Skip to main content
Log in

Changes in micro RNA expression in a wild tuber-bearing Solanum species induced by 5-Azacytidine treatment

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

Abstract

Phenotypic plasticity is often postulated as a principal characteristic of tuber-bearing wild Solanum species. The hypotheses to explore this observation have been developed based on the presence of genetic variation. In this context, evolutionary changes and adaptation are impossible without genetic variation. However, epigenetic effects, which include DNA methylation and microRNAs expression control, could be another source of phenotypic variation in ecologically relevant traits. To achieve a detailed mechanistic understanding of these processes, it is necessary to separate epigenetic from DNA sequence-based effects and to evaluate their relative importance on phenotypic variability. We explored the potential relevance of epigenetic effects in individuals with the same genotype. For this purpose, a clone of the wild potato Solanum ruiz-lealii, a non-model species in which natural methylation variability has been demonstrated, was selected and its DNA methylation was manipulated applying 5-Azacytidine (AzaC), a demethylating agent. The AzaC treatment induced early flowering and changes in leaf morphology. Using quantitative real-time PCR, we identified four miRNAs up-regulated in the AzaC-treated plants. One of them, miRNA172, could play a role on the early flowering phenotype. In this work, we showed that the treatment with AzaC could provide meaningful results allowing to study both the phenotypic plasticity in tuber-bearing Solanum species and the inter-relation between DNA methylation and miRNA accumulations in a wide range of species.

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

Access this article

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

Similar content being viewed by others

References

  • Ahluwalia JK, Hariharan M, Bargaje R, Pillai B, Brahmachari V (2009) Incomplete penetrance and variable expressivity: is there a microRNA connection? BioEssays 31:981–992

    Article  PubMed  CAS  Google Scholar 

  • Alvarez NMB, Peralta IE, Salas A, Spooner DM (2008) A morphological study of species boundaries of the wild potato Solanum brevicaule complex: replicated field trials in Peru. Plant Syst Evol 274:37–45

    Article  Google Scholar 

  • Aukerman MJ, Sakai H (2003) Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. Plant Cell 15:2730–2741

    Article  PubMed  CAS  Google Scholar 

  • Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297

    Article  PubMed  CAS  Google Scholar 

  • Bazzini AA, Almasia NI, Manacorda CA, Mongelli VC, Conti G, Maroniche GA, Rodriguez MC, Distéfano AJ, Hopp HE, del Vas M, Asurmendi S (2009) Virus infection alters transcriptional activity of miR164a promoter in plants. BMC Plant Biol 9:152. ISSN:1471-2229

    Google Scholar 

  • Bazzini AA, Manacorda CA, Tohge T, Conti G, Rodriguez MC, Nunes-Nesi A, Villanueva S, Fernie AR, Carrari F, Asurmendi S (2011) Metabolic and miRNA profiling of TMV infected plants reveals biphasic temporal changes. Plos One 6:e28466

    Article  PubMed  CAS  Google Scholar 

  • Bedogni MC, Camadro EL (2009) Morphological and molecular evidence of natural interspecific hybridization in the diploid potato Solanum kurtzianum from Argentina. Botany 87:78–87

    Article  Google Scholar 

  • Benetti R, Gonzalo S, Jaco I, Muñoz P, Gonzalez S, Schoeftner S, Murchison E, Andl T, Chen T, Klatt P, Li E, Serrano M, Millar S, Hannon G, Blasco MA (2008) A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2-dependent regulation of DNA methyltransferases. Nat Struct Mol Biol 15:268–279

    Article  PubMed  CAS  Google Scholar 

  • Berger Y, Harpaz-Saad S, Brand A, Melnik H, Sirding N, Alvarez JP, Zinder M, Samach A, Eshed Y, Ori N (2009) The NAC-domain transcription factor GOBLET specifies leaflet boundaries in compound tomato leaves. Development 136:823–832

    Article  PubMed  CAS  Google Scholar 

  • Bossdorf O, Arcuri D, Richards CL, Pigliucci M (2010) Experimental alteration of DNA methylation affects the phenotypic plasticity of ecologically relevant traits in Arabidopsis thaliana. Evol Ecol 24:541–553

    Article  Google Scholar 

  • Brown JCL, De Decker MM, Fieldes MA (2008) A comparative analysis of developmental profiles for DNA methylation in 5-azacytidine-induced early-flowering flax lines and their control. Plant Sci 175:217–225

