Molecular Biology Reports

, Volume 41, Issue 7, pp 4623–4629 | Cite as

Differential regulation of microRNAs in response to osmotic, salt and cold stresses in wheat

  • Om Prakash Gupta
  • Nand Lal Meena
  • Indu Sharma
  • Pradeep Sharma


MicroRNAs (miRNAs) are tiny non-coding regulatory molecules that modulate plant’s gene expression either by cleaving or repressing their mRNA targets. To unravel the plant actions in response to various environmental factors, identification of stress related miRNAs is essential. For understanding the regulatory behaviour of various abiotic stresses and miRNAs in wheat genotype C-306, we examined expression profile of selected conserved miRNAs viz. miR159, miR164, miR168, miR172, miR393, miR397, miR529 and miR1029 tangled in adapting osmotic, salt and cold stresses. The investigation revealed that two miRNAs (miR168, miR397) were down-regulated and miR172 was up-regulated under all the stress conditions. However, miR164 and miR1029 were up-regulated under cold and osmotic stresses in contrast to salt stress. miR529 responded to cold alone and does not change under osmotic and salt stress. miR393 showed up-regulation under osmotic and salt, and down-regulation under cold stress indicating auxin based differential cold response. Variation in expression level of studied miRNAs in presence of target genes delivers a likely elucidation of miRNAs based abiotic stress regulation. In addition, we reported new stress induced miRNAs Ta-miR855 using computational approach. Results revealed first documentation that miR855 is regulated by salinity stress in wheat. These findings indicate that diverse miRNAs were responsive to osmotic, salt and cold stress and could function in wheat response to abiotic stresses.


miRNAs Wheat Drought Cold Salt 

Supplementary material

11033_2014_3333_MOESM1_ESM.doc (34 kb)
Supplementary material 1 (DOC 33 kb)


