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Epigenetic responses to drought stress in rice (Oryza sativa L.)

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Abstract

Cytosine methylation polymorphism plays a key role in gene regulation, mainly in expression of genes in crop plants. The differential expression of cytosine methylation over drought stress response was analyzed in rice using drought susceptible but agronomically superior lines IR 20 and CO 43, and drought tolerant genotypes PL and PMK 3 and their F1 hybrids. The parents and hybrids were subjected to two moisture regimes viz., one under drought condition and another under control condition. The cytosine methylation polymorphism in genomic DNA was quantified under both the conditions at the reproductive stage of the plant using the Methylation Sensitive Amplified Polymorphism (MSAP) technique devised by Xiong et al. (261:439–446, 1999). The results depicted that under drought condition, hyper-methylation was predominant in the drought susceptible genotypes while drought tolerant genotypes presented hypo-methylation behavior. While imposing drought, spikelet sterility per cent was positively correlated to percentage of methylation whereas, panicle length, number of seed per panicle, panicle weight, 100 seed weight, and yield/plant were negatively correlated indicating the role of epigenetic regulation in yield attributing traits in response to drought. Thus, methylation can be considered as an important epigenetic regulatory mechanism in rice plants to adapt drought situation. From this study, we speculate that the hyper- methylation may be an indicator of drought susceptibility and the hypo-methylation for drought tolerance and this methylation polymorphism can be effectively used in drought screening program.

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References

  • Bird A (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16:6–21

    Article  CAS  PubMed  Google Scholar 

  • Boyko A, Kovalchuk I (2008) Epigenetic control of plant stress response. Environ Mol Mutagen 49:61–72

    Article  CAS  PubMed  Google Scholar 

  • Boyko A, Blevins T, Yao Y, Golubov A, Bilichak A, Ilnytskyy Y, Hollander J, Meins F Jr, Kovalchuk I (2010) Transgenerational adaptation of Arabidopsis to stress requires DNA methylation and the function of Dicer-like proteins. PLoS One 5(3):e9514

    Article  PubMed  PubMed Central  Google Scholar 

  • Cao D, Gao X, Liu J, Kimatu JN, Geng S, Wang X, Zhao J, Shi D (2011) Methylation sensitive amplified polymorphism (MSAP) reveals that alkali stress triggers more DNA hypomethylation levels in cotton (Gossypium hirsutum L.) roots than salt stress. Afr J Biotechnol 10(82):18971–18980

    Google Scholar 

  • Chen L, Chen J (2008) Changes of cytosine methylation induced by wide hybridization and allopolyploidy in Cucumis. Genome 51(10):789–799

    Article  CAS  PubMed  Google Scholar 

  • Chinnusamy V, Zhu JK (2009) Epigenetic regulation of stress responses in plants. Curr Opin Plant Biol 12(2):133–139

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Coolen M, Statham A, Gardiner-Garden M, Clark S (2007) Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements. Nucleic Acids Res 35:1–14

    Article  Google Scholar 

  • Deneberg S, Grövdal M, Karimi M, Jansson M, Nahi H, Corbacioglu A, Gaidzik V, Döhner K, Paul C, Ekström TJ, Hellström-Lindberg E, Lehmann S (2010) Gene-specific and global methylation patterns predict outcome in patients with acute myeloid leukemia. Leukemia 24(5):932–941

    Article  CAS  PubMed  Google Scholar 

  • Dowen RH, Pelizzola M et al (2012) Widespread dynamic DNA methylation in response to biotic stress. PNAS 109(32):2183–2191

    Article  Google Scholar 

  • Gawel NJ, Jarret RL (1991) A modified CTAB DNA extraction procedure for Musa and Ipomoea plant. Mol Biol Rep 9:262–266

    Article  CAS  Google Scholar 

  • Grativol C, Hemerly AS, Ferreira PCG (2012) Genetic and epigenetic regulation of stress responses in natural plant populations. Biochim Biophys 1819:176–185

    Article  CAS  Google Scholar 

  • Huizinga DH, Omosegbon O, Omery B, Crowell DN (2008) Isoprenylcysteine methylation and demethylation regulate abscisic acid signaling in Arabidopsis. Plant Cell Online 20(10):2714–2728

    Article  CAS  Google Scholar 

  • Kile ML, Baccarelli A, Tarantini L, Hoffman E, Wright RO, Christiani DC (2010) Correlation of global and gene-specific DNA methylation in maternal-infant pairs. PLoS One 5(10):e13730

    Article  PubMed  PubMed Central  Google Scholar 

  • Klose RJ, Bird AP (2006) Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci 31(2):89–97

    Article  CAS  PubMed  Google Scholar 

  • Kovalchuk I, Abramov V et al (2004) Molecular aspects of plant adaptation to life in the Chernobyl zone. Plant Physiol 135(1):357–363

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Labra M, Ghiani A, Citterio S, Sgorbati S, Sala F, Vannini C, Ruffini-Castiglione M, Bracale M (2002) Analysis of cytosine methylation pattern in response to water deficit in pea root tips. Plant Biol Stuttg 4:694–699

    Article  CAS  Google Scholar 

  • Lin MJ, Tang LY, Reddy MN, Shen CK (2005) DNA methyltransferase gene dDnmt2 and longevity of Drosophila. J Biol Chem 280:861–864

    Article  CAS  PubMed  Google Scholar 

  • Madlung A, Comai L (2004) The effect of stress on genome regulation and structure. Ann Bot 94:481–495

