Skip to main content

Advertisement

SpringerLink
Log in

Novel and conserved heat-responsive microRNAs in wheat (Triticum aestivum L.)

  • Original Paper
  • Published:
Functional & Integrative Genomics Aims and scope Submit manuscript

Abstract

MicroRNAs (miRNAs) are small endogenous RNAs of ~22 nucleotides that have been shown to play regulatory role by negatively affecting the expression of genes at the post-transcriptional level. Information of miRNAs on some important crops like soybean, Arabidopsis, and rice, etc. are available, but no study on heat-responsive novel miRNAs has yet been reported in wheat (Triticum aestivum L.). In the present investigation, a popular wheat cultivar HD2985 was used in small RNA library construction and Illumina HiSeq 2000 was used to perform high-throughput sequencing of the library after cluster generation; 110,896,604 and 87,743,861 reads were generated in the control (22 °C) and heat-treated (42 °C for 2 h) samples, respectively. Forty-four precursor and mature miRNAs were found in T. aestivum from miRBase v 19. The frequencies of the miRNA families varied from 2 (tae-miR1117) to 60,672 (tae-miR159b). We identify 1052 and 902 mature miRNA sequences in HD2985 control and HS-treated samples by mapping on reference draft genome of T. aestivum. Maximum identified miRNAs were located on IWGSC_CSS_3B_scaff (chromosome 3B). We could identify 53 and 46 mature miRNA in the control and HS samples and more than 516 target genes by mapping on the reference genome of Oryza sativa, Zea mays, and Sorghum bicolor. Using different pipelines and plant-specific criteria, 37 novel miRNAs were identified in the control and treated samples. Six novel miRNA were validated using qRT-PCR to be heat-responsive. A negative correlation was, however, observed between the expression of novel miRNAs and their targets. Target prediction and pathway analysis revealed their involvement in the heat stress tolerance. These novel miRNAs are new additions to miRNA database of wheat, and the regulatory network will be made use of in deciphering the mechanism of thermotolerance in wheat.

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
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10
Fig. 11
Fig. 12
Fig. 13

Similar content being viewed by others

Abbreviations

NGS:

Next-generation sequencing

RISC:

RNA-induced silencing complex

miRNA:

MicroRNA

HS:

Heat stress

HSF:

Heat shock factor

HSP:

Heat shock protein

CDPK:

Calcium-dependent protein kinase

qRT-PCR:

Quantitative real-time PCR

SAGs:

Stress-associated genes

SAPs:

Stress-associated proteins

References

  • Allen E, Xie Z, Gustafson AM, Sung GH, Spatafora JW, Carrington JC (2004) Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nat Genet 36:1282–1292

    Article  CAS  PubMed  Google Scholar 

  • Barakat A, Wall PK, Diloreto S, Depamphilis CW, Carlson JE (2007) Conservation and divergence of microRNAs in Populus. BMC Genomics 8:481. doi:10.1186/1471-2164-8-481

    Article  PubMed Central  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Berezikov E, Cuppen E, Plasterk RH (2006) Approaches to microRNA discovery. Nat Genet 38:S2–S7. doi:10.1038/ng1794

    Article  CAS  PubMed  Google Scholar 

  • Carra A, Mica E, Gambino G, Pindo M, Moser C, Enrico MP, Schubert A (2009) Cloning and characterization of small non-coding RNAs from grape. Plant J 59:750–763

    Article  CAS  PubMed  Google Scholar 

  • Carrington JC, Ambros V (2003) Role of microRNAs in plant and animal development. Sci 301:336–338

    Article  CAS  Google Scholar 

  • Carthew RW, Sontheimer EJ (2009) Origins and mechanisms of miRNAs and siRNAs. Cell 136:642–655

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Coraggio I, Tuberosa R (2004) Molecular basis of plant adaptation to abiotic stress and approaches to enhance tolerance to hostile environments. Handb Plant Biotechnol. doi:10.1002/0470869143.kc022

    Google Scholar 

  • Dai X, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39:W155–W159. doi:10.1093/nar/gkr319

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Ding Y, Tao Y, Zhu C (2013) Emerging roles of microRNAs in the mediation of drought stress response in plants. J Exp Bot 64(11):3077–3086

