F, Su Z-H (2016) Application of somatic embryogenesis in woody plants. Frontiers of Plant Science 07, 938
| Application of somatic embryogenesis in woody plants.Crossref | GoogleScholarGoogle Scholar |
Henderson IR, Jacobsen SE (2007) Epigenetic inheritance in plants. Nature 447, 418
| Epigenetic inheritance in plants.Crossref | GoogleScholarGoogle Scholar | 17522675PubMed |
Hirochika H (1993) Activation of tobacco retrotransposons during tissue culture. EMBO Journal 12, 2521–2528.
| Activation of tobacco retrotransposons during tissue culture.Crossref | GoogleScholarGoogle Scholar | 8389699PubMed |
Hirochika H, Sugimoto K, Otsuki Y, Tsugawa H, Kanda M (1996) Retrotransposons of rice involved in mutations induced by tissue culture. Proceedings of the National Academy of Sciences of the United States of America 93, 7783–7788.
| Retrotransposons of rice involved in mutations induced by tissue culture.Crossref | GoogleScholarGoogle Scholar | 8755553PubMed |
Hirochika H, Okamoto H, Kakutani T (2000) Silencing of retrotransposons in Arabidopsis and reactivation by the ddm1 mutation. The Plant Cell 12, 357–368.
| Silencing of retrotransposons in Arabidopsis and reactivation by the ddm1 mutation.Crossref | GoogleScholarGoogle Scholar | 10715322PubMed |
Hsieh T-F, Ibarra CA, Silva P, Zemach A, Eshed-Williams L, Fischer RL, Zilberman D (2009) Genome-wide demethylation of Arabidopsis endosperm. Science 324, 1451–1454.
| Genome-wide demethylation of Arabidopsis endosperm.Crossref | GoogleScholarGoogle Scholar | 19520962PubMed |
Hua-Van A, Le Rouzic A, Maisonhaute C, Capy P (2005) Abundance, distribution and dynamics of retrotransposable elements and transposons: similarities and differences. Cytogenetic and Genome Research 110, 426–440.
| Abundance, distribution and dynamics of retrotransposable elements and transposons: similarities and differences.Crossref | GoogleScholarGoogle Scholar | 16093695PubMed |
Huang Y-Y, Lee C-P, Fu JL, Chang BC-H, Matzke AJ, Matzke M (2014) De novo transcriptome sequence assembly from coconut leaves and seeds with a focus on factors involved in RNA-directed DNA methylation. G3: Genes, Genomes, Genetics g3, 114.013409
Hung Y-H, Liu F, Zhang X-Q, Xiao W, Hsieh T-F (2018) Sexual and non-sexual reproduction: inheritance and stability of epigenetic variations and consequences for breeding application. In ‘Plant epigenetics coming of age for breeding applications. Vol. 88’, 1st edn. (Eds P Gallusci, E Bucher, M Mirouze) pp. 117–163. (Academic Press: New York, NY, USA)
Ikeuchi M, Sugimoto K, Iwase A (2013) Plant callus: mechanisms of induction and repression. Plant Cell 25, 113.116053
Ikeuchi M, Ogawa Y, Iwase A, Sugimoto K (2016) Plant regeneration: cellular origins and molecular mechanisms. Development 143, 1442–1451.
| Plant regeneration: cellular origins and molecular mechanisms.Crossref | GoogleScholarGoogle Scholar | 27143753PubMed |
Ito H (2012) Small RNAs and transposon silencing in plants. Development, Growth & Differentiation 54, 100–107.
| Small RNAs and transposon silencing in plants.Crossref | GoogleScholarGoogle Scholar |
Ito H, Kim J-M, Matsunaga W, Saze H, Matsui A, Endo TA, Harukawa Y, Takagi H, Yaegashi H, Masuta Y (2016) A stress-activated transposon in Arabidopsis induces transgenerational abscisic acid insensitivity. Scientific Reports 6, 23181
| A stress-activated transposon in Arabidopsis induces transgenerational abscisic acid insensitivity.Crossref | GoogleScholarGoogle Scholar | 26976262PubMed |
Jain SM (1997) Micropropagation of selected somaclones of Begonia and Saintpaulia. Journal of Biosciences 22, 585–592.
| Micropropagation of selected somaclones of Begonia and Saintpaulia.Crossref | GoogleScholarGoogle Scholar |
Jaligot E, Rival A, Beulé T, Dussert S, Verdeil J-L (2000) Somaclonal variation in oil palm (Elaeis guineensis Jacq.): the DNA methylation hypothesis. Plant Cell Reports 19, 684–690.
| Somaclonal variation in oil palm (Elaeis guineensis Jacq.): the DNA methylation hypothesis.Crossref | GoogleScholarGoogle Scholar | 30754806PubMed |
Jaligot E, Beulé T, Rival A (2002) Methylation-sensitive RFLPs: characterisation of two oil palm markers showing somaclonal variation-associated polymorphism. Theoretical and Applied Genetics 104, 1263–1269.
| Methylation-sensitive RFLPs: characterisation of two oil palm markers showing somaclonal variation-associated polymorphism.Crossref | GoogleScholarGoogle Scholar | 12582579PubMed |
Jaligot E, Beulé T, Baurens F-C, Billotte N, Rival A (2004) Search for methylation-sensitive amplification polymorphisms associated with the ‘mantled’ variant phenotype in oil palm (Elaeis guineensis Jacq.). Genome 47, 224–228.
| Search for methylation-sensitive amplification polymorphisms associated with the ‘mantled’ variant phenotype in oil palm (Elaeis guineensis Jacq.).Crossref | GoogleScholarGoogle Scholar | 15060619PubMed |
Jaligot E, Rival A, Beulé T, Tregear J, Finnegan J (2007) A marker-based strategy for the assessment of epigenetic instability in oil palm. In ‘Proceedings of the PIPOC international oil palm congress: agriculture, biotechnology and sustainability, Kuala Lumpur, Malaysia’. pp. 313–323. (cirad Agricultural Research for Development: Montpellier, France)
Jiménez VM (2005) Involvement of plant hormones and plant growth regulators on in vitro somatic embryogenesis. Plant Growth Regulation 47, 91–110.