    Article  CAS  Google Scholar 

  • Burn JE, Bagnall DJ, Metzger JD, Dennis ES, Peacock WJ (1993) DNA methylation, vernalization, and the initiation of flowering. Proc Natl Acad Sci USA 90:287–291

    Article  PubMed  CAS  Google Scholar 

  • Cocciolone SM, Chopra S, Flint-Garcia SA, McMullen MD, Peterson T (2001) Tissue-specific patterns of a maize Myb transcription factor are epigenetically regulated. Plant J 5:467–478

    Article  Google Scholar 

  • Correll DS (1962) The potato and its wild relatives. Contributions from the Texas Research Foundation, Botanical Studies 4:1–606

    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 

  • Di Rienzo JA (2009) fgStatistics, version 2009. Córdoba, Argentina. http://sites.google.com/site/fgstatistics

  • Egger G, Liang G, Aparicio A, Jones PA (2004) Epigenetics in human disease and prospects for epigenetic therapy. Nature 429:457–463

    Article  PubMed  CAS  Google Scholar 

  • Erazzú LE, Camadro EL, Clausen AM (2009) Persistence over time, overlapping distribution and molecular indications of interspecific hybridization in wild potato populations of Northwest Argentina. Euphytica 168:249–262

    Article  Google Scholar 

  • Eriksson S, Böhlenius H, Moritz T, Nilsson O (2006) GA4 is the active gibberellin in the regulation of LEAFY transcription and Arabidopsis floral initiation. Plant Cell 18:2172–2181

    Article  PubMed  CAS  Google Scholar 

  • Fieldes MA, Amyot LM (1999) Epigenetic control of early flowering in flax lines induced by 5-azacytidine applied to germinating seed. J Heredity 90:199–206

    Article  CAS  Google Scholar 

  • Fieldes MA, Schaeffer SM, Krech MJ, Brown JCL (2005) DNA hypomethylation in 5-azacytidine-induced early-flowering lines of flax. Theor Appl Genet 111:136–149

    Article  PubMed  CAS  Google Scholar 

  • Gutierrez L, Bussell JD, Pǎcurar DI, Schwambach J, Pǎcurar M, Bellini C (2009) Phenotypic plasticity of adventitious rooting in Arabidopsis is controlled by complex regulation of AUXIN RESPONSE FACTOR transcripts and microRNA abundance. Plant Cell 21:3119–3132

    Article  PubMed  CAS  Google Scholar 

  • Ha M, Lu J, Tian L, Ramachandran V, Kasschau KD, Chapman EJ, Carrington JC, Chen X, Wang XJ, Chen ZJ (2009) Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids. Proc Natl Acad Sci USA 106:17835–17840

    Article  PubMed  CAS  Google Scholar 

  • Hijmans RJ, Spooner DM, Salas AR, Guarino L, de la Cruz J (2002) Atlas of wild potatoes. International Plant Genetic Resources Institute, Rome

    Google Scholar 

  • Iwase Y, Shiraya T, Takeno K (2010) Flowering and dwarfism induced by DNA demethylation in Pharbitis nil. Physiol Plant 139:118–127

    Article  PubMed  CAS  Google Scholar 

  • Jacobs MMJ, van den Berg RG, Vleeshouwers VGAA, Visser M, Mank R, Sengers M, Hoekstra R, Vosman B (2008) AFLP analysis reveals a lack of phylogenetic structure within Solanum section Petota. BMC Evol Biol 8:145

    Article  PubMed  Google Scholar 

  • Jacobsen SE, Meyerowitz EM (1997) Hypermethylated SUPERMAN epigenetic alleles in Arabidopsis. Science 277:1100–1103

    Article  PubMed  CAS  Google Scholar 

  • Janoušek B, Široký J, Vyskot B (1996) Epigenetic control of sexual phenotype in a dioecious plant, Melandrium album. Mol Gen Genet 250:483–490

    Article  PubMed  Google Scholar 

  • Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 57:19–53

    Article  PubMed  CAS  Google Scholar 

  • Jung J-H, Seo Y-H, Pil JS, Reyes JL, Yun J, Chua NH, Park CM (2007) The GIGANTEA-regulated microRNA172 mediates photoperiodic flowering independent of CONSTANS in Arabidopsis. Plant Cell 19:2736–2748

    Article  PubMed  CAS  Google Scholar 

  • Kalisz S, Purugganan MD (2004) Epialleles via DNA methylation: consequences for plant evolution. Trends Ecol Evol 19:309–314

