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Functional & Integrative Genomics

, Volume 18, Issue 6, pp 645–657 | Cite as

MicroRNAs in durum wheat seedlings under chronic and short-term nitrogen stress

  • Diana L. Zuluaga
  • Vittoria Liuzzi
  • Pasquale Luca Curci
  • Gabriella Sonnante
Original Article

Abstract

Nitrogen is an essential macronutrient for plant growth and reproduction. In durum wheat, an appropriate nitrogen soil availability is essential for an optimal seed development. miRNAs contribute to the environmental change adaptation of plants through the regulation of important genes involved in stress processes. In this work, nitrogen stress response was evaluated in durum wheat seedlings of Ciccio and Svevo cultivars. Eight small RNA libraries from leaves and roots of chronically stressed plants were sequenced to detect conserved and novel miRNAs. A total of 294 miRNAs were identified, 7 of which were described here for the first time. The expression level of selected miRNAs and target genes was analyzed by qPCR in seedlings subjected to chronic (Ciccio and Svevo, leaves and roots) or short-term (Svevo roots) stress conditions. Some miRNAs showed an immediate stress response, and their level of expression was either maintained or returned to a basal level during a long-term stress. Other miRNAs showed a gradual up- or downregulation during the short-term stress. The newly identified miRNA ttu-novel-106 showed an immediate strongly downregulation after nitrogen stress, which was negatively correlated with the expression of MYB-A, its putative target gene. PHO2 gene was significantly upregulated after 24–48-h stress, corresponding to a downregulation of miR399b. Ttu-miR399b putative binding sites in the 5′ UTR region of the Svevo PHO2 gene were identified in the A and B genomes. Both MYB-A and PHO2 genes were validated for their cleavage site using 5′ RACE assay.

Keywords

Abiotic stress Triticum turgidum subsp. durum seedlings miRNA expression Target genes Leaves and roots 

Notes

Acknowledgements

We thank Donatella Danzi, Domenico De Paola, and Anita Morgese for their assistance.

Funding information

This research was supported by the MIUR projects PON01_01145 ISCOCEM “Sviluppo tecnologico e innovazione per la sostenibilità e competitività della cerealicoltura meridionale”; PON PONa3_00025 prot. no. 1424/29 BIOforIU “Infrastruttura multidisciplinare per lo studio e la valorizzazione della Biodiversità marina e terrestre nella prospettiva della Innovation Union”; PRIN 2010–2011 DD 23/10/2012 n. 719 “Identificazione e caratterizzazione di geni utili ad incrementare la produttività e sostenibilità del frumento duro”; and by the Puglia Region D.G.R. n. 1719 of 02.02.2011, Project Code 73 BioNet-PTP “Biodiversità per la valorizzazione e sicurezza delle produzioni alimentari tipiche pugliesi”.