| Involvement of plant hormones and plant growth regulators on in vitro somatic embryogenesis.Crossref | GoogleScholarGoogle Scholar |
Johnson L, Mollah S, Garcia BA, Muratore TL, Shabanowitz J, Hunt DF, Jacobsen SE (2004) Mass spectrometry analysis of Arabidopsis histone H3 reveals distinct combinations of post-translational modifications. Nucleic Acids Research 32, 6511–6518.
| Mass spectrometry analysis of Arabidopsis histone H3 reveals distinct combinations of post-translational modifications.Crossref | GoogleScholarGoogle Scholar | 15598823PubMed |
Junker A, Mönke G, Rutten T, Keilwagen J, Seifert M, Thi TMN, Renou JP, Balzergue S, Viehöver P, Hähnel U (2012) Elongation‐related functions of LEAFY COTYLEDON1 during the development of Arabidopsis thaliana. The Plant Journal 71, 427–442.
Kaeppler S, Phillips R (1993a) DNA methylation and tissue culture-induced variation in plants. In Vitro Cellular & Developmental Biology. Plant 29, 125–130.
| DNA methylation and tissue culture-induced variation in plants.Crossref | GoogleScholarGoogle Scholar |
Kaeppler S, Phillips R (1993b) Tissue culture-induced DNA methylation variation in maize. Proceedings of the National Academy of Sciences of the United States of America 90, 8773–8776.
| Tissue culture-induced DNA methylation variation in maize.Crossref | GoogleScholarGoogle Scholar | 8415605PubMed |
Kaeppler SM, Kaeppler HF, Rhee Y (2000) Epigenetic aspects of somaclonal variation in plants. Plant Molecular Biology 43, 179–188.
| Epigenetic aspects of somaclonal variation in plants.Crossref | GoogleScholarGoogle Scholar | 10999403PubMed |
Kakutani T, Jeddeloh JA, Flowers SK, Munakata K, Richards EJ (1996) Developmental abnormalities and epimutations associated with DNA hypomethylation mutations. Proceedings of the National Academy of Sciences of the United States of America 93, 12406–12411.
| Developmental abnormalities and epimutations associated with DNA hypomethylation mutations.Crossref | GoogleScholarGoogle Scholar | 8901594PubMed |
Karp A (1991) On the current understanding of somaclonal variation. In ‘Oxford surveys of plant molecular cell biology. Vol. 7’. (Ed. BJ Miflin) pp. 1–58. (Oxford University Press: London, UK)
Kashkush K, Feldman M, Levy AA (2003) Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nature Genetics 33, 102
| Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat.Crossref | GoogleScholarGoogle Scholar | 12483211PubMed |
Kato M, Takashima K, Kakutani T (2004) Epigenetic control of CACTA transposon mobility in Arabidopsis thaliana. Genetics 168, 961–969.
| Epigenetic control of CACTA transposon mobility in Arabidopsis thaliana.Crossref | GoogleScholarGoogle Scholar | 15514067PubMed |
Kim HJ, Triplett BA (2001) Cotton fiber growth in planta and in vitro. Models for plant cell elongation and cell wall biogenesis. Plant Physiology 127, 1361–1366.
| Cotton fiber growth in planta and in vitro. Models for plant cell elongation and cell wall biogenesis.Crossref | GoogleScholarGoogle Scholar | 11743074PubMed |
Komatsu M, Shimamoto K, Kyozuka J (2003) Two-step regulation and continuous retrotransposition of the rice LINE-type retrotransposon Karma. The Plant Cell 15, 1934–1944.
| Two-step regulation and continuous retrotransposition of the rice LINE-type retrotransposon Karma.Crossref | GoogleScholarGoogle Scholar | 12897263PubMed |
Kornberg RD (1974) Chromatin structure: a repeating unit of histones and DNA. Science 184, 868–871.
| Chromatin structure: a repeating unit of histones and DNA.Crossref | GoogleScholarGoogle Scholar | 4825889PubMed |
Kour G, Kour B, Kaul S, Dhar MK (2009) Genetic and epigenetic instability of amplification-prone sequences of a novel B chromosome induced by tissue culture in Plantago lagopus L. Plant Cell Reports 28, 1857–1867.
| Genetic and epigenetic instability of amplification-prone sequences of a novel B chromosome induced by tissue culture in Plantago lagopus L.Crossref | GoogleScholarGoogle Scholar | 19847437PubMed |
Kouzarides T (2007) Chromatin modifications and their function. Cell 128, 693–705.
| Chromatin modifications and their function.Crossref | GoogleScholarGoogle Scholar | 17320507PubMed |
Krishna H, Alizadeh M, Singh D, Singh U, Chauhan N, Eftekhari M, Sadh RK (2016) Somaclonal variations and their applications in horticultural crops improvement. 3 Biotech 6, 54
| Somaclonal variations and their applications in horticultural crops improvement.Crossref | GoogleScholarGoogle Scholar | 28330124PubMed |
Kumar V, Van Staden J (2017) New insights into plant somatic embryogenesis: an epigenetic view. Acta Physiologiae Plantarum 39, 194
| New insights into plant somatic embryogenesis: an epigenetic view.Crossref | GoogleScholarGoogle Scholar |
Kumar V, Moyo M, Van Staden J (2016) Enhancing plant regeneration of Lachenalia viridiflora, a critically endangered ornamental geophyte with high floricultural potential. Scientia Horticulturae 211, 263–268.