    Article  PubMed  Google Scholar 

  • Khraiwesh B, Zhu J-K, Zhu J (2012) Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants. Biochim Biophys Acta 1819:137–148

    Article  PubMed  CAS  Google Scholar 

  • King GJ (1995) Morphological development in Brassica oleracea is modulated by in vivo treatment with 5-azacytidine. J Hort Sci 70:333–342

    CAS  Google Scholar 

  • Kondo H, Miura T, Wada KC, Takeno K (2007) Induction of flowering by 5-azacytidine in some plant species: Relationship between the stability of photoperiodically induced flowering and flower-inducing effect of DNA demethylation. Physiol Plant 131:462–469

    Article  PubMed  CAS  Google Scholar 

  • Kondo H, Shiraya T, Wada KC, Takeno K (2010) Induction of flowering by DNA demethylation in Perilla frutescens and Silene armeria: heritability of 5-azacytidine-induced effects and alteration of the DNA methylation state by photoperiodic conditions. Plant Sci 178:321–326

    Article  CAS  Google Scholar 

  • Li C, Zhang K, Zeng X, Jackson S, Zhou Y, Hong Y (2009) A cis element within Flowering Locus T mRNA determines its mobility and facilitates trafficking of heterologous viral RNA. J Virol 83:3540–3548

    Article  PubMed  CAS  Google Scholar 

  • Lin MK, Belanger H, Lee YJ, Varkonyi-Gasic E, Taoka K, Miura E, Xoconostle-Cázares B, Gendler K, Jorgensen RA, Phinney B, Lough TJ, Lucas WJ (2007) FLOWERING LOCUS T protein may act as the long-distance florigenic signal in the Cucurbits. Plant Cell 19:1488–1506

    Article  PubMed  CAS  Google Scholar 

  • Marfil CF, Camadro EL, Masuelli RW (2009) Phenotypic instability and epigenetic variability in a diploid potato of hybrid origin, Solanum ruiz-lealii. BMC Plant Biol 9:21

    Article  PubMed  Google Scholar 

  • Martin A, Adam H, Díaz-Mendoza M, Źurczak M, González-Schain ND, Suárez-López P (2009) Graft-transmissible induction of potato tuberization by the microRNA miR172. Development 136:2873–2881

    Article  PubMed  CAS  Google Scholar 

  • Masuelli RW, Camadro EL, Erazzú LE, Bedogni MC, Marfil CF (2009) Homoploid hybridization in the origin and evolution of wild diploid potato species. Plant Syst Evol 277:143–151

    Article  Google Scholar 

  • Mathieu J, Yant LJ, Mürdter F, Küttner F, Schmid M (2009) Repression of flowering by the miR172 target SMZ. PLoS Biol 7:e1000148

    Article  PubMed  Google Scholar 

  • McClelland M, Nelson M, Raschke E (1994) Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases. Nuc Acids Res 22:3640–3659

    Article  CAS  Google Scholar 

  • Megraw M, Baev V, Rusinov V, Jensen ST, Kalantidis K, Hatzigeorgiou AG (2006) MicroRNA promoter element discovery in Arabidopsis. RNA 12:1612–1619

    Article  PubMed  CAS  Google Scholar 

  • Miller JT, Spooner DM (1999) Collapse of species boundaries in the wild potato Solanum brevicaule complex (Solanaceae, sect. Petota): Molecular data. Plant Syst Evol 214:103–130

    Article  Google Scholar 

  • Mlotshwa S, Yang Z, Kim Y, Chen X (2006) Floral patterning defects induced by Arabidopsis APETALA2 and microRNA172 expression in Nicotiana benthamiana. Plant Mol Biol 61:781–793

    Article  PubMed  CAS  Google Scholar 

  • Nicot N, Hausman J-F, Hoffmann L, Evers D (2005) Housekeeping gene selection for real-time RT-PCR normalization in potato during biotic and abiotic stress. J Exp Bot 56:2907–2914

    Article  PubMed  CAS  Google Scholar 

  • Pfaffl MW, Horgan GW, Dempfle L (2002) Relative expression software tool (REST) for group-wise comparison and statistical analysis of relative expression results in real-time PCR. Nuc Acids Res 30:e36

    Article  Google Scholar 

  • Raimondi JP, Peralta IE, Masuelli RW, Feingold S, Camadro EL (2005) Examination of the hybrid origin of the wild potato Solanum ruiz-lealii Brücher. Plant Syst Evol 253:33–51

