Skip to main content
SpringerLink
Log in

Leaf patterning of Clivia miniata var. variegata is associated with differential DNA methylation

  • Original Article
  • Published:
Plant Cell Reports Aims and scope Submit manuscript

Abstract

Key message

Leaf patterns (yellow, green and striped) of Clivia miniata var. variegata might be caused by differential DNA methylation in CCGG sites in response to heterogeneous environmental pressure.

Abstract

Clivia miniata is an important ornamental plant. Clivia miniata var. variegata (Cmvv) is a variegated leaf mutant of C. miniata. Typical Cmvv has attractive green- and yellow-stripped leaves. The study has revealed that an explant of Cmvv, even a full-green explant, could regenerate plants of three different types: yellow, green, and striped; normal-appearing chloroplasts were found in guard cells but not in mesophyll cells of all the three types of Cmvv using confocal laser scanning microscopy (CLSM). Thus, we speculated that cells of the three types of Cmvv had an identical mutation and the mutation might disturb mesophyll cell chloroplast biogenesis after symplastic isolation of guard cells. Using CLSM and methylation-sensitive amplification polymorphism (MSAP), we found that (a) striped leaves of Cmvv are due to sectorial decreases in chlorophyll levels and the decreases are associated with CG hypermethylation; (b) extent of epigenetic divergence among the three types of Cmvv leaves is positively correlated with intensity of leaf-color difference; and (c) green stripes of two plants are clustered in one group based on the MSAP profiles, but green and yellow stripes of a plant are not. Sequencing analysis indicated that CG hypermethylation in gene bodies of CPSAR1 and ycf2 might lead to gene silencing and yellow leaves/stripes of Cmvv. All together, it is possible that cytosine methylation involved regulating leaf color of Cmvv, also striped pattern of Cmvv might be caused by differential DNA methylation in response to heterogeneous environmental pressure. Furthermore, a novel leaf-color epigenetic hypothesis was proposed in this article.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10
Fig. 11

Similar content being viewed by others

Abbreviations

Cmvv :

Clivia miniata var. Variegata

MSAP:

Methylation-sensitive amplification polymorphism

MZEs:

Mature zygotic embryos

MS:

Murashige and Skoog

KT:

Kinetin

NAA:

a-Naphthaleneacetic acid

BA:

6-Benzyladenine

2,4-D:

2,4-Dichlorophenoxyacetic acid

IM:

Initiation media

IM1 :

Initiation media supplemented with BA 1.11 μM + NAA 5.37 μM + 2,4-D 2.26 μM

IM2 :

Initiation media supplemented with BA 2.22 μM + NAA 5.37 μM + 2,4-D 1.13 μM

RM:

Regeneration media

RM1 :

Regeneration media containing KT 9.29 μM + NAA 2.69 μM

RM2 :

Regeneration media containing KT 9.29 μM + 5.37 μM

CLSM:

Confocal laser scanning microscopy

YP:

Expanding yellow leaves in young group

GP:

Expanding green leaves in young group

SP:

Expanding striped leaves in young group

YP2 :

Expanded yellow leaves in mature group

GP2 :

Expanded green leaves in mature group

SP2 :

Expanded striped leaves in mature group

YS1–3 :

Yellow stripes of expanded striped leaves in reference group

GS1–3 :

Green stripes of expanded striped leaves in reference group

PAGE:

Polyacrylamide gel electrophoresis

CE:

Capillary electrophoresis

PGRs:

Plant growth regulators

References

  • Aluru MR, Stessman DJ, Spalding MH, Rodermel SR (2007) Alterations in photosynthesis in Arabidopsis lacking IMMUTANS, a chloroplast terminal oxidase. Photosynth Res 91:11–23

    Article  PubMed  CAS  Google Scholar 

  • Bailey S, Thompson E, Nixon PJ, Horton P, Mullineaux CW et al (2002) A critical role for the Var2 FtsH homologue of Arabidopsis thaliana in the photosystem II repair cycle in vivo. J Biol Chem 277:2006–2011