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mandrioli M (2004) Epigenetic tinkering and evolution: is there any continuity in the functional role of cytosine methylation from invertebrates to vertebrates? Cell Mol Life Sci 61:2425–2427

    Article  CAS  PubMed  Google Scholar 

  • Matzke M, Kanno T, Daxinger L, Huettel B, Matzke AJM (2009) RNA-mediated chromatin-based silencing in plants. Curr Opin Plant Biol 21(3):367–376

    Article  CAS  Google Scholar 

  • Maughan PJ, SaghaiMaroof MA, Buss GR, Heustis GM (1996) Amplified fragment length polymorphism AFLP in soybean: species diversity, inheritance and near isogenic line analysis. Theor Appl Genet 93:392–401

    Article  CAS  PubMed  Google Scholar 

  • McCue AD, Nuthikattu S et al (2012) Gene expression and stress response mediated by the epigenetic regulation of a transposable element small RNA. PLoS Genet 8(2):e1002474

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mirouze M, Paszkowski J (2011) Epigenetic contribution to stress adaptation in plants. Curr Opin Plant Biol 14(3):267–274

    Article  CAS  PubMed  Google Scholar 

  • Msogoya T, Grout B (2012) Cytosine DNA methylation changes drought stress responses in tissue culture derived banana (Musa AAA-East Africa) plants. J Appl Biosci 49:3383–3387

    Google Scholar 

  • Ooi SKT, Bestor TH (2008) The colorful history of active DNA demethylation. Cell 133(7):1145–1148

    Article  CAS  PubMed  Google Scholar 

  • Radchuk VV, Sreenivasulu N, Radchuk RI, Wobus U, Weschke W (2005) The methylation cycle and its possible functions in barley endosperm development. Plant Mol Biol 59:289–307

    Article  CAS  PubMed  Google Scholar 

  • Raja P, Sanville BC et al (2008) Viral genome methylation as an epigenetic defense against gemini viruses. J Virol 82(18):8997–9007

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Saze H, Tsugane K et al (2012) DNA methylation in plants: relationship to small RNAs and histone modifications, and functions in transposon inactivation. Plant Cell Physiol 53(5):766–784

    Article  CAS  PubMed  Google Scholar 

  • Shen H et al (2012) Genome-Wide Analysis of DNA Methylation and gene expression changes in two Arabidopsis ecotypes and their reciprocal hybrids. Plant Cell doi:10.1105/tpc.111.094870

    Google Scholar 

  • Simmen MW, Leitgeb S, Charlton J, Jones SJM, Harris BR, Clark VH, Bird A (1999) Non-methylated transposable elements and methylated genes in a chordate genome. Science 283:1164–1167

    Article  CAS  PubMed  Google Scholar 

  • Smart RE, Bingham GE (1974) Rapid estimates of relative water content. Plant Physiol 53(2):258–260

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Steward N, Ito M, Yamakuchi Y, Koizumi N, Sano H (2002) Periodic DNA methylation in maize nucleosomes and demethylation by environmental stress. J Biol Chem 277:37741–37746

    Article  CAS  PubMed  Google Scholar 

  • Suzuki H, Toyota M, Sato H, Sonoda T, Sakauchi F, Mori M (2006) Roles and causes of abnormal DNA methylation in gastrointestinal cancers. Asian Pac J Cancer Prev 7:177–185

    PubMed  Google Scholar 

  • Tricker PJ, Gibbings JG et al (2012) Low relative humidity triggers RNA-directed de novo DNA methylation and suppression of genes controlling stomatal development. J Exp Bot 63(10):3799–3813

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Uthup TK, Ravindran M et al (2011) Divergent DNA methylation patterns associated with abiotic stress in Hevea brasiliensis. Mol Plant 4(6):996–1013

    Article  CAS  PubMed  Google Scholar 

  • Vining KJ, Pomraning KR et al (2012) Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression. BMC Genomics 13(1):27

    Google Scholar 

  • Vos P, Hogers R, Bleeker M, Reijans M, Van De Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang WS, Pan YJ, Zhao XQ, Dwivedi D, Zhu LH, Ali J, Fu BY, Li ZK (2011) Drought-induced site specific DNA methylation and its association with drought tolerance in rice (Oryza sativa L.). J Exp Bot 62(6):1951–1960

    Google Scholar 

  • Xiong LZ, Xu CG, Saghai-Maroof MA, Zhang Q (1999) Patterns of cytosine methylation in an elite rice hybrid and its parental lines, detected by a methylation-sensitive amplification polymorphism technique. Mol Gen Genet 261:439–446

    Article  CAS  PubMed  Google Scholar 

  • Zhang M, Xu C, Wettstein DV, Liu B (2011) Tissue-specific differences in cytosine methylation and their association with differential gene expression in sorghum. Plant Physiol 156(4):1955–1966

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgement

The authors are grateful to the Rockefeller foundation for the research grant RF Grant FS # 114 (2000–2005). The author Gayacharan is also thankful to Department of Biotechnology, (Govt. of India) for the fellowship and contingency grant during research period at Tamil Nadu Agriculture University, Coimbatore.

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Authors and Affiliations

  1. Division of Plant Genetic Resources, Indian Agricultural Research Institute, New Delhi, 110012, India

    Gayacharan

  2. Department of Plant Genetic Resources, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, 641 003, India

    A. John Joel

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  1. Gayacharan
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Correspondence to A. John Joel.

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Gayacharan, Joel, A.J. Epigenetic responses to drought stress in rice (Oryza sativa L.). Physiol Mol Biol Plants 19, 379–387 (2013). https://doi.org/10.1007/s12298-013-0176-4

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