| Enhancing plant regeneration of Lachenalia viridiflora, a critically endangered ornamental geophyte with high floricultural potential.Crossref | GoogleScholarGoogle Scholar |
Kumar V, Moyo M, Van Staden J (2017) Somatic embryogenesis in Hypoxis hemerocallidea: an important African medicinal plant. South African Journal of Botany 108, 331–336.
| Somatic embryogenesis in Hypoxis hemerocallidea: an important African medicinal plant.Crossref | GoogleScholarGoogle Scholar |
Lafos M, Kroll P, Hohenstatt ML, Thorpe FL, Clarenz O, Schubert D (2011) Dynamic regulation of H3K27 trimethylation during Arabidopsis differentiation. PLoS Genetics 7, e1002040
| Dynamic regulation of H3K27 trimethylation during Arabidopsis differentiation.Crossref | GoogleScholarGoogle Scholar | 21490956PubMed |
Landey RB, Cenci A, Georget F, Bertrand B, Camayo G, Dechamp E, Herrera JC, Santoni S, Lashermes P, Simpson J (2013) High genetic and epigenetic stability in Coffea arabica plants derived from embryogenic suspensions and secondary embryogenesis as revealed by AFLP, MSAP and the phenotypic variation rate. PLoS One 8, e56372
| High genetic and epigenetic stability in Coffea arabica plants derived from embryogenic suspensions and secondary embryogenesis as revealed by AFLP, MSAP and the phenotypic variation rate.Crossref | GoogleScholarGoogle Scholar |
Landey RB, Cenci A, Guyot R, Bertrand B, Georget F, Dechamp E, Herrera J-C, Aribi J, Lashermes P, Etienne H (2015) Assessment of genetic and epigenetic changes during cell culture ageing and relations with somaclonal variation in Coffea arabica. Plant Cell, Tissue and Organ Culture 122, 517–531.
| Assessment of genetic and epigenetic changes during cell culture ageing and relations with somaclonal variation in Coffea arabica.Crossref | GoogleScholarGoogle Scholar |
Larkin PJ, Scowcroft WR (1981) Somaclonal variation – a novel source of variability from cell cultures for plant improvement. Theoretical and Applied Genetics 60, 197–214.
| Somaclonal variation – a novel source of variability from cell cultures for plant improvement.Crossref | GoogleScholarGoogle Scholar | 24276737PubMed |
Law JA, Jacobsen SE (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nature Reviews. Genetics 11, 204
| Establishing, maintaining and modifying DNA methylation patterns in plants and animals.Crossref | GoogleScholarGoogle Scholar | 20142834PubMed |
Law RD, Suttle JC (2005) Chromatin remodeling in plant cell culture: patterns of DNA methylation and histone H3 and H4 acetylation vary during growth of asynchronous potato cell suspensions. Plant Physiology and Biochemistry 43, 527–534.
| Chromatin remodeling in plant cell culture: patterns of DNA methylation and histone H3 and H4 acetylation vary during growth of asynchronous potato cell suspensions.Crossref | GoogleScholarGoogle Scholar | 15922608PubMed |
Lee S-I, Kim N-S (2014) Transposable elements and genome size variations in plants. Genomics & Informatics 12, 87
| Transposable elements and genome size variations in plants.Crossref | GoogleScholarGoogle Scholar |
Lee JJ, Woodward AW, Chen ZJ (2007) Gene expression changes and early events in cotton fibre development. Annals of Botany 100, 1391–1401.
| Gene expression changes and early events in cotton fibre development.Crossref | GoogleScholarGoogle Scholar | 17905721PubMed |
Li Y, Butenko Y, Grafi G (2005) Histone deacetylation is required for progression through mitosis in tobacco cells. The Plant Journal 41, 346–352.
| Histone deacetylation is required for progression through mitosis in tobacco cells.Crossref | GoogleScholarGoogle Scholar | 15659094PubMed |
Li B, Carey M, Workman JL (2007a) The role of chromatin during transcription. Cell 128, 707–719.
| The role of chromatin during transcription.Crossref | GoogleScholarGoogle Scholar | 17320508PubMed |
Li X, Yu X, Wang N, Feng Q, Dong Z, Liu L, Shen J, Liu B (2007b) Genetic and epigenetic instabilities induced by tissue culture in wild barley (Hordeum brevisubulatum (Trin.) Link). Plant Cell, Tissue and Organ Culture 90, 153–168.
| Genetic and epigenetic instabilities induced by tissue culture in wild barley (Hordeum brevisubulatum (Trin.) Link).Crossref | GoogleScholarGoogle Scholar |
Li W, Liu H, Cheng ZJ, Su YH, Han HN, Zhang Y, Zhang XS (2011) DNA methylation and histone modifications regulate de novo shoot regeneration in Arabidopsis by modulating WUSCHEL expression and auxin signaling. PLOS Genetics 7, e1002243
| DNA methylation and histone modifications regulate de novo shoot regeneration in Arabidopsis by modulating WUSCHEL expression and auxin signaling.Crossref | GoogleScholarGoogle Scholar | 21876682PubMed |
Li H-L, Guo D, Zhu J-H, Wang Y, Peng S-Q (2017) Identification and expression analysis of genes involved in histone acetylation in Hevea brasiliensis. Tree Genetics & Genomes 13, 98
| Identification and expression analysis of genes involved in histone acetylation in Hevea brasiliensis.Crossref | GoogleScholarGoogle Scholar |
Lindroth AM, Shultis D, Jasencakova Z, Fuchs J, Johnson L, Schubert D, Patnaik D, Pradhan S, Goodrich J, Schubert I, Jenuwein T, Khorasanizadeh S, Jacobsen SE (2011) Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3. The EMBO journal 30, 1874
| Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3.Crossref | GoogleScholarGoogle Scholar |
Liu Z, Han F, Tan M, Shan X, Dong Y, Wang X, Fedak G, Hao S, Liu B (2004) Activation of a rice endogenous retrotransposon Tos17 in tissue culture is accompanied by cytosine demethylation and causes heritable alteration in methylation pattern of flanking genomic regions. Theoretical and Applied Genetics 109, 200–209.