    Article  PubMed  CAS  Google Scholar 

  • Bairu MW, Aremu AO, Staden JV (2011) Somaclonal variation in plants: causes and detection methods. Plant Growth Regul 63:147–173

    Article  CAS  Google Scholar 

  • Bang WY, Hata A, Jeong IS, Umeda T, Masuda T (2009) AtObgC, a plant ortholog of bacterial Obg, is a chloroplast-targeting GTPase essential for early embryogenesis. Plant Mol Biol 71:379–390

    Article  PubMed  CAS  Google Scholar 

  • Bao JZ, Liu CG, Sun Y, Li FT, Chen XL (2011) Hybrid breeding and cultivation management techniques of Clivia miniata var. variegata. Chin Hortic Abstr 9:143–144

    Google Scholar 

  • Chen M, Choi Y, Voytas DF, Rodermel SR (2000) Mutations in the Arabidopsis VAR2 locus cause leaf variegation due to the loss of a chloroplast FtsH protease. Plant J 22:303–313

    Article  PubMed  Google Scholar 

  • Chuartzman SG, Nevo R, Shimoni E, Charuvi D, Kiss V et al (2008) Thylakoid membrane remodeling during state transitions in Arabidopsis. Plant Cell 20:1029–1039

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Cocciolone SM, Cone K (1993) CPl-Bh, an anthocyanin regulatory gene of maize that leads to variegated pigmentation. Genetics 135:575–588

    PubMed  CAS  PubMed Central  Google Scholar 

  • Cubas P, Vincent C, Coen E (1999) An epigenetic mutation responsible for natural variation in floral symmetry. Nature 401:157–161

    Article  PubMed  CAS  Google Scholar 

  • Flores PS, Otoni WC, Dhingra OD, de Souza Diniz SPS, dos Santos TM, Bruckner CH (2012) In vitro selection of yellow passion fruit genotypes for-resistance to Fusarium vascular wilt. Plant Cell Tiss Organ Cult 108:37–45

    Article  CAS  Google Scholar 

  • Forth D, Pyke KA (2006) The suffulta mutation in tomato reveals a novel method of plastid replication during fruit ripening. J Exp Bot 57:1971–1979

    Article  PubMed  CAS  Google Scholar 

  • Garcia C, Khan NZ, Nannmark U, Aronsson H (2010) The chloroplast protein CPSAR1, dually localized in the stroma and the inner envelope membrane, is involved in thylakoid biogenesis. Plant J 63:73–85

    PubMed  CAS  Google Scholar 

  • Garstka M, Drożak A, Rosiak M, Venema JH, Kierdaszuk B et al (2005) Light-dependent reversal of dark-chilling induced changes in chloroplast structure and arrangement of chlorophyll–protein complexes in bean thylakoid membranes. BBA 1710:13–23

    PubMed  CAS  Google Scholar 

  • Gesteira AS, Otoni WC, Barros EG, Moreira MA (2002) RAPD-based detection of genomic instability in soybean plants derived from somatic embryogenesis. Plant Breed 121:269–271

    Article  CAS  Google Scholar 

  • Guo DP, Zhu ZJ, Hu XX, Zheng SJ (2005) Effect of cytokinins on shoot regeneration from cotyledon and leaf segment of stem mustard (Brassica juncea var. tsatsai). Plant Cell Tiss Org Cult 83:123–127

    Article  CAS  Google Scholar 

  • Guo WL, Wu R, Zhang YF, Liu XM, Wang HY et al (2007) Tissue culture-induced locus-specific alteration in DNA methylation and its correlation with genetic variation in Codonopsis lanceolata Benth. et Hook. f. Plant Cell Rep 26:1297–1307

    Article  PubMed  CAS  Google Scholar 

  • Han C, Coe EH Jr, Martienssen RA (1992) Molecular cloning and characterization of iojap (ij), a pattern striping gene of maize. EMBO J 11:4037–4046

    PubMed  CAS  PubMed Central  Google Scholar 

  • Ieven M, Vlietinck AJ, Vanden Berghe DA, Totte J, Dommisse R et al (1982) Plant antiviral agents. III. Isolation of alkaloids from Clivia miniata Regel (Amaryllidaceae). J Nat Prod 45:564–573