Supplementary material

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References

  1. Alptekin B, Langridge P, Budak H (2017) Abiotic stress miRNomes in the Triticeae. Funct Integr Genomics 17:145–170CrossRefGoogle Scholar
  2. Blanco A, Mangini G, Giancaspro A, Giove S, Colasuonno P, Simeone R, Signorile A, De Vita P, Mastrangelo AM, Cattivelli L, Gadaleta A (2012) Relationships between grain protein content and grain yield components through quantitative trait locus analyses in a recombinant inbred line population derived from two elite durum wheat cultivars. Mol Breed 30:79–92CrossRefGoogle Scholar
  3. Budak H, Khan Z, Kantar M (2015) History and current status of wheat miRNAs using next generation sequencing and their roles in development and stress. Brief Funct Genomics 14:189–198CrossRefGoogle Scholar
  4. Cercós M, Gómez-Cadenas A, Ho T-HD (1999) Hormonal regulation of a cysteine proteinase gene, EBP1, in barley aleurone layers: Cis- and trans-acting elements involved in the co-ordinated gene expression regulated by gibberellins and abscisic acid. Plant J 19:107–118CrossRefGoogle Scholar
  5. Chinnusamy V, Zhu J, Zhou T, Zhu JK (2007) Small RNAs: big role in abiotic stress tolerance of plants. In: Jenks MA, Hasegawa PM, Jain SM (eds) Advances in molecular breeding toward drought and salt tolerant. Crops. Springer, The Netherlands, pp 223–260Google Scholar
  6. Curci PL, Aiese Cigliano R, Zuluaga DL, Janni M, Sanseverino W, Sonnante G (2017) Transcriptomic response of durum wheat to nitrogen starvation. Sci Rep 7:1176CrossRefGoogle Scholar
  7. De Giorgio D, Fornaro F (2012) Nitrogen fertilization and root growth dynamics in durum wheat. Ital J Agron 7:207–213Google Scholar
  8. De Paola D, Cattonaro F, Pignone D, Sonnante G (2012) The miRNAome of globe artichoke: conserved and novel micro RNAs and target analysis. BMC Genomics 13:41CrossRefGoogle Scholar
  9. De Paola D, Zuluaga DL, Sonnante G (2016) The miRNAome of durum wheat: isolation and characterisation of conserved and novel microRNAs and their target genes. BMC Genomics 17:505CrossRefGoogle Scholar
  10. Diaz I, Vicente-Carbajosa J, Abraham Z, Martinez M, Isabel-LaMoneda I, Carbonero P (2002) The GAMYB protein from barley interacts with the DOF transcription factor BPBF and activates endosperm-specific genes during seed development. Plant J 29:453–464CrossRefGoogle Scholar
  11. Gao S, Guo C, Zhang Y, Zhang F, Du X, Gu J, Xiao K (2016) Wheat microRNA member TaMIR444a is nitrogen deprivation-responsive and involves plant adaptation to the nitrogen-starvation stress. Plant Mol Biol Rep 34:931–946CrossRefGoogle Scholar
  12. Gubler F, Kalla R, Roberts JK, Jacobsen JV (1995) Gibberellin-regulated expression of a myb gene in barley aleurone cells: evidence of myb transactivation of a high-pI α-amylase gene promoter. Plant Cell 7:1879–1891PubMedPubMedCentralGoogle Scholar
  13. Hackenberg M, Shi BJ, Gustafson P, Langridge P (2013) Characterization of phosphorus-regulated miR399 and miR827 and their isomirs in barley under phosphorus-sufficient and phosphorus-deficient conditions. BMC Plant Biol 13(1):214CrossRefGoogle Scholar
  14. Kantar M, Unver T, Budak H (2010) Regulation of barley miRNAs upon dehydration stress correlated with target gene expression. Funct Integr Genomics 10:493–507CrossRefGoogle Scholar
  15. Kolde R. (2011) Package ‘pheatmap’. http://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf
  16. Kubaláková M, Kovářová P, Suchánková P, Číhalíková J, Bartoš J, Lucretti S, Watanabe N, Kianian SF, Doležel J (2005) Chromosome sorting in tetraploid wheat and its potential for genome analysis. Genetics 170:823Y829CrossRefGoogle Scholar
  17. Le S, Josse J, Husson F (2008) FactoMineR: an R package for multivariate analysis. J Stat Softw 25:1–18CrossRefGoogle Scholar
