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MicroRNA as a Tool for Mitigating Abiotic Stress in Rice (Oryza sativa L.)

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Book cover Recent Approaches in Omics for Plant Resilience to Climate Change

Abstract

Oryza sativa, a model plant species is one of the most imperative food crops of the globe which feeds over two billion people including Indians. Plants are subjected to multiple stresses in chorus leading to colossal changes in the molecular landscape of a cell. Being sessile rice crop is persistently exposed to various abiotic stresses with devastating effect on its survival and productivity. Abiotic stresses can change growth, development and productivity of plants. Rice has developed extremely complex molecular machineries to sense a range of stress signals and bring forth an exact response to minimize the harm. Augmentation of rice productivity can significantly elevate the economic status of India. Recently, non-protein–coding microRNAs have acknowledged tremendous attention due to their value in negative gene regulation. In plants, despite regulating developmental, physiological and biological processes like immune responses, cell differentiation and fate determination, microRNAs have also been allied with varied biotic and abiotic stresses. Modification of miRNA regulatory landscape can significantly modify the product of a stress response which can consequently prove to be essential in understanding the molecular architecture of plant stress response repertoire and the cross-talk between diverse stress responses. The miRNA-mediated post-transcriptional gene silencing is one of the methods to establish plant abiotic stress tolerance. This review provides an up-date on microRNAs, role of miRNA on abiotic stress response in rice, rice miRNA-directed regulatory network and the genetic engineering perspectives of miRNAs applications in rice tolerance to various abiotic stress environments.

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References

  • Achard P, Herr A, Baulcombe DC, Harberd NP (2004) Modulation of floral development by a gibberellins regulated microRNA. Development 131:3357–3365

    Article  CAS  PubMed  Google Scholar 

  • Achard P, Gong F, Cheminant S, Alioua M, Hedden P, Genschik P (2008) The cold-inducible CBF1 factor-dependent signaling pathway modulates the accumulation of the growth-repressing DELLA proteins via its effect on gibberellin metabolism. Plant Cell 20:2117–2129

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X et al (2003a) A uniform system for microRNAs annotation. RNA 9:277–279

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ambros V, Lee RC, Lavanway A, Williams PT, Jewell D (2003b) MicroRNAs and other tiny endogenous RNAs in C. elegans. Curr Biol 13:807–818

    Article  CAS  PubMed  Google Scholar 

  • Apel K, Hirt H (2004) Reactive oxygen species: metabolism, oxidative stress, and signal trans- duction. Annu Rev Plant Biol 55:373–399

    Article  CAS  PubMed  Google Scholar 

  • Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815

    Article  Google Scholar 

  • Barrera-Figueroa BE, Gao L, Wu Z, Zhou X, Zhu J, Jin H, Liu R, Zhu JK (2012) High throughput sequencing reveals novel and abiotic stress-regulated microRNAs in the inflorescences of rice. BMC Plant Biol 12:132

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Bartels D, Sunkar R (2005) Drought and salt tolerance in plants. Crit Rev Plant Sci 24:23–58

    Article  CAS  Google Scholar 

  • Ben Chaabane S, Liu R, Chinnusamy V, Kwon Y, Park JH, Kim SY, Zhu JK, Yang SW, Lee BH (2013) STA1, an Arabidopsis pre-mRNA processing factor 6 homolog, is a new player involved in miRNA biogenesis. Nucleic Acids Res 41:1984–1997

    Article  CAS  Google Scholar 

  • Bielewicz D, Kalak M, Kalyna M, Windels D, Barta A, Vazquez F, Jarmolowski A (2013) Introns of plant pri-miRNAs enhance miRNA biogenesis. EMBO Rep 14:622–628

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Blumwald E, Grover A (2006) Salt tolerance. In: Halford NG (ed) Plant biotechnology: current and future uses of genetically modified crops. Wiley, England, pp 206–224

    Chapter  Google Scholar 

  • Bologna NG, Mateos JL, Bresso EG, Palatnik JF (2009) A loopto ‐ base processing mechanism underlies the biogenesis of plant microRNAs miR319 and miR159. EMBO J 28:3646–3656

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bologna NG, Schapire AL, Palatnik JF (2013a) Processing of plant microRNA precursors. Brief Funct Genomics 12:37–45