    Article  PubMed  CAS  Google Scholar 

  • Jakubiec A, Notaise J, Tournier V, Héricourt F, Block MA et al (2004) Assembly of Turnip Yellow Mosaic Virus replication complexes: interaction between the proteinase and polymerase domains of the replication proteins. J Virol 78:7945–7957

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Jin S, Mushke R, Zhu H, Tu L, Lin Z, Zhang Y, Zhang X (2008) Detection of somaclonal variation of cotton (Gossypium hirsutum) using cytogenetics, flow cytometry and molecular markers. Plant Cell Rep 27:1303–1316

    Article  PubMed  CAS  Google Scholar 

  • Karan R, DeLeon T, Biradar H, Subudhi PK (2012) Salt stress induced variation in DNA methylation pattern and its influence on gene expression in contrasting rice genotypes. PLoS One 7:e40203

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Krizova K, Fojtova M, Depicker A, Kovarik A (2009) Cell culture-induced gradual and frequent epigenetic reprogramming of invertedly repeated tobacco transgene epialleles1[W]. Plant Physiol 149:1493–1504

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Mamun EA, Cantrill LC, Overall RL, Sutton BG (2005) Cellular organisation and differentiation of organelles in pre-meiotic rice anthers. Cell Biol Int 29:792–802

    Article  PubMed  Google Scholar 

  • Manning K, Tör M, Poole M, Hong Y, Thompson AJ et al (2006) A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat Genet 8:48–952

    Google Scholar 

  • Miguel C, Marum L (2011) An epigenetic view of plant cells cultured in vitro: somaclonal variation and beyond. J Exp Bot 62:3713–3725

    Article  PubMed  CAS  Google Scholar 

  • Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 15:473–497

    Article  CAS  Google 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 Rep 31:597–620

    Article  PubMed  CAS  Google Scholar 

  • Nehra NS, Kartha KK, Stushnott C, Giles KL (1992) The influence of plant growth regulator concentrations and callus age on somaclonal variation in callus culture regenerants of strawberry. Plant Cell, Tissue Organ Cult 29:257–268

    Article  CAS  Google Scholar 

  • Palevitz BA, Hepler PK (1985) Changes in dye coupling of stomatal cells of Allium and Commelina demonstrated by microinjection of Lucifer yellow. Planta 164:473–479

    Article  PubMed  CAS  Google Scholar 

  • Peksa O, Skaloud P (2008) Changes in chloroplast structure in lichenized algae. Symbiosis 46:153–160

    Google Scholar 

  • Peschke VM, Phillips RL (1992) Genetic implications of somaclonal variation in plants. Adv Genet 30:41–75

    Article  CAS  Google Scholar 

  • Pfluger J, Zambryski PC (2001) Cell growth: the power of symplastic isolation. Curr Biol 11:R436–R439

    Article  PubMed  CAS  Google Scholar 

  • Pigliucci M (2005) Evolution of phenotypic plasticity: where are we going now? Trends Ecol Evol 20:481–486

    Article  PubMed  Google Scholar 

  • Pyke KA, Leech RM (1994) A genetic analysis of chloroplast division and expansion in Arabidopsis thaliana. Plant Physiol 104:201–207

    PubMed  CAS  PubMed Central  Google Scholar 

  • Qian XW, Yuan YL, Rong P, Zhu XY, Liu YT (2014) Analysis of methylation-sensitive amplified polymorphism in cotton genome under salt stress based on capillary electrophoresis. Chin J Biochem Mol Biol 30:298–306

    CAS  Google Scholar 

  • Ran Y, Hammett KRW, Murray BG (2001) Hybrid identification in Clivia (Amaryllidaceae) using chromosome banding and genomic in situ hybridization. Ann Bot 87:823–830

    Article  CAS  Google Scholar 

  • Rapp RA, Wendel JF (2005) Epigenetics and plant evolution. New Phytol 168:81–91