  18. Lex A, Gehlenborg N, Strobelt H, Vuillemot R, Pfister H (2014) UpSet: visualization of intersecting sets. IEEE Trans Vis Comput Graph 20:1983–1992CrossRefGoogle Scholar
  19. Liang G, He H, Yu D (2012) Identification of nitrogen starvation-responsive microRNAs in Arabidopsis thaliana. PLoS One 7:e48951CrossRefGoogle Scholar
  20. Liang WW, Huang JH, Li CP, Yang LT, Ye X, Lin D, Chen LS (2017) MicroRNA-mediated responses to long-term magnesium-deficiency in Citrus sinensis roots revealed by Illumina sequencing. BMC Genomics 18:657CrossRefGoogle Scholar
  21. Lin SI, Chiang SF, Lin WY, Chen JW, Tseng CY, Wu PC, Chiou TJ (2008) Regulatory network of microRNA399 and PHO2 by systemic signaling. Plant Physiol 147:732–746CrossRefGoogle Scholar
  22. Liu Z, Kumari S, Zhang L, Zheng Y, Ware D (2012) Characterization of miRNAs in response to short-term waterlogging in three inbred lines of Zea mays. PLoS One 7:e39786CrossRefGoogle Scholar
  23. Liu H, Able AJ, Able JA (2017a) Water-deficit stress-responsive microRNAs and their targets in four durum wheat genotypes. Funct Integr Genomics 17:237–251CrossRefGoogle Scholar
  24. Liu H, Able AJ, Able JA (2017b) Genotypic water-deficit stress responses in durum wheat: association between physiological traits, microRNA regulatory modules and yield components. Funct Plant Biol 44:538–551CrossRefGoogle Scholar
  25. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-delta delta C(T)) method. Methods 25:402–408CrossRefGoogle Scholar
  26. Maathuis F (2009) Physiological functions of mineral macronutrients. Curr Opin Plant Biol 12:250–258CrossRefGoogle Scholar
  27. Markham NR, Zuker M (2008) UNAFold: software for nucleic acid folding and hybridization. Methods Mol Biol 453:3–31CrossRefGoogle Scholar
  28. Masclaux-Daubresse C, Daniel-Vedele F, Dechorgnat J, Chardon F, Gaufichon L, Suzuki A (2010) Nitrogen uptake, assimilation and remobilization in plants: challenges for sustainable and productive agriculture. Ann Bot 105:1141–1157CrossRefGoogle Scholar
  29. Meyer C, Stitt M (2001) Nitrate reductase and signalling. In: Lea PJ, Morot-Gaudry JF (eds) Plant nitrogen. Springer, New York, pp 37–59CrossRefGoogle Scholar
  30. Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, Bowman JL, Cao X, Carrington JC, Chen X, Green PJ, Griffiths-Jones S, Jacobsen SE, Mallory AC, Martienssen RA, Poethig RS, Qi Y, Vaucheret H, Voinnet O, Watanabe Y, Weigel D, Zhu JK (2008) Criteria for annotation of plant microRNAs. Plant Cell 20:3186–3190CrossRefGoogle Scholar
  31. Millar AA, Gubler F (2005) The Arabidopsis GAMYB-like genes, MYB33 and MYB65, are microRNA-regulated genes that redundantly facilitate anther development. Plant Cell 17:705–721CrossRefGoogle Scholar
  32. Nguyen GN, Rothstein SJ, Spangenberg G, Kant S (2015) Role of microRNAs involved in plant response to nitrogen and phosphorous limiting conditions. Front Plant Sci 6:629PubMedPubMedCentralGoogle Scholar
  33. Nischal L, Mohsin M, Khan I, Kardam H, Wadhwa A, Abrol YP, Iqbal M, Ahmad A (2012) Identification and comparative analysis of microRNAs associated with low-N tolerance in rice genotypes. PLoS One 7:e50261CrossRefGoogle Scholar
  34. Ouyang X, Hong X, Zhao X, Zhang W, He X, Ma W, Teng W, Tong Y (2016) Knock out of the PHOSPHATE2 gene TaPHO2-A1 improves phosphorus uptake and grain yield under low phosphorus conditions in common wheat. Sci Rep 6:29850CrossRefGoogle Scholar
  35. Patade VY, Suprasanna P (2010) Short-term salt and PEG stresses regulate expression of MicroRNA, miR159 in sugarcane leaves. J Crop Sci Biotech 13:177–182CrossRefGoogle Scholar
  36. Paul S, Datta SK, Datta K (2015) MiRNA regulation of nutrient homeostasis in plants. Front Plant Sci 6:232CrossRefGoogle Scholar