    Article  CAS  PubMed  Google Scholar 

  • Dryanova A, Zakharov A, Gulick PJ (2008) Data mining for miRNAs and their targets in the Triticeae. Genome 51(6):433–443

    Article  CAS  PubMed  Google Scholar 

  • Dugas DV, Bartel B (2008) Sucrose induction of Arabidopsis miR398 represses two Cu/Zn superoxide dismutases. Plant Mol Biol 67:1009–1014

    Article  Google Scholar 

  • Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL et al (2007) High throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS One 2:e219

    Article  PubMed Central  PubMed  Google Scholar 

  • Gibson LR, Paulsen GM (1999) Yield components of wheat grown under high temperature stress during reproductive growth. Crop Sci 39(6):1841–1846

    Article  Google Scholar 

  • Guan Q, Lu X, Zeng H, Zhang Y, Zhu J (2013) Heat stress induction of miR398 triggers a regulatory loop that is critical for thermotolerance in Arabidopsis. Plant J 74(5):840–851

    Article  CAS  PubMed  Google Scholar 

  • Jia X, Wang WX, Ren L, Chen QJ, Mendu V, Willcut B, Dinkins R, Tang X, Tang G (2009) Differential and dynamic regulation of miR398 in response to ABA and salt stress in Populus tremula and Arabidopsis thaliana. Plant Mol Biol 71:51–59

    Article  CAS  PubMed  Google Scholar 

  • Jia J, Zhao S, Kong X, Li Y, Zhao G et al (2013) Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 496:91–95

    Article  CAS  PubMed  Google Scholar 

  • Khvorova A, Reynolds A, Jayasena SD (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell 115:209–216

    Article  CAS  PubMed  Google Scholar 

  • Kidner CA, Martienssen RA (2005) The developmental role of microRNA in plants. Curr Opin Plant Biol 8:38–44

    Article  CAS  PubMed  Google Scholar 

  • Klevebring D, Street NR, Fahlgren N, Kasschau KD, Carrington JC, Lundeberg J, Jansson S (2009) A genome-wide profiling of Populus small RNAs. BMC Genomics 10:620. doi:10.1186/1471-2164-10-620

    Article  PubMed Central  PubMed  Google Scholar 

  • Kozomara A, Griffiths-Jones S (2011) miRBase: integrating microRNA annotation and deep-sequencing data. NAR 39(Database Issue):D152–D157

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Kumar RR, Goswami S, Sharma SK, Singh K, Gadpayle KA, Singh SD, Pathak H, Rai RD (2013a) Differential expression of heat shock protein and alteration in osmolyte accumulation under heat stress in wheat. J Plant Biochem Biotechnol 22:16–26

    Article  CAS  Google Scholar 

  • Kumar RR, Sharma SK, Goswami S, Singh GP, Singh R, Singh K, Pathak H, Rai RD (2013b) Characterization of differentially expressed stress associated proteins in starch granule development under heat stress in wheat (Triticum aestivum L.). Indian J Biochem Biophys 50:126–138

    CAS  PubMed  Google Scholar 

  • Kumar RR, Singh GP, Goswami S, Pathak H, Rai RD (2014) Proteome analysis of wheat (Triticum aestivum) for the identification of differentially expressed heat-responsive proteins. Aus J Crop Sci 8(6):973–986

    CAS  Google Scholar 

  • Kurtoglu KY, Kantar M, Budak H (2014) New wheat microRNA using whole-genome sequence. Funct Integr Genomics 14(2):363–379

    Article  CAS  PubMed  Google Scholar 

  • Lopez-Gomollon S, Mohorianu I, Szittya G, Moulton V, Dalmay T (2012) Diverse correlation patterns between microRNAs and their targets during tomato fruit development indicates different modes of microRNA actions. Planta 236(6):1875–1887. doi:10.1007/s00425-012-1734-7

    Article  CAS  PubMed  Google Scholar 

  • Lu S, Sun YH, Shi R, Clark C, Li L et al (2005) Novel and mechanical stress-responsive microRNAs in Populus trichocarpa that are absent from Arabidopsis. Plant Cell 17:2186–2203