    Article  PubMed  CAS  Google Scholar 

  • Rodríguez López CM, Wetten AC, Wilkinson MJ (2010) Progressive erosion of genetic and epigenetic variation in callus-derived cocoa (Theobroma cacao) plants. New Phytol 186:856–868

    Article  PubMed  Google Scholar 

  • Rosso D, Bode R, Li W, Krol M, Saccon D et al (2009) Photosynthetic redox imbalance governs leaf sectoring in the Arabidopsis thaliana variegation mutants immutans, spotty, var1, and var2. Plant Cell 21:3473–3492

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Ruiz-García L, Cervera MT, Martínez-Zapater JM (2005) DNA methylation increases throughout Arabidopsis development. Planta 222:301–306

    Article  PubMed  Google Scholar 

  • Ruppel NJ, Kropp KN, Davis PA, Martin AE, Luesse DR, Hangarter RP (2013) Mutations in GERANYLGERANYL DIPHOSPHATE SYNTHASE 1 affect chloroplast development in Arabidopsis thaliana (Brassicaceae)1. Am J Bot 100:2074–2084

    Article  PubMed  CAS  Google Scholar 

  • Sakamoto W (2003) Leaf-variegated mutations and their responsible genes in Arabidopsis thaliana. Genes Genet Syst 78:1–9

    Article  PubMed  CAS  Google Scholar 

  • Sewram V, Raynor MW, Mulholland DA, Raidoo DM (2001) Supercritical fluid extraction and analysis of compounds from Clivia miniata for uterotonic activity. Planta Med 67:451–455

    Article  PubMed  CAS  Google Scholar 

  • Sivanesan I, Lim MY, Jeong BR (2011) Somatic embryogenesis and plant regeneration from leaf and petiole explants of Campanula punctata Lam. var. rubriflora Makino. Plant Cell Tiss Organ Cult 107:365–369

    Article  Google Scholar 

  • Telias A, Lin-Wang K, Stevenson DE, Cooney JM, Hellens RP et al (2011) Apple skin patterning is associated with differential expression of MYB10. BMC Plant Biol 11:93

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Turck F, Coupland G (2013) Natural variation in epigenetic gene regulation and its effects on plant developmental traits. Evolution 68:620–631

    Article  PubMed  Google Scholar 

  • Valledor L, Hasbún R, Meijón M, Rodríguez JL, Santamaría E et al (2007) Involvement of DNA methylation in tree development and micropropagation. Plant Cell, Tissue Organ Cult 91:75–86

    Article  CAS  Google Scholar 

  • Vanyushin BF, Ashapkin VV (2011) DNA methylation in higher plants: past, present and future. BBA 1809(8):360–368

    PubMed  CAS  Google Scholar 

  • Vaughn KC (1987) Two immunological approaches to the detection of ribulose-1,5-bisphosphate carboxylase in guard cell chloroplasts. Plant Physiol 84:188–196

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Veale DJH, Oliver DW, Arangies NS, Furman KI (1989) Preliminary isolated organ studies using an aqueous extract of Clivia miniata leaves. J Ethnopharmacol 27:341–346

    Article  PubMed  CAS  Google Scholar 

  • Wang Q-M, Wang L (2012) An evolutionary view of plant tissue culture: somaclonal variation and selection. Plant Cell Rep 31:1535–1547

    Article  PubMed  CAS  Google Scholar 

  • Wang Q-M, Wang Y-Z, Sun L-L, Gao F-Z, Sun W et al (2012a) Direct and indirect organogenesis of Clivia miniata and assessment of DNA methylation changes in various regenerated plantlets. Plant Cell Rep 31:1283–1296

    Article  PubMed  CAS  Google Scholar 

  • Wang Q-M, Gao F-Z, Gao X, Zou F-Y, Sui X et al (2012b) Regeneration of Clivia miniata and assessment of clonal fidelity of plantlets. Plant Cell, Tissue Organ Cult 109:191–200

