Advertisement

miRNAs: The Game Changer in Producing Salinity Stress-Tolerant Crops

  • Ratanesh Kumar
  • Sudhir Kumar
  • Neeti Sanan-Mishra
Chapter

Abstract

The problem of soil salinity is emerging as the most damaging factor for crop growth and productivity. An increased salt concentration causes both osmotic and ionic stress to the plants, which inhibits their growth rate and yields. The genetic processes that coordinate the plant’s response to salinity have been explained by mechanisms that regulate the signaling cascades, cellular homeostasis, osmoticum maintenance and metabolic processes. This involves modulation of the gene expression. The microRNAs (miRNAs) represent an important class of endogenous posttranscriptional regulators. They play an important role in plant biology by regulating every aspect of development, metabolism and environmental responses. This review discusses the available information on the salt stress-responsive genes and their role in the adaptive response to salt stress. It also discusses the role of miRNAs as potential regulators in salt stress response. The application of miRNA-based strategies for improving plants is also described.

Keywords

MicroRNA Origin Function Oryza sativa Salt stress Target gene Posttranscriptional regulation Signaling molecules Transporters miRNA application Osmolytes Hormones 

Abbreviations

ABA

Abscisic acid

ABREs

ABA-responsive cis-elements

AGO

Argonaute

AP2

Apetala 2

AREB/ABF

ABA-responsive element-binding protein/ABRE-binding factor

AtHK1

Arabidopsis thaliana histidine kinase1

Ca2+

Calcium ion

CAD

C-terminal CDPK activation domain

CBC

Cap-binding complex

CBL

Calcineurin B-like

CDPKs.

Ca2+-dependent protein kinases

CIPKs

CBL-interacting protein kinases

CKs

Cytokinins

CSDs

Cu/Zn superoxide dismutases

D bodies

Dicing bodies

DAG

Diacylglycerol

DCL

Dicer-like

GAs

Gibberellins

GST

Glutathione S-transferase

H2O2

Hydrogen peroxide

HD-ZIP

Homeodomain-leucine zipper protein

HEN1

Hua enhancer1

HST

Hasty

HYL1

Hyponastic leaves1

IAA

Indole acetic acid

IP3

Inositol 1,4,5-trisphosphate

JA

Jasmonic acid

MAPK

Mitogen-activated protein kinase

miRNAs

MicroRNAs

NAC

NAM, ATAF1 2, CUC2

NF-YA5

Nuclear factor YA5

NO

Nitric oxide

O2

Superoxide

OsSPL14

Oryza sativa squamosa promoter binding protein-like 14

PI

Phosphatidylinositol

PI-4,5-P2 or PIP2

PI-4,5-biphosphate

PI-4-P or PIP

PI-4-monophosphate

Pi-PLC

Phosphoinositide phospholipase C

Pre-miRNA

Precursor miRNAs

Pri-miRNA

Primary miRNAs

RISC

RNA-induced silencing complex

RLKs

Receptor-like kinases

RNA Pol II

RNA polymerase II

RNAi

RNA interference

ROS

Reactive oxygen species

SA

Salicylic acid

SE

Serrate

SIMK

Salt stress-inducible MAPK

siRNAs

Short interfering RNAs

SmD3-bodies

Small nuclear RNA-binding protein D3 bodies

SnRK2

Sucrose non-fermenting 1-related protein kinase2

SOD

Superoxide dismutase

SOS

Salt overly sensitive

TGH

Tough

UBC

Ubiquitin-conjugating enzyme

Notes

Acknowledgments

We apologize to colleagues whose work could not be included owing to space constraints. The study on miRNAs in our lab was supported by financial grants from the Department of Biotechnology.

