Skip to main content
SpringerLink
Log in

Analysis of methylation-sensitive amplified polymorphism in different cotton accessions under salt stress based on capillary electrophoresis

  • Research Article
  • Published:
Genes & Genomics Aims and scope Submit manuscript

Abstract

A methylation-sensitive amplification polymorphism method based on capillary electrophoresis was used to analyze DNA methylation levels in three cotton accessions, two salt-tolerant accessions CCRI 35 and Zhong 07 and one salt-sensitive accession CCRI 12. Many categories of DNA methylation happened in the three cotton accessions under salt treatment, including hypermethylation, hypomethylation, and other patterns. Hypermethylation happened at a significantly higher rate than that of hypomethylation in salt-tolerant accessions CCRI 35 and Zhong 07. On the contrary, in salt-sensitive accession CCRI 12, hypomethylation happened at a significantly higher rate than that of hypermethylation. In general, the global DNA methylation level significantly increased under salt stress in both salt-tolerant accessions CCRI 35 and Zhong 07, whereas there was no significant difference in the salt-sensitive accessions CCRI 12. Our results suggested that salt-tolerant cotton might have a mechanism of increasing the methylation level when responding to salt stress; the increase of the global level of DNA methylation and also different methylation patterns might play important roles in tolerance to salt stress in cotton. Some interesting genes were found through cloning and analysis of differently methylated DNA sequences, which might contribute to salt tolerance in cotton.

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

Similar content being viewed by others

References

  • Aina R, Sgorbati S, Santagostino A, Labra A, Ghiani A, Citterio S (2004) Specific hypomethylation of DNA is induced by heavy metals in white clover and industrial hemp. Physiol Plantarum 121:472–480

    Article  CAS  Google Scholar 

  • Angers B, Castonguay E, Massicotte R (2010) Environmentally induced phenotypes and DNA methylation: how to deal with unpredictable conditions until the next generation and after. Mol Ecol 19:1283–1295

    Article  CAS  PubMed  Google Scholar 

  • Bilichak A, Ilnystkyy Y, Hollunder J, Kovalchuk I (2012) The progeny of Arabidopsis thaliana plants exposed to salt exhibit changes in DNA methylation, histone modifications and gene expression. PLoS ONE 7:e30515

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Bonasio R, Tu S, Reinberg D (2010) Molecular signals of epigenetic states. Science 330:612–616

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Boyko A, Kathiria P, Zemp FJ, Yao Y, Pogribny I, Kovalchuk I (2007) Transgenerational changes in the genome stability and methylation in pathogen-infected plants. Nucleic Acids Res 35:1714–1725

    Article  PubMed Central  CAS  PubMed  Google Scholar 

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

    CAS  Google Scholar 

  • Choi CS, Sano H (2007) Abiotic-stress induces demethylation and transcriptional activation of a gene encoding a glycerophosphodiesterase-like protein in tobacco plants. Mol Genet Genomics 277:589–600

    Article  CAS  PubMed  Google Scholar 

  • Cui MH, Yoo KS, Hyoung S, Nguyen HTK, Kim YY, Kim HJ, Ok SH, Yoo SD, Shin JS (2013) An Arabidopsis R2R3-MYB transcription factor, AtMYB20, negatively regulates type 2C serine/threonine protein phosphatases to enhance salt tolerance. FEBS Lett 587:1773–1778

    Article  CAS  PubMed  Google Scholar 

  • Dyachenko OV, Zakharchenko NS, Shevchuk TV, Bohnert HJ, Cushman JC, Buryanov YI (2006) Effect of hypermethylation of CCWGG sequences in DNA of Mesembryanthemum crystallinum plants on their adaptation to salt stress. Biochemistry (Moscow) 71:461–465

    Article  CAS  Google Scholar 

  • Flowers TJ, Yeo AR (1995) Breeding for salinity resistance in crop plants: where next? Aust J Plant Physiol 22:875–884

    Article  Google Scholar 

  • Gao S, Zhang YL, Yang L, Song JB, Yang ZM (2014) AtMYB20 is negatively involved in plant adaptive response to drought stress. Plant Soil 376:433–443