| Activation of a rice endogenous retrotransposon Tos17 in tissue culture is accompanied by cytosine demethylation and causes heritable alteration in methylation pattern of flanking genomic regions.Crossref | GoogleScholarGoogle Scholar | 15071728PubMed |
Liu X, Huang J, Wang Y, Khanna K, Xie Z, Owen HA, Zhao D (2010) The role of floral organs in carpels, an Arabidopsis loss‐of‐function mutation in MicroRNA160a, in organogenesis and the mechanism regulating its expression. The Plant Journal 62, 416–428.
| The role of floral organs in carpels, an Arabidopsis loss‐of‐function mutation in MicroRNA160a, in organogenesis and the mechanism regulating its expression.Crossref | GoogleScholarGoogle Scholar | 20136729PubMed |
Liu X, Yu C-W, Duan J, Luo M, Wang K, Tian G, Cui Y, Wu K (2012) HDA6 directly interacts with DNA methyltransferase MET1 and maintains transposable element silencing in Arabidopsis. Plant Physiology 158, 119–129.
| HDA6 directly interacts with DNA methyltransferase MET1 and maintains transposable element silencing in Arabidopsis.Crossref | GoogleScholarGoogle Scholar | 21994348PubMed |
LoSchiavo F, Pitto L, Giuliano G, Torti G, Nuti-Ronchi V, Marazziti D, Vergara R, Orselli S, Terzi M (1989) DNA methylation of embryogenic carrot cell cultures and its variations as caused by mutation, differentiation, hormones and hypomethylating drugs. Theoretical and Applied Genetics 77, 325–331.
| DNA methylation of embryogenic carrot cell cultures and its variations as caused by mutation, differentiation, hormones and hypomethylating drugs.Crossref | GoogleScholarGoogle Scholar | 24232608PubMed |
Lotan T, Ohto M-a, Yee KM, West MA, Lo R, Kwong RW, Yamagishi K, Fischer RL, Goldberg RB, Harada JJ (1998) Arabidopsis LEAFY COTYLEDON1 is sufficient to induce embryo development in vegetative cells. Cell 93, 1195–1205.
| Arabidopsis LEAFY COTYLEDON1 is sufficient to induce embryo development in vegetative cells.Crossref | GoogleScholarGoogle Scholar | 9657152PubMed |
Lu X, Chen X, Mu M, Wang J, Wang X, Wang D, Yin Z, Fan W, Wang S, Guo L (2016) Genome-wide analysis of long noncoding RNAs and their responses to drought stress in cotton (Gossypium hirsutum L.). PLoS One 11, e0156723
| Genome-wide analysis of long noncoding RNAs and their responses to drought stress in cotton (Gossypium hirsutum L.).Crossref | GoogleScholarGoogle Scholar | 27907011PubMed |
Machczyńska J, Orłowska R, Mańkowski DR, Zimny J, Bednarek PT (2014) DNA methylation changes in triticale due to in vitro culture plant regeneration and consecutive reproduction. Plant Cell, Tissue and Organ Culture 119, 289–299.
| DNA methylation changes in triticale due to in vitro culture plant regeneration and consecutive reproduction.Crossref | GoogleScholarGoogle Scholar |
Makarevitch I, Eichten SR, Briskine R, Waters AJ, Danilevskaya ON, Meeley RB, Myers CL, Vaughn MW, Springer NM (2013) Genomic distribution of maize facultative heterochromatin marked by trimethylation of H3K27. The Plant Cell 25, 112.106427
Makarevitch I, Waters AJ, West PT, Stitzer M, Hirsch CN, Ross-Ibarra J, Springer NM (2015) Transposable elements contribute to activation of maize genes in response to abiotic stress. PLOS Genetics 11, e1004915
| Transposable elements contribute to activation of maize genes in response to abiotic stress.Crossref | GoogleScholarGoogle Scholar | 26452261PubMed |
Matzke M, Kanno T, Daxinger L, Huettel B, Matzke AJ (2009) RNA-mediated chromatin-based silencing in plants. Current Opinion in Cell Biology 21, 367–376.
| RNA-mediated chromatin-based silencing in plants.Crossref | GoogleScholarGoogle Scholar | 19243928PubMed |
Mehrpooyan F, Othman R, Harikrishna J (2012) Tissue and temporal expression of miR172 paralogs and the AP2-like target in oil palm (Elaeis guineensis Jacq.). Tree Genetics & Genomes 8, 1331–1343.
| Tissue and temporal expression of miR172 paralogs and the AP2-like target in oil palm (Elaeis guineensis Jacq.).Crossref | GoogleScholarGoogle Scholar |
Meijón M, Valledor L, Santamaría E, Testillano PS, Risueño MC, Rodríguez R, Feito I, Cañal MJ (2009) Epigenetic characterization of the vegetative and floral stages of azalea buds: dynamics of DNA methylation and histone H4 acetylation. Journal of Plant Physiology 166, 1624–1636.
| Epigenetic characterization of the vegetative and floral stages of azalea buds: dynamics of DNA methylation and histone H4 acetylation.Crossref | GoogleScholarGoogle Scholar | 19523713PubMed |
Meijón M, Feito I, Valledor L, Rodríguez R, Cañal MJ (2010) Dynamics of DNA methylation and Histone H4 acetylation during floral bud differentiation in azalea. BMC Plant Biology 10, 10
| Dynamics of DNA methylation and Histone H4 acetylation during floral bud differentiation in azalea.Crossref | GoogleScholarGoogle Scholar | 20067625PubMed |
Méndez-Hernández HA, Ledezma-Rodríguez M, Avilez-Montalvo RN, Juárez-Gómez YL, Skeete A, Avilez-Montalvo J, De-la-Peña C, Loyola-Vargas VM (2019) Signaling overview of plant somatic embryogenesis. Frontiers of Plant Science 10, 77
| Signaling overview of plant somatic embryogenesis.Crossref | GoogleScholarGoogle Scholar |
Miguel C, Marum L (2011) An epigenetic view of plant cells cultured in vitro: somaclonal variation and beyond. Journal of Experimental Botany 62, 3713–3725.