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Lu S, Sun YH, Chiang VL (2008) Stress-responsive microRNAs in Populus. Plant J 55:131–151

    Article  CAS  PubMed  Google Scholar 

  • Lu S, Yang C, Chiang VL (2011) Conservation and diversity of microRNA-associated copper-regulatory networks in Populus trichocarpa. J Integr Plant Biol 53:879–891

    Article  CAS  PubMed  Google Scholar 

  • Lukasik A, Pietrykowska H, Paczek L, Szweykowska-Kulinska Z, Zielenkiewicz P (2013) High-throughput sequencing identification of novel and conserved miRNAs in the Brassica oleracea leaves. BMC Genomics 14(1):801. doi:10.1186/1471-2164-14-801

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Mayer KF, Rogers J, Dolezel J, Pozniak C, Eversole K, Feuillet C et al (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Sci 345(6194):1251788. doi:10.1126/science.1251788

    Article  Google Scholar 

  • Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, Bowman J, Cao X, Carrington JC, Chen X, Green PJ et al (2008) Criteria for annotation of plant microRNAs. Plant Cell 20:3186–3190

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Mutum RD, Balyan SC, Kansal S, Agarwal P, Kumar S, Kumar M, Raghuvanshi S (2013) Evolution of variety specific regulatory schema for expression of osamiR408 in indica rice varieties under drought stress. FEBS J 280(7):1717–1730

    Article  CAS  PubMed  Google Scholar 

  • Palatnik JF, Allen E, Wu X, Schommer C, Schwab R et al (2003) Control of leaf morphogenesis by microRNAs. Nature 425:257–263

    Article  CAS  PubMed  Google Scholar 

  • Pandey B, Gupta O, Pandey D, Sharma I, Sharma P (2013) Identification of new stress-induced microRNA and their targets in wheat using computational approach. Plant Signaling Behav 8:e23932, PMID:23511197

    Article  Google Scholar 

  • Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29(9):e45–e45

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Qin D, Wu H, Peng H, Yao Y, Ni Z, Li Z, Sun Q (2008) Heat stress-responsive transcriptome analysis in heat susceptible and tolerant wheat (Triticum aestivum L.) by using wheat genome array. BMC Genomics 9(1):432. doi:10.1186/1471-2164-9-432

    Article  PubMed Central  PubMed  Google Scholar 

  • Rajagopalan R, Vaucheret H, Trejo J, Bartel DP (2006) A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev 20:3407–3425

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Shaik R, Ramakrishna W (2013) Machine learning approaches distinguish multiple stress conditions using stress responsive genes and identify candidate genes for broad resistance in rice. Plant Physiol 164(1):481–495. doi:10.1104/pp.113

    Article  PubMed Central  PubMed  Google Scholar 

  • Shukla LI, Chinnusamy V, Sunkar R (2008) The role of microRNAs and other endogenous small RNAs in plant stress responses. Biochim Biophys Acta Gene Regul Mech 1779(11):743–748

    Article  CAS  Google Scholar 

  • Song C, Wang C, Zhang C, Korir N, Yu H, Ma Z, Fang J (2010) Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata). BMC Genomics 11(1):431–443. doi:10.1186/1471-2164-11-431

    Article  PubMed Central  PubMed  Google Scholar 

  • Srivastava N, Chaudhary S, Kumar V, Katudia K, Vaidya K, Vyas MK, Chikara SK (2012) Evaluation of the yield, quality and integrity of total RNA extracted by four different extraction methods in rice (Oryza sativa). Res Rev J Crop Sci Technol 1:1–9

    Google Scholar 

  • Stief A, Altmann S, Hoffmann K, Pant BD, Scheible WR, Baurle I (2014) Arabidopsis miR156 regulates tolerance to recurring environmental stress through SPL transcription factors. Plant Cell Online 26(4):1792–1807

    Article  CAS  Google Scholar 

  • Sun W, Julie Li Y-S, Huang HD, Shyy JYJ, Chien S (2010) microRNA: a master regulator of cellular processes for bioengineering systems. Ann Rev Biomed Eng 12:1–27