  37. Qu B, He X, Wang J, Zhao Y, Teng W, Shao A, Zhao X, Ma W, Wang J, Li B, Li Z, Tong Y (2015) A wheat CCAAT box-binding transcription factor increases the grain yield of wheat with less fertilizer input. Plant Physiol 167:411–423CrossRefGoogle Scholar
  38. R Core Team (2017) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.gbif.org/tool/81287/r-a-language-and-environment-for-statistical-computing
  39. Rubio-Somoza I, Martinez M, Abraham Z, Diaz I, Carbonero P (2006) Ternary complex formation between HvMYBS3 and other factors involved in transcriptional control in barley seeds. Plant J 47:269–281CrossRefGoogle Scholar
  40. Shriram V, Kumar V, Devarumath RM, Khare TS, Wani SH (2016) MicroRNAs as potential targets for abiotic stress tolerance in plants. Front Plant Sci 7:817CrossRefGoogle Scholar
  41. Stracke R, Werber M, Weisshaar B (2001) The R2R3-MYB gene family in Arabidopsis thaliana. Curr Opin Plant Biol 4:447–456CrossRefGoogle Scholar
  42. Tedone L, Ali SA, De Mastro G (2018) Optimization of nitrogen in durum wheat in the Mediterranean climate: the agronomical aspect and greenhouse gas (GHG) emissions. In: Amanullah (ed) Nitrogen in agriculture. InTech, London, pp 132–162Google Scholar
  43. Tsay YF, Chiu CC, Tsai CB, Ho CH, Hsu PK (2007) Nitrate transporters and peptide transporters. FEBS Lett 581:2290–2300CrossRefGoogle Scholar
  44. Tsuji H, Aya K, Ueguchi-Tanaka M, Shimada Y, Nakazono M, Watanabe R, Nishizawa NK, Gomi K, Shimada A, Kitano H, Ashikari M, Matsuoka M (2006) GAMYB controls different sets of genes and is differentially regulated by microRNA in aleurone cells and anthers. Plant J 47:427–444CrossRefGoogle Scholar
  45. Washio K (2003) Functional dissections between GAMYB and Dof transcription factors suggest a role for protein-protein associations in the gibberellin-mediated expression of the RAmy1A gene in the rice aleurone. Plant Physiol 133:850–863CrossRefGoogle Scholar
  46. Wu J, Zhang JH, Huang MH, Zhu MH, Tong ZK (2016) Expression analysis of miR164 and its target gene NAC1 in response to low nitrate availability in Betula luminifera. Hereditas (Beijing) 38:155–162Google Scholar
  47. Xie Q, Frugis G, Colgan D, Chua NH (2000) Arabidopsis NAC1 transduces auxin signal downstream of TIR1 to promote lateral root development. Genes Dev 14:3024–3036CrossRefGoogle Scholar
  48. 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:e28009CrossRefGoogle Scholar
  49. Yang S, Sweetman JP, Amirsadeghi S, Barghchi M, Huttly AK, Chung W, Twell D (2001) Novel anther-specific myb genes from tobacco as putative regulators of phenylalanine ammonia-lyase expression. Plant Physiol 126:1738–1753CrossRefGoogle Scholar
  50. Zadoks JC, Chang TT, Konzak CF (1974) A decimal code for the growth stages of cereals. Weed Res 14:415–421CrossRefGoogle Scholar
  51. Zhao M, Ding H, Zhu JK, Zhang F, Li W (2011) Involvement of miR169 in the nitrogen-starvation responses in Arabidopsis. New Phytol 190:906–915CrossRefGoogle Scholar
  52. Zhao M, Tai H, Sun S, Zhang F, Xu Y, Li WX (2012) Cloning and characterization of maize miRNA involved in response to nitrogen deficiency. PLoS One 7:e29669CrossRefGoogle Scholar
  53. Zhao Y, Guo L, Lu W, Li X, Chen H, Guo C, Xiao K (2015) Expression pattern analysis of microRNAs in root tissue of wheat (Triticum aestivum L.) under normal nitrogen and low nitrogen conditions. J Plant Biochem Biotech 24:143–153CrossRefGoogle Scholar
  54. Zuluaga DL, De Paola D, Janni M, Curci PL, Sonnante G (2017) Durum wheat miRNAs in response to nitrogen starvation at the grain filling stage. PLos One 12:e0183253CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Institute of Biosciences and BioresourcesNational Research CouncilBariItaly

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