| An epigenetic view of plant cells cultured in vitro: somaclonal variation and beyond.Crossref | GoogleScholarGoogle Scholar | 21617249PubMed |
Mirouze M, Paszkowski J (2011) Epigenetic contribution to stress adaptation in plants. Current Opinion in Plant Biology 14, 267–274.
| Epigenetic contribution to stress adaptation in plants.Crossref | GoogleScholarGoogle Scholar | 21450514PubMed |
Mirouze M, Reinders J, Bucher E, Nishimura T, Schneeberger K, Ossowski S, Cao J, Weigel D, Paszkowski J, Mathieu O (2009) Selective epigenetic control of retrotransposition in Arabidopsis. Nature 461, 427
| Selective epigenetic control of retrotransposition in Arabidopsis.Crossref | GoogleScholarGoogle Scholar | 19734882PubMed |
Miura A, Yonebayashi S, Watanabe K, Toyama T, Shimada H, Kakutani T (2001) Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature 411, 212
| Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis.Crossref | GoogleScholarGoogle Scholar | 11346800PubMed |
Mordhorst AP, Toonen MA, de Vries SC, Meinke D (1997) Plant embryogenesis. Critical Reviews in Plant Sciences 16, 535–576.
| Plant embryogenesis.Crossref | GoogleScholarGoogle Scholar |
Neelakandan AK, Wang K (2012) Recent progress in the understanding of tissue culture-induced genome level changes in plants and potential applications. Plant Cell Reports 31, 597–620.
| Recent progress in the understanding of tissue culture-induced genome level changes in plants and potential applications.Crossref | GoogleScholarGoogle Scholar | 22179259PubMed |
Negin B, Shemer O, Sorek Y, Williams LE (2017) Shoot stem cell specification in roots by the WUSCHEL transcription factor. PLoS One 12, e0176093
| Shoot stem cell specification in roots by the WUSCHEL transcription factor.Crossref | GoogleScholarGoogle Scholar | 28445492PubMed |
Ngezahayo F, Xu C, Wang H, Jiang L, Pang J, Liu B (2009) Tissue culture-induced transpositional activity of mPing is correlated with cytosine methylation in rice. BMC Plant Biology 9, 91
| Tissue culture-induced transpositional activity of mPing is correlated with cytosine methylation in rice.Crossref | GoogleScholarGoogle Scholar | 19604382PubMed |
Nic-Can GI, López-Torres A, Barredo-Pool F, Wrobel K, Loyola-Vargas VM, Rojas-Herrera R, De-la-Peña C (2013) New insights into somatic embryogenesis: LEAFY COTYLEDON1, BABY BOOM1 and WUSCHEL-RELATED HOMEOBOX4 are epigenetically regulated in Coffea canephora. PLoS One 8, e72160
| New insights into somatic embryogenesis: LEAFY COTYLEDON1, BABY BOOM1 and WUSCHEL-RELATED HOMEOBOX4 are epigenetically regulated in Coffea canephora.Crossref | GoogleScholarGoogle Scholar | 23977240PubMed |
Ogas J, Cheng J-C, Sung ZR, Somerville C (1997) Cellular differentiation regulated by gibberellin in the Arabidopsis thaliana pickle mutant. Science 277, 91–94.
| Cellular differentiation regulated by gibberellin in the Arabidopsis thaliana pickle mutant.Crossref | GoogleScholarGoogle Scholar | 9204906PubMed |
Ogas J, Kaufmann S, Henderson J, Somerville C (1999) PICKLE is a CHD3 chromatin-remodeling factor that regulates the transition from embryonic to vegetative development in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America 96, 13839–13844.
| PICKLE is a CHD3 chromatin-remodeling factor that regulates the transition from embryonic to vegetative development in Arabidopsis.Crossref | GoogleScholarGoogle Scholar | 10570159PubMed |
Okushima Y, Overvoorde PJ, Arima K, Alonso JM, Chan A, Chang C, Ecker JR, Hughes B, Lui A, Nguyen D (2005) Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19. The Plant Cell 17, 444–463.
| Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19.Crossref | GoogleScholarGoogle Scholar | 15659631PubMed |
Ong-Abdullah M, Ordway JM, Jiang N, Ooi S-E, Kok S-Y, Sarpan N, Azimi N, Hashim AT, Ishak Z, Rosli SK (2015) Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm. Nature 525, 533
| Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm.Crossref | GoogleScholarGoogle Scholar | 26352475PubMed |
Pang M, Woodward AW, Agarwal V, Guan X, Ha M, Ramachandran V, Chen X, Triplett BA, Stelly DM, Chen ZJ (2009) Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.). Genome Biology 10, R122
| Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.).Crossref | GoogleScholarGoogle Scholar | 19889219PubMed |
Park S-Y, Murthy H, Chakrabarthy D, Paek K-Y (2009) Detection of epigenetic variation in tissue-culture-derived plants of Doritaenopsis by methylation-sensitive amplification polymorphism (MSAP) analysis. In Vitro Cellular & Developmental Biology. Plant 45, 104–108.
| Detection of epigenetic variation in tissue-culture-derived plants of Doritaenopsis by methylation-sensitive amplification polymorphism (MSAP) analysis.Crossref | GoogleScholarGoogle Scholar |
Peng H, Zhang J (2009) Plant genomic DNA methylation in response to stresses: potential applications and challenges in plant breeding. Progress in Natural Science 19, 1037–1045.
| Plant genomic DNA methylation in response to stresses: potential applications and challenges in plant breeding.Crossref | GoogleScholarGoogle Scholar |
Peschke VM, Phillips RL, Gengenbach BG (1987) Discovery of transposable element activity among progeny of tissue culture-derived maize plants. Science 238, 804–807.