  1. 1.
    Kawaguchi R, Girke T, Bray EA, Bailey-Serres J (2004) Differential mRNA translation contributes to gene regulation under non-stress and dehydration stress conditions in Arabidopsis thaliana. Plant J 38:823–839CrossRefPubMedGoogle Scholar
  2. 2.
    Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297CrossRefPubMedGoogle Scholar
  3. 3.
    Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu JK (2005) Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulates salt tolerance in Arabidopsis. Cell 123:1279–1291PubMedCentralCrossRefPubMedGoogle Scholar
  4. 4.
    Navarro L, Dunoyer P, Jay F, Arnold B, Dharmasiri N, Estelle M, Voinnet O, Jones JD (2006) A plant miRNA contributes to antibacterial resistance by repressing auxin signalling. Science 312:436–439CrossRefPubMedGoogle Scholar
  5. 5.
    Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M, Dunoyer P, Yamamoto YY, Sieburth L, Voinnet O (2008) Widespread translational inhibition by plant miRNAs and siRNAs. Science 320:1185–1190CrossRefPubMedGoogle Scholar
  6. 6.
    Abdel-Ghany SE, Pilon M (2008) MicroRNA-mediated systemic down-regulation of copper protein expression in response to low copper availability in Arabidopsis. J Biol Chem 28:15932–15945CrossRefGoogle Scholar
  7. 7.
    Voinnet O (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 36:669–687CrossRefGoogle Scholar
  8. 8.
    Wu G, Park MY, Conway SR, Wang JW, Weigel D, Poethig RS (2009) The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell 138:750–759PubMedCentralCrossRefPubMedGoogle Scholar
  9. 9.
    Vazquez F, Legrand S, Windels D (2010) The biosynthetic pathways and biological scopes of plant small RNAs. Trends Plant Sci 15:337–345CrossRefPubMedGoogle Scholar
  10. 10.
    Surekha-Katiyar A, Shang G, Adam VS, Hailing J (2007) A novel class of bacteria-induced small RNAs in Arabidopsis. Genes Dev 21:3123–3134CrossRefGoogle Scholar
  11. 11.
    Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 57:19–53CrossRefPubMedGoogle Scholar
  12. 12.
    Sunkar R, Zhu JK (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16:2001–2019PubMedCentralCrossRefPubMedGoogle Scholar
  13. 13.
    Zhao B, Liang R, Ge L, Li W, Xiao H, Lin H, Ruan K, Jin Y (2007) Identification of drought-induced microRNAs in rice. Biochem Biophys Res Commun 354:585–590CrossRefPubMedGoogle Scholar
  14. 14.
    Zhou X, Wang G, Zhang W (2007) UV-B responsive microRNA genes in Arabidopsis thaliana. Mol Syst Biol 3:103–112PubMedCentralCrossRefPubMedGoogle Scholar
  15. 15.
    Huang SQ, Peng J, Qiu CX, Yang ZM (2009) Heavy metal-regulated new microRNAs from rice. J Inorg Biochem 3:282–287CrossRefGoogle Scholar
  16. 16.
    Gupta OP, Sharma P, Gupta RK, Sharma I (2014) MicroRNA mediated regulation of metal toxicity in plants: present status and future perspectives. Plant Mol Biol 84:1–18CrossRefPubMedGoogle Scholar
  17. 17.
    Jones-Rhoades MW, Bartel DP (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14:787–799CrossRefPubMedGoogle Scholar
  18. 18.
    Pant BD, Musialak-Lange M, Nuc P, May P, Buhtz A, Kehr J, Walther D, Scheible WR (2009) Identification of nutrient-responsive Arabidopsis and rapeseed microRNAs by comprehensive real-time polymerase chain reaction profiling and small RNA sequencing. Plant Physiol 150:1541–1555PubMedCentralCrossRefPubMedGoogle Scholar
  19. 19.
    Xu Z, Zhong S, Li X, Li W, Rothstein SJ, Zhang S, Bi Y, Xie C (2011) Genome-wide identification of microRNAs in response to low nitrate availability in maize leaves and roots. PLoS ONE 6:e28009PubMedCentralCrossRefPubMedGoogle Scholar
  20. 20.
    Yang X, Li L (2011) miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants. Bioinformatics 27:2614–2615PubMedGoogle Scholar
  21. 21.
    Zhou L, Liu Y, Liu Z, Kong D, Duan M, Luo L (2010) Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa. J Exp Bot 61:4157–4168CrossRefPubMedGoogle Scholar
  22. 22.
    Gupta OP, Sharma P, Gupta RK, Sharma I (2014) Current status on role of miRNAs during plant–fungus interaction. Physiol Mol Plant Pathol 85:1–7CrossRefGoogle Scholar
  23. 23.
    Gupta OP, Permar V, Koundal V, Singh UD, Praveen S (2012) MicroRNA regulated defense responses in Triticum aestivum L. during Puccinia graminis f. sp. tritici infection. Mol Biol Rep 39:817–822CrossRefPubMedGoogle Scholar
  24. 24.
    Pandey B, Gupta OP, Pandey DM, Sharma I, Sharma P (2013) Identification of new stress-induced microRNA and their targets in wheat using computational approach. Plant Sig Behav 8:e23932CrossRefGoogle Scholar
  25. 25.
    Xin MM, Wang Y, Yao YY, Xie CJ, Peng HR, Ni ZF, Sun QX (2010) Diverse set of microRNAs are responsive to powdery mildew infection and heat stress in wheat (Triticum aestivum L.). BMC Plant Biol 10:123–134PubMedCentralCrossRefPubMedGoogle Scholar
  26. 26.
    Reyes JL, Chua NH (2007) ABA induction of miR159 controls transcript levels of two MYB factors during Arabidopsis seed germination. Plant J 49:592–606CrossRefPubMedGoogle Scholar
  27. 27.
    Liu HH, Tian X, Li YJ, Wu CA, Zheng CC (2008) Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana. RNA 14:836–843PubMedCentralCrossRefPubMedGoogle Scholar
  28. 28.