    Article  CAS  PubMed  Google Scholar 

  • Bologna NG, Schpire AL, Zhai J, Chorostecki U, Boisbouvier J, Meyers BC, Palatnik JF (2013b) Multiple RNA recognition patterns during microRNA biogenesis in plants. Genome Res 23:1675–1689

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Breakfield NW, Corcoran DL, Petricka JJ, Shen J, Sae-Seaw J, Rubio-Somoza I, Weigel D, Ohler U, Benfey PN (2012) High resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis. Genome Res 22:163–176

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cai X, Davis EJ, Ballif J, Liang M, Bushman E, Haroldsen V et al (2006) Mutant identification and characterization of the laccase gene family in Arabidopsis. J Exp Bot 57(11):2563–2569

    Article  CAS  PubMed  Google Scholar 

  • Canto-Pastor A, Molla-Morales E, Ernst W, Dahl J, Zhai Y, Yan B, Meyers C, Shanklin J, Martienssen R (2015) Efficient transformation and artificial miRNA gene silencing in Lemna minor. Plant Biol 17:59–65

    Article  CAS  PubMed  Google Scholar 

  • Chaves MM, Flexas J, Pinheiro C (2009) Photosynthesis under drought and salt stress: regulation mechanisms from whole plant to cell. Ann Bot 103:551–560

    Article  CAS  PubMed  Google Scholar 

  • Chen X (2004) A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303:2022–2025

    Article  CAS  PubMed  Google Scholar 

  • Chen X (2010) Plant microRNAs at a glance. Semin Cell Dev Biol 21:781

    Article  PubMed  Google Scholar 

  • Chen ZH, Bao ML, Sun YZ, Yang YJ, Xu XH, Wang JH, Zhu MY (2011) Regulation of auxin response by miR393-targeted transport inhibitor response protein 1 is involved in normal development in Arabidopsis. Plant Mol Biol 77:619–629

    Article  CAS  PubMed  Google Scholar 

  • Chinnusamy V, Zhu J, Zhu JK (2007) Cold stress regulation of gene expression in plants. Trends Plant Sci 12:444–451

    Article  CAS  PubMed  Google Scholar 

  • Chinnusamy V, Zhu J-K, Sunkar R (2010) Gene regulation during cold stress acclimation in plants. Methods Mol Biol 639:39–55

    Google Scholar 

  • Cui N, Sun X, Sun M, Jia B, Duanmu H, Lv D, Duan X, Zhu Y (2015) Overexpression of OsmiR156k leads to reduced tolerance to cold stress in rice (Oryza sativa). Mol Breed 35:214

    Article  CAS  Google Scholar 

  • Devi SJSR, Madhav MS, Kumar GR, Goel AK, Umakanth B, Jahnavi B, Viraktamath BC (2013) Identification of abiotic stress miRNA transcription factor binding motifs (TFBMs) in rice. Gene 531:15–22

    Article  CAS  PubMed  Google Scholar 

  • Devos K (2005) Updating the “Crop Circle”. Curr Opin Plant Biol 8:155–162

    Article  CAS  PubMed  Google Scholar 

  • Ding YF, Chen Z, Zhu C (2011) Microarray-based analysis of cadmium-responsive microRNAs in rice (Oryza sativa). J Exp Bot 62:3563–3573

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ding Y, Qu A, Gong S, Huang S, Lv B, Zhu C (2013) Molecular identification and analysis of Cd-responsive MicroRNAs in rice. J Agric Food Chem 61:11668–11675

    Article  CAS  PubMed  Google Scholar 

  • Dong CH et al (2009) Disruption of Arabidopsis CHY1 reveals an important role of metabolic status in plant cold stress signaling. Mol Plant 2:59

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Eamens AL, Smith NA, Curtin SJ, Wang M, Waterhouse PM (2009) The Arabidopsis thaliana double-stranded RNA binding protein DRB1 directs guide strand selection from microRNAs duplexes. RNA 15:2219–2235

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Eamens AL, McHale M, Waterhouse PM (2014) The use of artificial microRNA technology to control gene expression in Arabidopsis thaliana. Arabidopsis Protoc Methods Mol Biol 1062:211–224