| Discovery of transposable element activity among progeny of tissue culture-derived maize plants.Crossref | GoogleScholarGoogle Scholar | 17814708PubMed |
Pfluger J, Wagner D (2007) Histone modifications and dynamic regulation of genome accessibility in plants. Current Opinion in Plant Biology 10, 645–652.
| Histone modifications and dynamic regulation of genome accessibility in plants.Crossref | GoogleScholarGoogle Scholar | 17884714PubMed |
Phillips RL, Kaeppler SM, Olhoft P (1994) Genetic instability of plant tissue cultures: breakdown of normal controls. Proceedings of the National Academy of Sciences of the United States of America 91, 5222–5226.
| Genetic instability of plant tissue cultures: breakdown of normal controls.Crossref | GoogleScholarGoogle Scholar | 8202472PubMed |
Pischke MS, Huttlin EL, Hegeman AD, Sussman MR (2006) A transcriptome-based characterization of habituation in plant tissue culture. Plant Physiology 140, 1255–1278.
| A transcriptome-based characterization of habituation in plant tissue culture.Crossref | GoogleScholarGoogle Scholar | 16489130PubMed |
Rhee Y, Sekhon RS, Chopra S, Kaeppler S (2010) Tissue culture-induced novel epialleles of a Myb transcription factor encoded by pericarp color1 in maize. Genetics 186, 843–855.
| Tissue culture-induced novel epialleles of a Myb transcription factor encoded by pericarp color1 in maize.Crossref | GoogleScholarGoogle Scholar | 20823340PubMed |
Rival A (2000) Somatic embryogenesis in oil palm. In ‘Somatic embryogenesis in woody plants. Forestry sciences. Vol. 67’. (Eds SM Jain, PK Gupta, RJ Newton) pp. 249–290. (Springer: Dordrecht, Netherlands)
Rodríguez López CM, Wetten AC, Wilkinson MJ (2010) Progressive erosion of genetic and epigenetic variation in callus‐derived cocoa (Theobroma cacao) plants. New Phytologist 186, 856–868.
| Progressive erosion of genetic and epigenetic variation in callus‐derived cocoa (Theobroma cacao) plants.Crossref | GoogleScholarGoogle Scholar | 20406408PubMed |
Rogers K, Chen X (2013) Biogenesis, turnover, and mode of action of plant microRNAs. The Plant Cell 25, 2383–2399.
| Biogenesis, turnover, and mode of action of plant microRNAs.Crossref | GoogleScholarGoogle Scholar | 23881412PubMed |
Roudier F, Teixeira FK, Colot V (2009) Chromatin indexing in Arabidopsis: an epigenomic tale of tails and more. Trends in Genetics 25, 511–517.
| Chromatin indexing in Arabidopsis: an epigenomic tale of tails and more.Crossref | GoogleScholarGoogle Scholar | 19850370PubMed |
Saze H 2008
Schellenbaum P, Mohler V, Wenzel G, Walter B (2008) Variation in DNA methylation patterns of grapevine somaclones (Vitis vinifera L.). BMC Plant Biology 8, 78
| Variation in DNA methylation patterns of grapevine somaclones (Vitis vinifera L.).Crossref | GoogleScholarGoogle Scholar | 18627604PubMed |
Seto E, Yoshida M (2014) Erasers of histone acetylation: the histone deacetylase enzymes. Cold Spring Harbor Perspectives in Biology 6, a018713
| Erasers of histone acetylation: the histone deacetylase enzymes.Crossref | GoogleScholarGoogle Scholar | 24691964PubMed |
Shilatifard A (2006) Chromatin modifications by methylation and ubiquitination: implications in the regulation of gene expression. Annual Review of Biochemistry 75, 243–269.
| Chromatin modifications by methylation and ubiquitination: implications in the regulation of gene expression.Crossref | GoogleScholarGoogle Scholar | 16756492PubMed |
Singh K, Kumar S, Ahuja PS (2009) Differential expression of Histone H3 gene in tea (Camellia sinensis (L.) O. Kuntze) suggests its role in growing tissue. Molecular Biology Reports 36, 537–542.
| Differential expression of Histone H3 gene in tea (Camellia sinensis (L.) O. Kuntze) suggests its role in growing tissue.Crossref | GoogleScholarGoogle Scholar | 18224457PubMed |
Singh R, Ong-Abdullah M, Low E-TL, Manaf MAA, Rosli R, Nookiah R, Ooi LC-L, Ooi SE, Chan K-L, Halim MA (2013) Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds. Nature 500, 335
| Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds.Crossref | GoogleScholarGoogle Scholar | 23883927PubMed |
Slotkin RK, Martienssen R (2007) Transposable elements and the epigenetic regulation of the genome. Nature Reviews. Genetics 8, 272
| Transposable elements and the epigenetic regulation of the genome.Crossref | GoogleScholarGoogle Scholar | 17363976PubMed |
Smith A, Hansey C, Kaeppler S (2012) TCUP: a novel hAT transposon active in maize tissue culture. Frontiers of Plant Science 3, 6
| TCUP: a novel hAT transposon active in maize tissue culture.Crossref | GoogleScholarGoogle Scholar |
Smulders M, De Klerk G (2011) Epigenetics in plant tissue culture. Plant Growth Regulation 63, 137–146.
| Epigenetics in plant tissue culture.Crossref | GoogleScholarGoogle Scholar |
Smýkal P, Valledor L, Rodriguez R, Griga M (2007) Assessment of genetic and epigenetic stability in long-term in vitro shoot culture of pea (Pisum sativum L.). Plant Cell Reports 26, 1985–1998.