    Li WX, Ono Y, Zhu J, He XJ, Wu JM, Iida K, Lu XY, Cui X, Hin H, Zhu JK (2008) The Arabidopsis NFYA5 transcription factor is regulated transcriptionally and post-transcriptionally to promote drought resistance. Plant Cell 20:2238–2251PubMedCentralCrossRefPubMedGoogle Scholar
  29. 29.
    Trindade I, Capitao C, Dalmay T, Fevereiro MP, Santos DM (2010) miR398 and miR408 are up-regulated in response to water deficit in Medicago truncatula. Planta 231:705–716CrossRefPubMedGoogle Scholar
  30. 30.
    Wang T, Chen L, Zhao M, Tian Q, Zhang WH (2011) Identification of drought-responsive microRNAs in Medicago truncatula by genome-wide high throughput sequencing. BMC Genomics 12:367–378PubMedCentralCrossRefPubMedGoogle Scholar
  31. 31.
    Eldem V, Celikkol-Akcay U, Ozhuner E, Bakir Y, Uranbey S, Akcay U, Unver T (2012) Genome-wide identification of miRNAs responsive to drought in peach (Prunus persica) by high-throughput deep sequencing. PLoS ONE 7:e50298PubMedCentralCrossRefPubMedGoogle Scholar
  32. 32.
    Kantar M, Lucas SJ, Budak H (2011) miRNA expression patterns of Triticum dicoccoides in response to shock drought stress. Planta 233:471–484CrossRefPubMedGoogle Scholar
  33. 33.
    Nageshbabu R, Jyothi MN, Sharadamma N, Sarika S, Rai DV, Devaraj VR (2013) Expression of miRNAs regulates growth and development of frenchbean (Phaseolus vulgaris) under salt and drought stress conditions. Int Res J Biol Sci 2:52–56Google Scholar
  34. 34.
    Wang M, Wang Q, Zhang B (2013) Response of miRNAs and their targets to salt and drought stresses in cotton (Gossypium hirsutum L.). Gene 30:26–32CrossRefGoogle Scholar
  35. 35.
    Li JS, Fu F, Ming AN, Feng SZ, Hui YS, Li WC (2013) Differential expression of microRNAs in response to drought stress in maize. J Integr Agric 12:1414–1422CrossRefGoogle Scholar
  36. 36.
    Bertolini E, Verelst W, Horner DS, Gianfranceschi L, Piccolo V, Inze D, Pe ME, Mica E (2013) Addressing the role of microRNAs in reprogramming leaf growth during drought stress in Brachypodium distachyon. Mol Plant 6:423–443PubMedCentralCrossRefPubMedGoogle Scholar
  37. 37.
    Ferreira TH, Gentile A, Vilela RD, Costa GGL, Dias L, Endres L, Menossi MM (2012) MicroRNAs associated with drought response in the bioenergy crop sugarcane (Saccharum spp.). PLoS ONE 7:e46703PubMedCentralCrossRefPubMedGoogle Scholar
  38. 38.
    Sunkar R (2010) MicroRNAs with macro-effects on plant stress responses. Semin Cell Dev Biol 21:805–811CrossRefPubMedGoogle Scholar
  39. 39.
    Dharmasiri N, Dharmasiri S, Estelle M (2005) The F-box protein TIR1 is an auxin receptor. Nature 435:441–445CrossRefPubMedGoogle Scholar
  40. 40.
    Sun G (2012) MicroRNAs and their diverse functions in plants. Plant Mol Biol 80:17–36CrossRefPubMedGoogle Scholar
  41. 41.
    Lu W, Li J, Liu F, Gu J, Guo C, Xu L, Zhang H, Xiao K (2011) Expression pattern of wheat miRNAs under salinity stress and prediction of salt-inducible miRNAs targets. Front Agric China 5:413–422CrossRefGoogle Scholar
  42. 42.
    Kong YM, Elling AA, Chen B, Deng XW (2010) Differential expression of microRNAs in maize inbred and hybrid lines during salt and drought stress. Am J Plant Sci 1:69–76CrossRefGoogle Scholar
  43. 43.
    Li B, Duan H, Li J, Deng XW, Yin W, Xia X (2013) Global identification of miRNAs and targets in Populus euphratica under salt stress. Plant Mol Biol 81:525–539CrossRefPubMedGoogle Scholar
  44. 44.
    Macovei A, Tuteja N (2012) MicroRNAs targeting DEAD-box helicases are involved in salinity stress response in rice (Oryza sativa L.). BMC Plant Biol 12:183–195PubMedCentralCrossRefPubMedGoogle Scholar
  45. 45.
    Min W, Qinglian W, Zhang B (2013) Response of miRNAs and their targets to salt and drought stresses in cotton (Gossypium hirsutum L.). Gene 530:26–32CrossRefGoogle Scholar
  46. 46.
    Ding D, Zhang L, Wang H, Liu Z, Zhang Z, Zheng Y (2009) Differential expression of miRNAs in response to salt stress in maize roots. Ann Bot 103:29–38PubMedCentralCrossRefPubMedGoogle Scholar
  47. 47.
    Lv DK, Bai X, Li Y, Ding XD, Ge Y, Cai H, Ji W, Wu N, Zhu YM (2012) 0) Profiling of cold-stress-responsive miRNAs in rice by microarrays. Gene 459:39–47CrossRefGoogle Scholar
  48. 48.
    Vaucheret H, Vazquez F, Crete P, Bartel DP (2004) The action of AGRONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev 18:1187–1197PubMedCentralCrossRefPubMedGoogle Scholar
  49. 49.
    Zhang J, Xu Y, Huan Q, Chong K (2009) Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response. BMC Genomics 10:449–465PubMedCentralCrossRefPubMedGoogle Scholar
  50. 50.
    Barakat A, Sriram A, Park J, Zhebentyayeva T, Main D, Abbott A (2012) Genome wide identification of chilling responsive microRNAs in Prunus persica. BMC Genomics 13:481–488PubMedCentralCrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Om Prakash Gupta
    • 1
  • Nand Lal Meena
    • 1
    • 2
    • 3
  • Indu Sharma
    • 3
  • Pradeep Sharma
    • 3
  1. 1.Quality and Basic Sciences DivisionDirectorate of Wheat ResearchKarnalIndia
  2. 2.Basic Sciences DivisionIndian Institute of Pulses ResearchKanpurIndia
  3. 3.Biotechnology LaboratoryDirectorate of Wheat ResearchKarnalIndia

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