    Article  CAS  Google Scholar 

  • Ferdous J, Hussain SS, Shi B‐J (2015) Role of microRNAs in plant drought tolerance. Plant Biotechnol J 13:293–305

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gao P, Bai X, Yang L, Lv D, Li Y, Cai H, Ji W, Guo D, Zhu Y (2010) Over-expression of osa-MIR396c decreases salt and alkali stress tolerance. Planta 231:991–1001

    Article  CAS  PubMed  Google Scholar 

  • Gao P, Bai X, Yang L, Lv D, Pan X, Li Y, Cai H, Ji W, Chen Q, Zhu Y (2011) Osa- MIR393: a salinity-and alkaline stress-related microRNA gene. Mol Biol Rep 38:237–242

    Article  PubMed  CAS  Google Scholar 

  • Goldgur Y et al (2007) Desiccation and zinc binding induce transition of tomato abscisic acid stress ripening 1, a water stress- and salt stress-regulated plant specific protein, from unfolded to folded state. Plant Physiol 143:617

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gong H, Hu WW, Jiao Y, Pua EC (2005) Molecular characterization of Phi-class mustard (Brassica juncea) glutathione S-transferase gene in Arabidopsis thaliana by 5′-deletion analysis of its promoter. Plant Cell Rep 24:439–447

    Article  CAS  PubMed  Google Scholar 

  • Grad Y, Aach J, Hayes GD, Reinhart BJ, Church GM, Ruvkun G, Kim J (2003) Computational and experimental identification of C. elegans microRNAs. Mol Cell 11:1253–1263

    Article  CAS  PubMed  Google Scholar 

  • Grover A, Minhas D (2000) Towards the production of abiotic stress tolerant transgenic rice plants: issues, progress and future research needs. Proc Natl Acad Sci U S A 1:13–32

    Google Scholar 

  • Hasanuzzaman M, Nahar K, Fujita M (2013) Plant response to salt stress and role of exogenous protectants to mitigate salt-induced damages. In: Ecophysiology and responses of plants under salt stress. Springer, New York, NY, pp 25–87

    Chapter  Google Scholar 

  • Hawker NP, Bowman JL (2004) Roles for class III HD-Zip and KANADI genes in Arabidopsis root development. Plant Physiol 135:2261–2270

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Iki T, Yoshikawa M, Nishikiori M, Jaudal MC, Matsumoto-Yokoyama E, Mitsuhara I, Meshi T, Ishikawa M (2010) In vitro assembly of plant RNAinduced silencing complexes facilitated by molecular chaperone HSP90. Mol Cell 39:282–291

    Article  CAS  PubMed  Google Scholar 

  • Iki T, Yoshikawa M, Meshi T, Ishikawa M (2012) Cyclophilin 40 facilitates HSP90-mediated RISC assembly in plants. EMBO J 31:267–278

    Article  CAS  PubMed  Google Scholar 

  • Jeong DH, Park S, Zhai J, Gurazada SG, De Paoli E, Meyers BC, Green PJ (2011) Massive analysis of rice small RNAs: mechanistic implications of regulated microRNAs and variants for differential target RNA cleavage. Plant Cell 23:4185–4207

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jian X, Zhang L, Li G, Zhang L, Wang X, Cao X, Fang X, Zha FC (2010) Identification of novel stress-regulated microRNAs from Oryza sativa L. Genomics 95:47–50

    Article  CAS  PubMed  Google Scholar 

  • Jiao Y, Wang Y, Xue D, Wang J, Yan M, Liu G, Dong G, Zeng D, Lu Z, Zhu X, Qian Q, Li J (2010) Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat Genet 42:541–544

    Article  CAS  PubMed  Google Scholar 

  • Jones-Rhoades MW, Bartel DP (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14:787–799

    Article  CAS  PubMed  Google Scholar 

  • Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAS and their regulatory roles in plants. Annu Rev Plant Biol 57:19–53

    Article  CAS  PubMed  Google Scholar 

  • Jouannet V, Moreno AB, Elmayan T, Vaucheret H, Crespi MD, Maizel A (2012) Cytoplasmic Arabidopsis AGO7 accumulates in membrane-associated siRNA bodies and is required for tasiRNA biogenesis. EMBO J 31:1704–1713