    Article  CAS  Google Scholar 

  • Sun F, Guo G, Du J, Guo W, Peng H, Ni Z, Sun Q, Yao Y (2014) Whole-genome discovery of miRNAs and their targets in wheat (Triticum aestivum L.). BMC Plant Biol 14:142

    Article  PubMed Central  PubMed  Google Scholar 

  • Sunkar R, Zhu JK (2001) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16:2001–2019

    Article  Google Scholar 

  • Sunkar R, Li YF, Jagadeeswaran G (2012) Functions of microRNAs in plant stress responses. Trends Plant Sci 17(4):196–203

    Article  CAS  PubMed  Google Scholar 

  • 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 231:705–716

    Article  CAS  PubMed  Google Scholar 

  • Voinnet O (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 136:669–687

    Article  CAS  PubMed  Google Scholar 

  • Wahid A, Gelani S, Ashraf M, Foolad MR (2007) Heat tolerance in plants: an overview. Env Exp Bot 61(3):199–223

    Article  Google Scholar 

  • Wang JW, Wang LJ, Mao YB, Cai WJ, Xue HW et al (2005) Control of root cap formation by microRNA-targeted auxin response factors in Arabidopsis. Plant Cell 17:2204–2216

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Wang Y, Sun F, Cao H, Peng H, Ni Z et al (2012) TamiR159 directed wheat TaGAMYB cleavage and its involvement in anther development and heat response. PLoS One 7(11):e48445. doi:10.1371/journal.pone.0048445

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Xin M, Wang Y, Yao Y, Xie C, Peng H, Ni Z, Sun Q (2010) Diverse set of microRNAs are responsive to powdery mildew infection and heat stress in wheat (Triticum aestivum L.). BMC Plant Biol 10:123–134

    Article  PubMed Central  PubMed  Google Scholar 

  • Yamasaki H, Abdel-Ghany SE, Cohu CM, Kobayashi Y, Shikanai T, Pilon M (2007) Regulation of copper homeostasis by micro-RNA in Arabidopsis. J Biol Chem 282:16369–16378

    Article  CAS  PubMed  Google Scholar 

  • Yao Y, Guo G, Ni Z, Sunkar R, Du J, Zhu JK, Sun Q (2007) Cloning and characterization of microRNAs from wheat (Triticum aestivum L.). Genome Biol 8:R96. doi:10.1186/gb-2007-8-6-r96

    Article  PubMed Central  PubMed  Google Scholar 

  • Zhai J, Zhao Y, Simon SA, Huang S, Petsch K, Arikit S et al (2013) Plant microRNAs display differential 3′ truncation and tailing modifications that are ARGONAUTE1 dependent and conserved across species. Plant Cell 25(7):2417–2428. doi:10.1105/tpc.113

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Zhang JZ, Ai XY, Guo WW, Peng SA, Deng XX, Hu CG (2012) Identification of miRNAs and their target genes using deep sequencing and degradome analysis in trifoliate orange (Poncirus trifoliata L. Raf). Mol Biotechnol 51(1):44–57. doi:10.1007/s12033-011-9439-x

    Article  CAS  PubMed  Google Scholar 

  • Zhao CZ, Xia H, Frazier TP, Yao YY, Bi YP et al (2010) Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.). BMC Plant Biol 10:3–15. doi:10.1186/1471-2229-10-3

    Article  PubMed Central  PubMed  Google Scholar 

  • Zhao X, Liu X, Guo C, Gu J, Xiao K (2013) Identification and characterization of microRNAs from wheat (Triticum aestivum L.) under phosphorus deprivation. J Plant Biochem Biotechnol 22(1):113–123

    Article  CAS  Google Scholar 

  • Zuker M (1989) On finding all suboptimal folding of an RNA molecule. Sci 244(4900):48–52

    Article  CAS  Google Scholar 

Download references

Acknowledgments

Financial assistance provided by the Indian Council of Agriculture Research (ICAR) under the National Initiative for Climate Resilient Agriculture (NICRA) project (Project 12/115 TG3079) is highly acknowledged. We also thank Director, Indian Agricultural Research Institute (IARI) for providing all the logistic support required for executing the research work.

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standards

Experiments comply with the current laws of the country in which they were performed.