    Article  CAS  Google Scholar 

  • Golldack D, Lüking I, Yang O (2011) Plant tolerance to drought and salinity: stress regulating transcription factors and their functional significance in the cellular transcriptional network. Plant Cell Rep 30:1383–1391

    Article  CAS  PubMed  Google Scholar 

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

    CAS  Google Scholar 

  • Guo WZ, Zhang TZ, Sheng XL, John Y, Kohel RJ (2003) Development of SCAR marker linked to a major QTL for high fiber strength and its molecular marker assisted selection in Upland cotton. Crop Sci 6:2252–2256

    Article  Google Scholar 

  • Hirose N, Takei K, Kuroha T, Kamada-Nobusada T, Hayashi H, Sakakibara H (2008) Regulation of cytokinin biosynthesis, compartmentalization and translocation. J Exp Bot 59:75–83

    Article  CAS  PubMed  Google Scholar 

  • Jiang YR, Lv YJ, Zhu SJ (2006) Advance in studies of the mechanism of salt tolerance and controlling of salt damage in Upland cotton. Cotton Sci 18:248–254

    Google Scholar 

  • Keyte AL, Percifield R, Liu B, Wendel JF (2006) Infraspecific DNA methylation polymorphism in cotton (Gossypium hirsutum L.). J Hered 97:444–450

    Article  CAS  PubMed  Google Scholar 

  • Kimatu JN, Diarso M, Song CD, Agboola RS, Pang JS, Qi X, Liu B (2011) DNA cytosine methylation alterations associated with aluminium toxicity and low pH in Sorghum bicolor. Afr J Agr Res 6:4579–4593

    Google Scholar 

  • Kovarik A, Koukalova B, Bezdek M, Opatrny Z (1997) Hypermethylation of tobacco heterochromatic loci in response to osmotic stress. Theor Appl Genet 95:301–306

    Article  Google Scholar 

  • Labra M, Grassi F, Imazio S, Fabio TD, Citterio S, Sgorbati S, Agradi E (2004) Genetic and DNA-methylation changes induced by potassium dichromate in Brassica napus L. Chemosphere 54:1049–1058

    Article  CAS  PubMed  Google Scholar 

  • Li XL, Lin ZX, Nie YC, Guo XP, Zhang XL (2009) MSAP analysis of epigenetic changes in cotton (Gossypium hirsutum L.) under salt stress. Acta Agro Sinica 35:588–596

    CAS  Google Scholar 

  • Lukens LN, Zhan SH (2007) The plant genome’s methylation status and response to stress, implications for plant improvement. Curr Opin Plant Biol 10:317–322

    Article  CAS  PubMed  Google Scholar 

  • Mahajan S, Tuteja N (2005) Cold, salinity and drought stresses: an overview. Arch Biochem Biophys 444:139–158

    Article  CAS  PubMed  Google Scholar 

  • Mastan SG, Rathore MS, Bhatt VD, Yadav P, Chikara J (2012) Assessment of changes in DNA methylation by methylation-sensitive amplification polymorphism in Jatropha curcas L. subjected to salinity stress. Gene 508:125–129

    Article  CAS  PubMed  Google Scholar 

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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Morgan SH, Maity PJ, Geilfus CM, Lindberg S, Mühling KH (2014) Leaf ion homeostasis and plasma membrane H+-ATPase activity in Vicia faba change after extra calcium and potassium supply under salinity. Plant Physiol Biochem 82:244–253

    Article  CAS  PubMed  Google Scholar 

  • Nishiyama R, Watanabe Y, Fujita Y, Le DT, Kojima M, Werner T, Vankova R, Yamaguchi-Shinozaki K, Shinozaki K, Kakimoto T, Sakakibara H, Schmülling T, Trana LSP (2011) Analysis of cytokinin mutants and regulation of cytokinin metabolic genes reveals important regulatory roles of cytokinins in drought, salt and abscisic Acid responses, and abscisic acid biosynthesis. Plant Cell 23:2169–2183