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kawaguchi Y, Kovacs JJ, McLaurin A, Vance JM, Ito A, Yao TP (2003) The deacetylase HDAC6 regulates aggresome formation and cell viability in response to misfolded protein stress. Cell 115:727–738

    Article  CAS  PubMed  Google Scholar 

  • Khraiwesh B, Zhu J, Zhu J (2012) Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants. Biochim Biophys Acta 1819:137–148

    Article  CAS  PubMed  Google Scholar 

  • Kim VN (2005) MicroRNA biogenesis: coordinated cropping and dicing. Nat Rev Mol Cell Biol 6:376–385

    Article  CAS  PubMed  Google Scholar 

  • Kim YJ, Zheng B, Yu Y, Won SY, Mo B, Chen X (2011) The role of Mediator in small and long noncoding RNA production in Arabidopsis thaliana. EMBO J 30:814–822

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lai EC (2003) MicroRNAs: runts of the genome assert themselves. Curr Biol 13:R925–R936

    Article  CAS  PubMed  Google Scholar 

  • Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75(5):843–854

    Article  CAS  PubMed  Google Scholar 

  • Li B, Qin Y, Duan H, Yin W, Xia X (2011a) Genome-wide characterization of new and drought stress responsive microRNAs in Populus euphratica. J Exp Bot 62:3765–3779

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li F, Pignatta D, Bendix C, Brunkard JO, Cohn MM, Tung J, Sun H, Kumar P, Baker B, Li H, Dong Y, Yin H, Wang N, Yang J, Liu X, Wang Y, Wu J, Li X (2011b) Characterization of the stress associated microRNAs in Glycine max by deep sequencing. BMC Plant Biol 11:170

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB, Bartel DP (2003) The microRNAs of Caenorhabditis elegans. Genes Dev 17:991–1008

    Article  CAS  Google Scholar 

  • Liu Q, Chen YQ (2010) A new mechanism in plant engineering: the potential roles of microRNAs in molecular breeding for crop improvement. Biotechnol Adv 28:301–307

    Article  CAS  PubMed  Google Scholar 

  • Liu HH, Tian X, Li YJ, Wu CA, Zheng CC (2008) Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana. RNA 14(5):836–843

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu Q, Zhang YC, Wang CY, Luo YC, Huang QJ, Chen SY, Chen YQ (2009) Expression analysis of phytohormone-regulated microRNAs in rice, implying their regulation roles in plant hormone signaling. FEBS Lett 583:723–728

    Article  CAS  PubMed  Google Scholar 

  • Lu C, Jeong DH, Kulkarni K, Pillay M, Nobuta K, German R, Green PJ (2008) Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs). Proc Natl Acad Sci U S A 105:4951–4956

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lv DK, Bai X, Li Y, Ding XD, Ge Y, Cai H, Ji W, Wu N, Zhu YM (2010) Profiling of cold-stress-responsive miRNAs in rice by microarrays. Gene 459(1–2):39–47

    Article  CAS  PubMed  Google Scholar 

  • Ma X, Xin Z, Wang Z et al (2015) Identification and comparative analysis of differentially expressed miRNAs in leaves of two wheat (Triticum aestivum L.) genotypes during dehydration stress. BMC Plant Biol 15:21

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Macovei A, Gill SS, Tuteja N (2012) microRNAs as promising tools for improving stress tolerance in rice. Plant Signal Behav 7:1296–1301

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Macrae IJ, Zhou K, Li F, Repic A, Brooks AN, Cande WZ, Adams PD, Doudna JA (2006) Structural basis for double-stranded RNA processing by Dicer. Science 311:195–198

    Article  CAS  PubMed  Google Scholar 

  • Mallory AC, Vaucheret H (2006) Functions of microRNAs and related small RNAs in plants. Nat Genet 38(Suppl):S31–S36

    Article  CAS  PubMed  Google Scholar 

  • Mane SP, Vasquez-Robinet C, Sioson AA, Heath LS, Grene R (2007) Early PLD {alpha}-mediated events in response to progressive drought stress in Arabidopsis: a transcriptome analysis. J Exp Bot 58:241