Availability of NGS raw data

The data sets supporting the results of this article are available in the National Center for Biotechnology Information (NCBI) repository [BioProject Database: PRJNA172054; http://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA172054].

Author information

Authors and Affiliations

  1. Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, 110012, India

    Ranjeet Ranjan Kumar, Sushil Kumar Sharma, Mahesh Kumar Nirjal, Suneha Goswami & Raj Deo Rai

  2. Division of Environmental Science, Indian Agricultural Research Institute, New Delhi, 110012, India

    Himanshu Pathak

  3. Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110012, India

    Yugal Kishore Kala & Gyanendra Pratap Singh

Authors
  1. Ranjeet Ranjan Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Himanshu Pathak
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sushil Kumar Sharma
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yugal Kishore Kala
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Mahesh Kumar Nirjal
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Gyanendra Pratap Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Suneha Goswami
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Raj Deo Rai
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ranjeet Ranjan Kumar.

Electronic supplementary materials

Below is the link to the electronic supplementary material.

ESM_1.tif

Flow chart of the work plan undertaken for the identification of conserved and novel heat-responsive miRNA in control and heat stress treated samples of HD2985 (thermotolerant) cultivar of wheat (Triticum aestivum L.). (DOCX 158 kb)

ESM_2.tif

Work-flow for novel miRNA discovery using the raw reads from the sequenced libraries of control and heat stress treated samples of HD2985 cultivar of wheat (Triticum aestivum L.); different pipeline analyzers were used for the identification of novel heat-responsive miRNAs from the potential candidates. (DOCX 45 kb)

ESM_3.xls

List of primers used for the comparative expression analysis of mature miRNAs and their target genes in control and heat stress treated samples of HD2985 (thermotolerant) cultivar of wheat (Triticum aestivum). (XLS 39 kb)

ESM_4.xls

List of miRNAs identified in control and heat stress treated samples of HD2985 (thermotolerant) cultivar using the reference draft genome of wheat (Triticum aestivum). (XLS 44 kb)

ESM_5.xls

A list of candidate miRNAs, identified targets and their functional annotation based on the reference draft genome of Triticum aestivum (retrieved from ftp://ftp.ensemblgenomes.org). (XLS 50 kb)

ESM_6.xls

List of miRNAs identified in control and heat stress treated samples of HD2985 (thermotolerant) cultivar of wheat based on homology search using the reference genome of rice (Oryza sativa). (XLS 48 kb)

ESM_7.xls

List of miRNAs identified in control and heat stress treated samples of HD2985 (thermotolerant) cultivar of wheat based on homology search using the reference genome of maize (Zea mays). (XLS 42 kb)

ESM_8.xls

List of miRNAs identified in control and heat stress treated samples of HD2985 (thermotolerant) cultivar of wheat based on homology search using the reference genome of sorghum (Sorghum bicolor). (XLS 41 kb)

ESM_9.xls

List of target genes of mature miRNAs identified by homology based search using the reference genome of T. aestivum, O. sativa, Z. mays and S. bicolor. (XLS 229 kb)

ESM_10.tif

Secondary structure analysis of validated heat-responsive miRNAs from wheat (Triticum aestivum); Flicker v3.0 was used for the prediction of secondary structure and structure analysis was performed using Zuker’s algorithm. (DOCX 95 kb)

ESM_11.xls

Novel miRNAs (identified based on homology search using the reference genome of O. sativa, Z. mays and S. bicolor) and their respective target genes identified in control sample of HD2985 cultivar of wheat. (XLS 122 kb)

ESM_12.xls

Novel miRNAs (identified based on homology search using the reference genome of O. sativa, Z. mays and S. bicolor) and their target genes identified in heat shock treated samples of HD2985 cultivar of wheat. (XLS 60 kb)

ESM_13.xls

List of mature miRNAs (identified in present investigation) involved in thermotolerance pathways along with their target genes. (XLS 335 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kumar, R.R., Pathak, H., Sharma, S.K. et al. Novel and conserved heat-responsive microRNAs in wheat (Triticum aestivum L.). Funct Integr Genomics 15, 323–348 (2015). https://doi.org/10.1007/s10142-014-0421-0

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10142-014-0421-0

Keywords

Search

Navigation