| Assessment of genetic and epigenetic stability in long-term in vitro shoot culture of pea (Pisum sativum L.).Crossref | GoogleScholarGoogle Scholar | 17668220PubMed |
Spanudakis E, Jackson S (2014) The role of microRNAs in the control of flowering time. Journal of Experimental Botany 65, 365–380.
| The role of microRNAs in the control of flowering time.Crossref | GoogleScholarGoogle Scholar | 24474808PubMed |
Stelpflug SC, Eichten SR, Hermanson PJ, Springer NM, Kaeppler SM (2014) Consistent and heritable alterations of DNA methylation are induced by tissue culture in maize. Genetics 198, 209–218.
| Consistent and heritable alterations of DNA methylation are induced by tissue culture in maize.Crossref | GoogleScholarGoogle Scholar | 25023398PubMed |
Stone SL, Braybrook SA, Paula SL, Kwong LW, Meuser J, Pelletier J, Hsieh T-F, Fischer RL, Goldberg RB, Harada JJ (2008) Arabidopsis LEAFY COTYLEDON2 induces maturation traits and auxin activity: implications for somatic embryogenesis. Proceedings of the National Academy of Sciences of the United States of America 105, 3151–3156.
| Arabidopsis LEAFY COTYLEDON2 induces maturation traits and auxin activity: implications for somatic embryogenesis.Crossref | GoogleScholarGoogle Scholar | 18287041PubMed |
Stroud H, Ding B, Simon SA, Feng S, Bellizzi M, Pellegrini M, Wang G-L, Meyers BC, Jacobsen SE (2013) Plants regenerated from tissue culture contain stable epigenome changes in rice. elife 2, e00354
| Plants regenerated from tissue culture contain stable epigenome changes in rice.Crossref | GoogleScholarGoogle Scholar | 23539454PubMed |
Sun Q Zhou D-X 2008
Tanurdzic M, Vaughn MW, Jiang H, Lee T-J, Slotkin RK, Sosinski B, Thompson WF, Doerge RW, Martienssen RA (2008) Epigenomic consequences of immortalized plant cell suspension culture. PLoS Biology 6, e302
| Epigenomic consequences of immortalized plant cell suspension culture.Crossref | GoogleScholarGoogle Scholar | 19071958PubMed |
Tessadori F, Chupeau M-C, Chupeau Y, Knip M, Germann S, van Driel R, Fransz P, Gaudin V (2007) Large-scale dissociation and sequential reassembly of pericentric heterochromatin in dedifferentiated Arabidopsis cells. Journal of Cell Science 120, 1200–1208.
| Large-scale dissociation and sequential reassembly of pericentric heterochromatin in dedifferentiated Arabidopsis cells.Crossref | GoogleScholarGoogle Scholar | 17376962PubMed |
Tian L, Fong MP, Wang JJ, Wei NE, Jiang H, Doerge R, Chen ZJ (2005) Reversible histone acetylation and deacetylation mediate genome-wide, promoter-dependent and locus-specific changes in gene expression during plant development. Genetics 169, 337–345.
| Reversible histone acetylation and deacetylation mediate genome-wide, promoter-dependent and locus-specific changes in gene expression during plant development.Crossref | GoogleScholarGoogle Scholar | 15371352PubMed |
Todorovska E (2007) Retrotransposons and their role in plant–genome evolution. Biotechnology, Biotechnological Equipment 21, 294–305.
| Retrotransposons and their role in plant–genome evolution.Crossref | GoogleScholarGoogle Scholar |
Uddenberg D Valladares S Abrahamsson M Sundström JF Sundås-Larsson A von Arnold S 2011
Urbański DF, Małolepszy A, Stougaard J, Andersen SU (2012) Genome‐wide LORE1 retrotransposon mutagenesis and high‐throughput insertion detection in Lotus japonicus. The Plant Journal 69, 731–741.
| Genome‐wide LORE1 retrotransposon mutagenesis and high‐throughput insertion detection in Lotus japonicus.Crossref | GoogleScholarGoogle Scholar | 22014280PubMed |
Valledor L, Hasbún R, Meijón M, Rodríguez JL, Santamaría E, Viejo M, Berdasco M, Feito I, Fraga MF, Canal MJ (2007a) Involvement of DNA methylation in tree development and micropropagation. Plant Cell, Tissue and Organ Culture 91, 75–86.
| Involvement of DNA methylation in tree development and micropropagation.Crossref | GoogleScholarGoogle Scholar |
Valledor L, Rodrıguez R, Sánchez P, Fraga M, Berdasco M, Hasbún R, Rodrıguez J, Pacheco J, Garcıa I, Uribe M (2007b) Propagation of Pinus genotypes regardless of age. In ‘Protocols of micropropagation for woody trees and fruits’. (Eds S Mohan Jain, H Haggman) pp. 137–146 (Springer, Dordrecht, Netherlands)
Valledor L, Meijón M, Hasbún R, Cañal MJ, Rodríguez R (2010) Variations in DNA methylation, acetylated histone H4, and methylated histone H3 during Pinus radiata needle maturation in relation to the loss of in vitro organogenic capability. Journal of Plant Physiology 167, 351–357.
| Variations in DNA methylation, acetylated histone H4, and methylated histone H3 during Pinus radiata needle maturation in relation to the loss of in vitro organogenic capability.Crossref | GoogleScholarGoogle Scholar | 19931210PubMed |
Vanyushin BF, Ashapkin VV (2011) DNA methylation in higher plants: past, present and future. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1809, 360–368.