    Article  CAS  PubMed  Google Scholar 

  • Mangrauthia SK, Bhogireddy S, Agarwal S, Prasanth VV, Voleti SR, Neelamraju S, Subrahmanyam D (2017) Genome-wide changes in microRNA expression during short and prolonged heat stress and recovery in contrasting rice cultivars. J Exp Bot 68(9):2399–2412

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mittal D, Chakrabarti S, Sarkar A, Singh A, Grover A (2009) Heat shock factor gene family in rice: genomic organization and transcript expression profiling in response to high temperature low temperature and oxidative stresses. Plant Physiol Biochem 47(9):785–795

    Article  CAS  PubMed  Google Scholar 

  • Mittal D, Madhyastha DA, Grover A (2012) Genome-wide transcriptional profiles during temperature and oxidative stress reveal coordinated expression patterns and overlapping regulons in rice. PLoS One 7(7):e40899

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mittler R, Vanderauwera S, Gollery M, Van Breusegem F (2004) Reactive oxygen gene network of plants. Trends Plant Sci 9:490–498

    Article  CAS  PubMed  Google Scholar 

  • Miura K, Furumoto T (2013) Cold signaling and cold response in plants. Int J Mol Sci 14:5312–5337

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Miura K, Ikeda M, Matsubara A, Song XJ, Ito M, Asano K, Matsuoka M, Kitano H, Ashikari M (2010) OsSPL14 promotes panicle branching and higher grain productivity in rice. Nat Genet 42:545–549

    Article  CAS  PubMed  Google Scholar 

  • Munns R (2010) Approaches to identifying genes for salinity tolerance and the importance of timescale. Methods Mol Biol 639:25–38

    Article  CAS  PubMed  Google Scholar 

  • Mutum RD, Balyan SC, Kansal S, Agarwal P, Kumar S, Kumar M et al (2013) Evolution of variety-specific regulatory schema for expression of osa-miR408 in indica rice varieties under drought stress. FEBS J 280:1717–1730

    Article  CAS  PubMed  Google Scholar 

  • Mutum RD, Kumar S, Balyan S, Kansal S, Mathur S, Raghuvanshi S (2016) Identification of novel miRNAs from drought tolerant rice variety Nagina 22. Sci Rep 6:30786. https://doi.org/10.1038/srep30786

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ni FT, Chu LY, Shao HB, Liu ZH (2009) Gene expression and regulation of higher plants under soil water stress. Curr Genomics 10:269–280

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nozawa M, Miura S, Nei M (2012) Origins and evolution of microRNA genes in plant species. Genome Biol Evol 4:230–239

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ossowski S, Schwab R, Weigel D (2008) Gene silencing in plants using artificial microRNAs and other small RNAs. Plant J 53:674–690

    Article  CAS  PubMed  Google Scholar 

  • Pan J, Huang D, Guo Z, Kuang Z, Zhang H, Xie X, Ma Z, Gao S, Lerdau MT, Chu C, Li L (2018) Overexpression of microRNA408 enhances photosynthesis, growth, and seed yield in diverse plants. J Integr Plant Biol. https://doi.org/10.1111/jipb.12634

    Article  CAS  PubMed  Google Scholar 

  • Pandita D (2018a) Plant miRNAs: micro structure and macro character. Res Rev J Agric Allied Sci 7(1):83–84

    Google Scholar 

  • Pandita D (2018b) RNA interference: what and why? J Genet Mol Biol 2(1):1–3

    Google Scholar 

  • Paterson AH, Bowers JE, Chapman BA (2004) Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci U S A 101:9903–9908

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pérez-Quintero AL, López C (2010) Artificial microRNAs and their applications in plant molecular biology. Agronomia Colombiana 28:373–381

    Google Scholar 

  • Raffaele S, Mongrand S, Gamas P, Niebel A, Ott T (2007) Genome-wide annotation of remorins, a plant-specific protein family: evolutionary and functional perspectives. Plant Physiol 145:593

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP (2002) MicroRNAs in plants. Genes Dev 16:1616–1626

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rogers K, Chen X (2013) Biogenesis, turnover, and mode of action of plant microRNAs. Plant Cell 25:2383–2399

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sailaja B, Voleti SR, Subrahmanyam D, Sarla N, Prasanth V, Bhadana VP, Mangrauthia SK (2014) Prediction and expression analysis of miRNAs associated with heat stress in Oryza sativa. Rice Sci 21(1):3–12