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Nishiyama R, Le DT, Watanabe Y, Matsui A, Tanaka M, Seki M, Yamaguchi-Shinozaki K, Shinozaki K, Tran LS (2012) Transcriptome analyses of a salt-tolerant cytokinin-deficient mutant reveal differential regulation of salt stress response by cytokinin deficiency. PLoS ONE 7:e32124

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Osabe K, Clement JD, Bedon F, Pettolino FA, Ziolkowski L, Llewellyn DJ, Finnegan EJ, Wilson IW (2014) Genetic and DNA methylation changes in cotton (Gossypium) genotypes and tissues. PLoS ONE 9:e86049

    Article  PubMed Central  PubMed  Google Scholar 

  • Paterson AH, Brubaker CL, Wendel JF (1993) A rapid method for extraction of cotton (Gossypium spp.) genomic DNA suitable for RFLP or PCR analysis. Plant Mol Biol Rep 11:122–127

    Article  CAS  Google Scholar 

  • Peng H, Zhang J (2009) Plant genomic DNA methylation in response to stresses: potential applications and challenges in plant breeding. Prog Nat Sci 19:1037–1045

    Article  CAS  Google Scholar 

  • Reyna-López GE, Simpson J, Ruiz-Herresa J (1997) Differences in DNA methylation patterns are detectable during the dimorphic transition of fungi by amplification of restriction polymorphisms. Mol Gen Genet 253:703–710

    Article  PubMed  Google Scholar 

  • Shan H, Chen S, Jiang J, Chen F, Chen Y, Gu C, Li P, Song A, Zhu X, Gao H, Zhou G, Li T, Yang X (2012) Heterologous expression of the Chrysanthemun R2R3-MYB transcription factor CmMYB2 enhances drought and salinity tolerance, increases hypersensitivity to ABA and delays flowering in Arabidopsis thaliana. Mol Biotechnol 51:160–173

    Article  CAS  PubMed  Google Scholar 

  • Shan XH, Wang XY, Yang G, Wu Y, Su SZ, Li SP, Liu HK, Yuan YP (2013) Analysis of the DNA methylation of Maize (Zea mays L.) in response to cold stress based on methylation-sensitive amplified polymorphisms. J Plant Biol 56:32–38

    Article  CAS  Google Scholar 

  • Shi WN, Liu DD, Hao LL, Wu CA, Guo XQ, Li H (2014) GhWRKY39, a member of the WRKY transcription factor family in cotton, has a positive role in disease resistance and salt stress tolerance. Plant Cell Tissue Organ Cult 118:17–32

    Article  CAS  Google Scholar 

  • Sun J, Wang MJ, Ding MQ, Deng SR, Liu MQ, Lu CF, Zhou XY, Shen X, Zheng XJ, Zhang ZK, Song J, Hu ZM, Xu Y, Chen SL (2010) H2O2 and cytosolic Ca2+ signals triggered by the PM H+-coupled system mediate K+/Na+ homeostasis in NaCl-stressed Populus euphratica cells. Plant Cell Environ 33:943–958

    Article  CAS  PubMed  Google Scholar 

  • Tan MP (2010) Analysis of DNA methylation of maize in response to osmotic and salt stress based on methylation-sensitive amplified polymorphism. Plant Physiol Biochem 48:21–26

    Article  CAS  PubMed  Google Scholar 

  • Türkana I, Demiral T (2009) Recent developments in understanding salinity tolerance. Environ Exp Bot 67:2–9

    Article  Google Scholar 

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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Wang WS, Zhao XQ, Pan YJ, Zhu LH, Fu BY, Li ZK (2011b) DNA methylation changes detected by methylation-sensitive amplified polymorphism in two contrasting rice genotypes under salt stress. J Genet Genomics 38:419–424

    Article  CAS  PubMed  Google Scholar 

  • Wikström N, Savolainen V, Chase MW (2001) Evolution of the angiosperms: calibrating the family tree. Proc Biol Sci 268:2211–2220

    Article  PubMed Central  PubMed  Google Scholar 

  • Xiong LZ, Xu CG, Saghai Maroof MA, Zhang QF (1999) Patterns of cytosine methylation pattern in an elite rice hybrid and its parental lines detected by a methylation-sensitive amplification polymorphism technique. Mol Gen Genet 261:139–446