    Article  Google Scholar 

  • Waters MT, Fray RG, Pyke KA (2004) Stromule formation is dependent upon plastid size, plastid differentiation status and the density of plastids within the cell. Plant J 39:655–667

    Article  PubMed  Google Scholar 

  • Wetzel CM, Jiang CZ, Meehan LJ, Voytas DF, Rodermel SR (1994) Nuclear-organelle interactions: the immutans variegation mutant of Arabidopsis is plastid autonomous and impaired in carotenoid biosynthesis. Plant J 6:161–175

    Article  PubMed  CAS  Google Scholar 

  • Wolfe KH (1994) Similarity between putative ATP-binding sites in land plant plastid ORF2280 proteins and the FtsH/CDC48 family of ATPases. Curr Genet 25(4):379–383

    Article  PubMed  CAS  Google Scholar 

  • Wu D, Wright DA, Wetzel C, Voytas DF, Rodermel S et al (1999) The IMMUTANS variegation locus of Arabidopsis defines a mitochondrial alternative oxidase homolog that functions during early chloroplast biogenesis. Plant Cell 11:43–55

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • YamaryoaY Dubots E, Albrieuxa C, BaldanbB Blocka MA (2008) Phosphate availability affects the tonoplast localization of PLDζ2, an Arabidopsis thaliana phospholipase D. FEBS Lett 582:685–690

    Article  Google Scholar 

  • Ye L (2006) Progress in the tissue culture and micropropagation of Clivia miniata Regel. Subtrop Agric Res 2:231–233

    Google Scholar 

  • Yu F, Park S, Rodermel SR (2004) The Arabidopsis FtsH metalloprotease gene family: interchangeability of subunits in chloroplast oligomeric complexes. Plant J 34:864–876

    Article  Google Scholar 

  • Yu F, Fu A, Aluru M, Park S, Xu Y et al (2007) Variegation mutants and mechanisms of chloroplast biogenesis. Plant, Cell Environ 30:350–365

    Article  CAS  Google Scholar 

  • Yu F, Liu X, Alsheikh M, Park S, Rodermel S (2008) Mutations in SUPPRESSOR OF VARIEGATION1, a factor required for normal chloroplast translation, suppress var2-mediated leaf variegation in Arabidopsis. Plant Cell 20:1786–1804

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Yu F, Park S-S, Liu X, Foudreec A, Fub A et al (2011) SUPPRESSOR OF VARIEGATION4, a new var2 suppressor locus, encodes a pioneer protein that is required for chloroplast biogenesis. Mol Plant 4:229–240

    Article  PubMed  CAS  Google Scholar 

  • Zhang Y-Y, Fischer M, Colot V, Bossdorf O (2013) Epigenetic variation creates potential for evolution of plant phenotypic plasticity. New Phytol 197:314–322

    Article  PubMed  CAS  Google Scholar 

  • Zhu JF, Yang SH (2002) Maternal inheritance of the striped-art Clivia miniata. J Chin Flowers Bonsai 5:9

    Google Scholar 

Download references

Acknowledgments

This work was supported by China Postdoctoral Science Foundation (2015M571330), Scientific Research Fund of Liaoning Provincial Education Department (L2015487) and Shengyang Agricultural University Scientific Research Fund of Young Teacher (20131002). Professor Bao Liu (Laboratory of Plant Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, China) kindly provided the facilities for MSAP analysis.

Author information

Authors and Affiliations

  1. College of Forestry, Shengyang Agricultural University, Shengyang, 110866, China

    Qin-Mei Wang, Yongbin Zhou, Jianguo Cui & Chengming Zhao

  2. Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China

    Li Wang & Yuzhang Wang

Authors
  1. Qin-Mei Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Li Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yongbin Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jianguo Cui
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yuzhang Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Chengming Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Qin-Mei Wang.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Communicated by W. Harwood.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 141 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wang, QM., Wang, L., Zhou, Y. et al. Leaf patterning of Clivia miniata var. variegata is associated with differential DNA methylation. Plant Cell Rep 35, 167–184 (2016). https://doi.org/10.1007/s00299-015-1877-7

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00299-015-1877-7

Keywords

Search

Navigation