    Article  Google Scholar 

  • Sanan-Mishra N, Kumar V, Sopory SK, Mukherjee SK (2009) Cloning and validation of novel miRNA from basmati rice indicates cross talk between abiotic and biotic stresses. Mol Genet Genomics 282:463–474

    Article  CAS  PubMed  Google Scholar 

  • Sasaki T, Burr B (2000) International rice genome sequencing project: the effort to completely sequence the rice genome. Curr Opin Plant Biol 3:138–141

    Article  CAS  PubMed  Google Scholar 

  • Sasaki T, Matsumoto T, Yamamoto K, Sakata K, Baba T, Katayose Y, Wu JZ, Niimura Y, Cheng ZK, Nagamura Y et al (2002) The genome sequence and structure of rice chromosome 1. Nature 420:312–316

    Article  CAS  PubMed  Google Scholar 

  • Schommer C, Palatnik JF, Aggarwal P, Chetelat A, Cubas P, Farmer EE, Nath U, Weigel D (2008) Control of jasmonate biosynthesis and senescence by miR319 targets. PLoS Biol 6:e230

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sharma N, Tripathi A, Sanan-Mishra N (2015) Profiling the expression domains of a rice-specific microRNA under stress. Front Plant Sci 6:333

    Article  PubMed  PubMed Central  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 11:743–748

    Article  CAS  Google Scholar 

  • Singh KB, Foley RC, O ate-Sanchez L (2002) Transcription factors in plant defense and stress responses. Curr Opin Plant Biol 5:430–436

    Article  CAS  PubMed  Google Scholar 

  • Singh P, Kaloudas D, Raines CA (2008) Expression analysis of the Arabidopsis CP12 gene family suggests novel roles for these proteins in roots and floral tissues. J Exp Bot 59:3975–3985

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Song L, Axtell MJ, Fedoroff NV (2010) RNA secondary structural determinants of miRNA precursor processing in Arabidopsis. Curr Biol 20:37–41

    Article  CAS  PubMed  Google Scholar 

  • Sun TP, Kamiya Y (1994) The Arabidopsis GA1 locus encodes the cyclase ent-kaurene synthetase A of gibberellin biosynthesis. Plant Cell Online 6:1509

    CAS  Google Scholar 

  • Sun M, Yang J, Cai X, Shen Y, Cui N, Zhu Y, Jia B, Sun X (2018) The opposite roles of OsmiR408 in cold and drought stress responses in Oryza sativa. Mol Breed 38:120

    Article  CAS  Google Scholar 

  • Sunkar R (2010) MicroRNAs with macro-effects on plant stress responses. Semin Cell Dev Biol 21:805–811

    Article  CAS  PubMed  Google Scholar 

  • Sunkar R, Zhu JK (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16:2001–2019

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sunkar R, Girke T, Jain PK, Zhu JK (2005) Cloning and characterization of microRNAs from rice. Plant Cell 17:1397–1411

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Taylor RS, Tarver JE, Hiscock SJ, Donoghue PCJ (2014) Evolutionary history of plant microRNAs. Trends Plant Sci 19:175–182

    Article  CAS  PubMed  Google Scholar 

  • The Rice Chromosome 10 Sequencing Consortium (2003) In-depth view of structure, activity, and evolution of rice chromosome 10. Science 300:1566–1569

    Article  CAS  Google Scholar 

  • Tiwari M, Sharma D, Trivedi PK (2014) Artificial microRNAs mediated gene silencing in plants: progress and perspectives. Plant Mol Biol 86:1–18

    Article  CAS  PubMed  Google Scholar 

  • Van Dyck L, Pearce DA, Sherman F (1994) PIM1 encodes a mitochondrial ATP dependent protease that is required for mitochondrial function in the yeast Saccharomyces cerevisiae. J Biol Chem 269:238

    PubMed  Google Scholar 

  • Wang JF, Zhou H, Chen YQ, Luo QJ, Qu LH (2004) Identification of 20 microRNAs from Oryza sativa. Nucleic Acids Res 32:1688–1695