Vaughn MW, Tanurdžić M, Lippman Z, Jiang H, Carrasquillo R, Rabinowicz PD, Dedhia N, McCombie WR, Agier N, Bulski A (2007) Epigenetic natural variation in Arabidopsis thaliana. PLoS Biology 5, e174
| Epigenetic natural variation in Arabidopsis thaliana.Crossref | GoogleScholarGoogle Scholar | 17579518PubMed |
Vazquez F (2006) Arabidopsis endogenous small RNAs: highways and byways. Trends in Plant Science 11, 460–468.
| Arabidopsis endogenous small RNAs: highways and byways.Crossref | GoogleScholarGoogle Scholar | 16893673PubMed |
Verhoeven KJ, Preite V (2014) Epigenetic variation in asexually reproducing organisms. Evolution 68, 644–655.
| Epigenetic variation in asexually reproducing organisms.Crossref | GoogleScholarGoogle Scholar | 24274255PubMed |
Vicient CM, Casacuberta JM (2017) Impact of transposable elements on polyploid plant genomes. Annals of Botany 120, 195–207.
| Impact of transposable elements on polyploid plant genomes.Crossref | GoogleScholarGoogle Scholar | 28854566PubMed |
Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O (2007) A unified classification system for eukaryotic transposable elements. Nature Reviews. Genetics 8, 973
| A unified classification system for eukaryotic transposable elements.Crossref | GoogleScholarGoogle Scholar | 17984973PubMed |
Williams L, Zhao J, Morozova N, Li Y, Avivi Y, Grafi G (2003) Chromatin reorganization accompanying cellular dedifferentiation is associated with modifications of histone H3, redistribution of HP1, and activation of E2F‐target genes. Developmental Dynamics 228, 113–120.
| Chromatin reorganization accompanying cellular dedifferentiation is associated with modifications of histone H3, redistribution of HP1, and activation of E2F‐target genes.Crossref | GoogleScholarGoogle Scholar | 12950085PubMed |
Withers LA, Alderson P (2013) ‘Plant tissue culture and its agricultural applications. Proceedings of Previous Easter Schools in Agricultural Science, 1st edn.’ (Butterworths-Heinemann: London, UK)
Yaacob JS, Loh H-S, Mat Taha R (2013) Protein profiling and histone deacetylation activities in somaclonal variants of oil palm (Elaeis guineensis Jacq.). Scientific World Journal 2013, 613635
Yang X, Zhang X (2010) Regulation of somatic embryogenesis in higher plants. Critical Reviews in Plant Sciences 29, 36–57.
| Regulation of somatic embryogenesis in higher plants.Crossref | GoogleScholarGoogle Scholar |
Yu Z, Haberer G, Matthes M, Rattei T, Mayer KF, Gierl A, Torres-Ruiz RA (2010) Impact of natural genetic variation on the transcriptome of autotetraploid Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the United States of America 107, 17809–17814.
| Impact of natural genetic variation on the transcriptome of autotetraploid Arabidopsis thaliana.Crossref | GoogleScholarGoogle Scholar | 20876110PubMed |
Yu X, Li X, Zhao X, Jiang L, Miao G, Pang J, Qi X, Liu B (2011) Tissue culture‐induced genomic alteration in maize (Zea mays) inbred lines and F1 hybrids. Annals of Applied Biology 158, 237–247.
| Tissue culture‐induced genomic alteration in maize (Zea mays) inbred lines and F1 hybrids.Crossref | GoogleScholarGoogle Scholar |
Zhang K, Sridhar VV, Zhu J, Kapoor A, Zhu J-K (2007) Distinctive core histone post-translational modification patterns in Arabidopsis thaliana. PLoS One 2, e1210
| Distinctive core histone post-translational modification patterns in Arabidopsis thaliana.Crossref | GoogleScholarGoogle Scholar | 18030344PubMed |
Zhang M, Kimatu JN, Xu K, Liu B (2010) DNA cytosine methylation in plant development. Journal of Genetics and Genomics 37, 1–12.
| DNA cytosine methylation in plant development.Crossref | GoogleScholarGoogle Scholar | 20171573PubMed |
Zhao J, Morozova N, Williams L, Libs L, Avivi Y, Grafi G (2001) Two phases of chromatin decondensation during dedifferentiation of plant cells distinction between competence for cell fate switch and a commitment for S phase. The Journal of Biological Chemistry 276, 22772–22778.
| Two phases of chromatin decondensation during dedifferentiation of plant cells distinction between competence for cell fate switch and a commitment for S phase.Crossref | GoogleScholarGoogle Scholar | 11274191PubMed |
Zheng Q, Zheng Y, Perry SE (2013) AGAMOUS-Like15 promotes somatic embryogenesis in Arabidopsis and soybean in part by the control of ethylene biosynthesis and response. Plant Physiology 161, 2113–2127.
| AGAMOUS-Like15 promotes somatic embryogenesis in Arabidopsis and soybean in part by the control of ethylene biosynthesis and response.Crossref | GoogleScholarGoogle Scholar | 23457229PubMed |
Zhou Y, Honda M, Zhu H, Zhang Z, Guo X, Li T, Li Z, Peng X, Nakajima K, Duan L (2015) Spatiotemporal sequestration of miR165/166 by Arabidopsis Argonaute10 promotes shoot apical meristem maintenance. Cell Reports 10, 1819–1827.
| Spatiotemporal sequestration of miR165/166 by Arabidopsis Argonaute10 promotes shoot apical meristem maintenance.Crossref | GoogleScholarGoogle Scholar | 25801022PubMed |
Zhu Q-H, Upadhyaya NM, Gubler F, Helliwell CA (2009) Over-expression of miR172 causes loss of spikelet determinacy and floral organ abnormalities in rice (Oryza sativa). BMC Plant Biology 9, 149
| Over-expression of miR172 causes loss of spikelet determinacy and floral organ abnormalities in rice (Oryza sativa).Crossref | GoogleScholarGoogle Scholar | 20017947PubMed |
Ziauddin A, Kasha K (1990) Long-term callus cultures of diploid barley (Hordeum vulgare). II. Effect of auxins on chromosomal status of cultures and regeneration of plants. Euphytica 48, 279–286.
| Long-term callus cultures of diploid barley (Hordeum vulgare). II. Effect of auxins on chromosomal status of cultures and regeneration of plants.Crossref | GoogleScholarGoogle Scholar |