    Article  Google Scholar 

  • Xu ML, Li XQ, Korban SS (2000) AFLP-based detection of DNA methylation. Plant Mol Biol Rep 18:361–368

    Article  CAS  Google Scholar 

  • Xu Q, Sun DX, Zhang Y (2005) F-MSAP: a practical system to detect methylation in chicken genome. Chin Sci Bull 50:2039–2044

    Article  CAS  Google Scholar 

  • Yang JL, Liu LW, Gong YQ, Huang DQ, Wang F, He LL (2007) Analysis of genomic DNA methylation level in radish under cadmium stress by methylation sensitive amplified polymorphism technique. J Plant Physiol Mol Biol 33:219–226

    CAS  Google Scholar 

  • Zemach A, McDaniel IE, Silva P, Zilberman D (2010) Genome-wide evolutionary analysis of eucaryotic DNA methylation. Science 328:916–919

    Article  CAS  PubMed  Google Scholar 

  • Zhang LN, Ye WW, Wang JJ, Fan BX (2010) Studies of salinity-tolerance with SSR markers on G. hirsutum L. Cotton Sci 22:175–180

    CAS  Google Scholar 

  • Zhao YL, Yu SX, Ye WW, Wang HM, Wang JJ, Fan BX (2010) Study on DNA cytosine methylation of cotton (Gossypium hirsutum L.) genome and its implication for salt tolerance. Agric Sci China 9:783–791

    Article  CAS  Google Scholar 

  • Zhao J, Gao Y, Zhang Z, Chen T, Guo W, Zhang T (2013) A receptor-like kinase gene (GbRLK) from Gossypium barbadense enhances salinity and drought-stress tolerance in Arabidopsis. BMC Plant Biol 13:110

    Article  PubMed Central  PubMed  Google Scholar 

  • Zhu JK (2001) Plant salt tolerance. Trends Plant Sci 6:66–71

    Article  CAS  PubMed  Google Scholar 

  • Zhu YN, Shi DQ, Ruan MB, Zhang LL, Meng ZH, Liu J, Yang WC (2013) Transcriptome analysis reveals crosstalk of responsive genes to multiple abiotic stresses in cotton (Gossypium hirsutum L.). PLoS ONE 8:e80218

    Article  PubMed Central  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

Research supported by the Natural Science Foundation of Jiangsu Province of China (BK20131204, BK20130429), the National Natural Science Foundation of China (31000729), the State Key Laboratory of Cotton Biology Open Fund (CB2015A09, CB2013A12), the State Foundation for Studying Abroad (2015), the National Practice Innovation Training Program Projects for College Students (2015).

Conflict of interest

The authors declare that they have no conflict of interest.

Author information

Authors and Affiliations

  1. School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People’s Republic of China

    Baohua Wang, Rong Fu, Mi Zhang, Lei Chang, Xinyu Zhu & Yafeng Wang

  2. State Key Laboratory of Cotton Biology; Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, People’s Republic of China

    Baoxiang Fan, Wuwei Ye & Youlu Yuan

  3. Xuzhou Institute of Agricultural Sciences of Xu-huai Region of Jiangsu, Xuzhou, 221131, Jiangsu, People’s Republic of China

    Zhenqian Ding

Authors
  1. Baohua Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Rong Fu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Mi Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Zhenqian Ding
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Lei Chang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Xinyu Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Yafeng Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Baoxiang Fan
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Wuwei Ye
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Youlu Yuan
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Baohua Wang.

Electronic supplementary material

Below are the links to the electronic supplementary material.

Table S1 (DOC 37 kb)

Table S2 (DOC 34 kb)

Table S3 (XLSX 10 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wang, B., Fu, R., Zhang, M. et al. Analysis of methylation-sensitive amplified polymorphism in different cotton accessions under salt stress based on capillary electrophoresis. Genes Genom 37, 713–724 (2015). https://doi.org/10.1007/s13258-015-0301-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13258-015-0301-6

Keywords

Search

Navigation