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang X, Yang Y, Yu C, Zhou J, Cheng Y, Yan C et al (2010) A highly efficient method for construction of rice artificial MicroRNA vectors. Mol Biotechnol 46:211–218

    Article  CAS  PubMed  Google Scholar 

  • Wang L, Song X, Gu L (2013) NOT2 proteins promote polymerase II-dependent transcription and interact with multiple microRNAs biogenesis factors in Arabidopsis. Plant Cell 25:715–727

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang S-t, X-l S, Hoshino Y, Yu Y, Jia B et al (2014) MicroRNA319 positively regulates cold tolerance by targeting OsPCF6 and OsTCP21 in rice (Oryza sativa L.). PLoS One 9(3):e91357

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wen-Wen K, Hong-Bo W, Jing L (2014) Biogenesis of plant microRNAs. J Northeast Agric Univ 21:84–96

    Google Scholar 

  • Wu L, Zhou H, Zhang Q, Zhang J, Ni F, Liu C, Qi Y (2010) DNA methylation mediated by a microRNA pathway. Mol Cell 38:465–475

    Article  CAS  PubMed  Google Scholar 

  • Xia K, Wang R, Ou X, Fang Z, Tian C, Duan J (2012) OsTIR1 and OsAFB2 downregulation via OsmiR393 overexpression leads to more tillers, early flowering and less tolerance to salt and drought in rice. PLoS One 7:e30039

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xie K, Shen J, Hou X, Yao J, Li X, Xiao J, Xiong L (2012) Gradual increase of miR156 regulates temporal expression changes of numerous genes during leaf development in rice. Plant Physiol 158:1382–1394

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xie F, Stewart CN Jr, Taki FA, He Q, Liu H, Zhang B (2014) High-throughput deep sequencing shows that microRNAs play important roles in switch grass responses to drought and salinity stress. Plant Biotechnol J 12:354–366

    Article  CAS  PubMed  Google Scholar 

  • Xie M, Zhang S, Yu B (2015) microRNA biogenesis, degradation and activity in plants. Cell Mol Life Sci 72:87–99

    Article  CAS  PubMed  Google Scholar 

  • Yamaguchi-Shinozaki K, Shinozaki K (2006) Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Annu Rev Plant Biol 57:781–803

    Article  CAS  PubMed  Google Scholar 

  • Yang CH, Li DY, Mao DH, Liu X, Ji CJ et al (2013a) Over expression of microRNA319 impacts leaf morphogenesis and leads to enhanced cold tolerance in rice (Oryza sativa L.). Plant Cell Environ 36:2207–2218

    Article  CAS  PubMed  Google Scholar 

  • Yang Z, Huang D, Tang W, Zheng Y, Liang K et al (2013b) Mapping of quantitative trait loci underlying cold tolerance in rice seedlings via high-throughput sequencing of pooled extremes. PLoS One 8(7):e68433

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ye C, Fukai S, Godwin I, Reinke R, Snell P, Schiller J, Basnayake J (2009) Cold tolerance in rice varieties at different growth stages. Crop Pasture Sci 60:328–338

    Article  Google Scholar 

  • Yi X, Zhang Z, Ling Y, Xu W, Su Z (2015) PNRD: a plant noncoding RNA database. Nucleic Acids Res 43(D1):D982–D989

    Article  CAS  PubMed  Google Scholar 

  • Yoshida S (1981) Growth and development of the rice plant. Fundamentals of rice crop science, vol 1. International Rice Research Institute, Los Banos, Philippines, pp 1–36

    Google Scholar 

  • Yoshikawa M, Iki T, Tsutsui Y, Miyashita K, Poethig RS, Habu Y, Ishikawa M (2013) 3’ fragment of miR173-programmed RISC-cleaved RNA is protected from degradation in a complex with RISC and SGS3. Proc Natl Acad Sci U S A 110:4117–4122

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yu J, Hu SN, Wang J, Wong GKS, Li SG, Liu B, Deng YJ, Dai L, Zhou Y, Zhang XQ et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp indica). Science 296:79–92

    Article  CAS  PubMed  Google Scholar 

  • Yu J, Wang J, Lin W, Li SG, Li H, Zhou J, Ni PX, Dong W, Hu SN, Zeng CQ et al (2005) The genomes of Oryza sativa: a history of duplications. PLoS Biol 3:266–281