    Article  Google Scholar 

  • Ramakers C, Ruijter JM, Deprez RH, Moorman AF (2003) Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neurosci Lett 339:62–66

    Article  PubMed  CAS  Google Scholar 

  • Sano H, Kamada I, Youssefian S, Katsumi M, Wabiko H (1990) A single treatment of rice seedlings with 5-azacytidine induces heritable dwarfism and undermethylation of genomic DNA. Mol Gen Genet 220:441–447

    Article  CAS  Google Scholar 

  • Sato F, Tsuchiya S, Meltzer SJ, Shimizu K (2011) MicroRNAs and epigenetics. FEBS J 278:1598–1609

    Article  PubMed  CAS  Google Scholar 

  • Schmid M, Uhlenhaut NH, Godard F, Demar M, Bressan R, Weigel D, Lohmann JU (2003) Dissection of floral induction pathways using global expression analysis. Development 130:6001–6012

    Article  PubMed  CAS  Google Scholar 

  • Sinkkonen L, Hugenschmidt T, Berninger P, Gaidatzis D, Mohn F, Artus-Revel CG, Zavolan M, Svoboda P, Filipowicz W (2008) MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells. Nat Struct Mol Biol 15:259–267

    Article  PubMed  CAS  Google Scholar 

  • Solis JS, Ulloa DM, Rodríguez LA (2007) Molecular description and similarity relationships among native germplasm potatoes (Solanum tuberosum ssp. tuberosum L.) using morphological data and AFLP markers. Elect J Biot 10:436–443

    CAS  Google Scholar 

  • Soppe WJJ, Jacobsen SE, Alonso-Blanco C, Jackson JP, Kakutani T, Koornneef M, Peeters AJ (2000) The late flowering phenotype of fwa mutants is caused by gain-of-function epigenetic alleles of a homeodomain gene. Mol Cell 6:791–802

    Article  PubMed  CAS  Google Scholar 

  • Spooner DM, Castillo RT (1997) Reexamination of series relationships of South American wild potatoes (Solanaceae: Solanum sect. Petota): evidence from chloroplast DNA restriction site variation. Amer J Bot 84:671–685

    Article  CAS  Google Scholar 

  • Spooner DM, McLean K, Ramsay G, Waugh R, Bryan GJ (2005) A single domestication for potato based on multilocus amplified fragment length polymorphism genotyping. Proc Natl Acad Sci USA 102:14694–14699

    Article  PubMed  CAS  Google Scholar 

  • Stokes TL, Kunkel BN, Richards EJ (2002) Epigenetic variation in Arabidopsis disease resistance. Genes Dev 16:171–182

    Article  PubMed  CAS  Google Scholar 

  • Stresemann C, Lyko F (2008) Modes of action of the DNA methyltransferase inhibitors azacytidine and decitabine. Int J Cancer 123:8–13

    Article  PubMed  CAS  Google Scholar 

  • Vyskot B, Koukalová B, Kovařík A, Sachambula L, Reynolds D, Bezděk M (1995) Meiotic transmission of a hypomethylated repetitive DNA family in tobacco. Theor Appl Genet 91:659–664

    Article  CAS  Google Scholar 

  • Wellmer F, Riechmann JL (2010) Gene networks controlling the initiation of flower development. Trends Genet 26:519–527

    Article  PubMed  CAS  Google Scholar 

  • Wu L, Zhou H, Zhang Q, Zhang J, Ni F, Liu C, Qi Y (2010) DNA methylation mediated by a microRNA pathway. Mol Cell 38:465–475

    Article  PubMed  CAS  Google Scholar 

  • Zhang W, Luo Y, Gong X, Zeng W, Li S (2009) Computational identification of 48 potato microRNAs and their targets. Comput Biol Chem 33:84–93

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by grants of Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT), Ministerio de Ciencia y Tecnología de Argentina PICT 2007-1294 and by INTA PE 243532. We are grateful to Ariel Bazzini and Carlos Manacorda (Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria Castelar) for valuable technical assistance with qPCR analysis, and Julia V. Sabio y García (Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria Castelar) for critical reading of the manuscript.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Carlos F. Marfil.

Additional information

Communicated by P. Kumar.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 872 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Marfil, C.F., Asurmendi, S. & Masuelli, R.W. Changes in micro RNA expression in a wild tuber-bearing Solanum species induced by 5-Azacytidine treatment. Plant Cell Rep 31, 1449–1461 (2012). https://doi.org/10.1007/s00299-012-1260-x

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00299-012-1260-x

Keywords

Navigation