    Article  CAS  Google Scholar 

  • Yue E, Liu Z, Li C et al (2017) Over expression of miR529a confers enhanced resistance to oxidative stress in rice (Oryza sativa L.). Plant Cell Rep 36:1171

    Article  CAS  PubMed  Google Scholar 

  • Zhang B (2015) MicroRNA: a new target for improving plant tolerance to abiotic stress. J Exp Bot 66:1749–1761

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang B, Wang Q (2015) MicroRNA-based biotechnology for plant improvement. J Cell Physiol 230:1–15

    Article  PubMed  CAS  Google Scholar 

  • Zhang BH, Pan XP, Wang QL, Cobb GP, Anderson TA (2005) Identification and characterization of new plant microRNAs using EST analysis. Cell Res 15:336–360

    Article  PubMed  Google Scholar 

  • Zhang B, Pan X, Cobb GP, Anderson TA (2006) Plant microRNA: a small regulatory molecule with big impact. Dev Biol 289:3–16

    Article  CAS  PubMed  Google Scholar 

  • Zhang YC, Yu Y, Wang CY et al (2013a) Overexpression of microRNAs OsmiR397 improves rice yield by increasing grain size and promoting panicle branching. Nat Biotechnol 31:848–852

    Article  CAS  PubMed  Google Scholar 

  • Zhang S, Yue Y, Sheng L, Wu Y, Fan G, Li A, Hu X, Shang Guan M, Wei C (2013b) PASmiR: a literature curated database for miRNA molecular regulation in plant response to abiotic stress. BMC Plant Biol 13:33

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang JP, Yu Y, Feng YZ, Zhou YF, Zhang F, Yang YW, Lei MQ, Zhang YC, Chen YQ (2017) MiR408 regulates grain yield and photosynthesis via a phytocyanin protein. Plant Physiol 175(3):1175–1185. https://doi.org/10.1104/pp.17.01169

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 354:585–590

    Article  CAS  PubMed  Google Scholar 

  • Zhao B, Ge L, Liang R, Li W, Ruan K, Lin H, Jin Y (2009) Members of miR-169 family are induced by high salinity and transiently inhibit the NF-YA transcription factor. BMC Mol Biol 10:29

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhao X, Zhang H, Li L (2013) Identification and analysis of the proximal promoters of microRNA genes in Arabidopsis. Genomics 101:187–194

    Article  CAS  PubMed  Google Scholar 

  • Zhou X, Wang G, Sutoh K, Zhu JK, Zhang W (2008) Identification of cold-inducible microRNAs in plants by transcriptome analysis. Biochim Biophys Acta 1779:780–788

    Article  CAS  PubMed  Google Scholar 

  • 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 61:4157–4168

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Zhu JK (2002) Salt and drought stress signal transduction in plants. Annu Rev Plant Biol 53:247–273

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zou J, Liu AL, Chen XB, Zhou XY, Gao GF, Wang WF, Zhang XW (2009) Expression analysis of nine rice heat shock protein genes under abiotic stresses and ABA treatment. J Plant Physiol 166(8):851–861

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

Dr. Saurabh Raghuvanshi is acknowledged for introducing me to the world of micro RNAs while working under his guidance as IASc-INSA-NASI Summer Research Teacher Fellow in 2014 at Laboratory of Structural Genomics & Bioinformatics, Department of Plant Molecular Biology, Delhi University, South Campus, New Delhi, India.

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  1. Government Department of School Education, Jammu, Jammu and Kashmir, India

    Deepu Pandita

  2. Mountain Research Centre for Field Crops, Khudwani, SKUAST-Kashmir, India

    Shabir Hussain Wani

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  1. Deepu Pandita
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  2. Shabir Hussain Wani
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  1. Mountain Research Centre for Field Crops, Khudwani, SKUAST-Kashmir, India

    Shabir Hussain Wani

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Pandita, D., Wani, S.H. (2019). MicroRNA as a Tool for Mitigating Abiotic Stress in Rice (Oryza sativa L.). In: Wani, S. (eds) Recent Approaches in Omics for Plant Resilience to Climate Change. Springer, Cham. https://doi.org/10.1007/978-3-030-21687-0_6

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