References

  1. Abe H, Urao T, Ito T, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2003) Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function as transcriptional activators in abscisic acid signaling. Plant Cell 15(1):63–78PubMedPubMedCentralCrossRefGoogle Scholar
  2. Abebe T, Guenzi AC, Martin B, Cushman JC (2003) Tolerance of mannitol-accumulating transgenic wheat to water stress and salinity. Plant Physiol 131(4):1748–1755PubMedPubMedCentralCrossRefGoogle Scholar
  3. Abeles FB, Morgan PW, Saltveit ME Jr (2012) Ethylene in plant biology. Academic, San DiegoGoogle Scholar
  4. 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(8):2117–2129PubMedPubMedCentralCrossRefGoogle Scholar
  5. Adams RP, Kendall E, Kartha K (1990) Comparison of free sugars in growing and desiccated plants of Selaginella lepidophylla. Biochem Syst Ecol 18(2–3):107–110CrossRefGoogle Scholar
  6. Afzal I, Basra S, Iqbal A (2005) The effect of seed soaking with plant growth regulators on seedling vigor of wheat under salinity stress. Stress Physiol Biochem 1:6–14Google Scholar
  7. Aleman L, Sun Y, Fokar M, Allen R (2007) Role of phytohormone signaling pathways in cotton fiber development. In: World cotton research conference-4, Lubbock, Texas, USA, 10–14 September 2007. International Cotton Advisory Committee (ICAC)Google Scholar
  8. Alonso-Peral MM, Li J, Li Y, Allen RS, Schnippenkoetter W, Ohms S, White RG, Millar AA (2010) The microRNA159-regulated GAMYB-like genes inhibit growth and promote programmed cell death in Arabidopsis. Plant Physiol 154(2):757–771PubMedPubMedCentralCrossRefGoogle Scholar
  9. Amor BB, Wirth S, Merchan F, Laporte P, d’Aubenton-Carafa Y, Hirsch J, Maizel A, Mallory A, Lucas A, Deragon JM (2009) Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses. Genome Res 19(1):57–69PubMedPubMedCentralCrossRefGoogle Scholar
  10. Arenas-Huertero C, Pérez B, Rabanal F, Blanco-Melo D, De la Rosa C, Estrada-Navarrete G, Sanchez F, Covarrubias AA, Reyes JL (2009) Conserved and novel miRNAs in the legume Phaseolus vulgaris in response to stress. Plant Mol Biol 70(4):385–401PubMedCrossRefPubMedCentralGoogle Scholar
  11. Aukerman MJ, Sakai H (2003) Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. Plant Cell 15(11):2730–2741PubMedPubMedCentralCrossRefGoogle Scholar
  12. Aung K, Lin S-I, Wu C-C, Huang Y-T, C-l S, Chiou T-J (2006) pho2, a phosphate over accumulator, is caused by a nonsense mutation in a microRNA399 target gene. Plant Physiol 141(3):1000–1011PubMedPubMedCentralCrossRefGoogle Scholar
  13. Baek D, Chun HJ, Kang S, Shin G, Park SJ, Hong H, Kim C, Kim DH, Lee SY, Kim MC (2016) A role for Arabidopsis miR399f in salt, drought, and ABA signaling. Mol Cell 39(2):111CrossRefGoogle Scholar
  14. Bagni N, Tassoni A (2001) Biosynthesis, oxidation and conjugation of aliphatic polyamines in higher plants. Amino Acids 20(3):301–317PubMedCrossRefPubMedCentralGoogle Scholar
  15. Baier M, Kandlbinder A, Golldack D, Dietz KJ (2005) Oxidative stress and ozone: perception, signalling and response. Plant Cell Environ 28(8):1012–1020CrossRefGoogle Scholar
  16. Bari R, Pant BD, Stitt M, Scheible W-R (2006) PHO2, microRNA399, and PHR1 define a phosphate-signaling pathway in plants. Plant Physiol 141(3):988–999PubMedPubMedCentralCrossRefGoogle Scholar
  17. Barrera-Figueroa BE, Gao L, Wu Z, Zhou X, Zhu J, Jin H, Liu R, Zhu J-K (2012) High throughput sequencing reveals novel and abiotic stress-regulated microRNAs in the inflorescences of rice. BMC Plant Biol 12(1):132PubMedPubMedCentralCrossRefGoogle Scholar
  18. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116(2):281–297PubMedCrossRefPubMedCentralGoogle Scholar
  19. Bieleski R (1982) Sugar alcohols. In: Plant carbohydrates. Springer, New York, pp 158–192CrossRefGoogle Scholar
  20. Blackman P, Davies W (1984) Age-related changes in stomatal response to cytokinins and abscisic acid. Ann Bot 54(1):121–126CrossRefGoogle Scholar
  21. Blumwald E (2000) Sodium transport and salt tolerance in plants. Curr Opin Cell Biol 12(4):431–434PubMedPubMedCentralCrossRefGoogle Scholar
  22. Blumwald E, Grover A (2006) Salt tolerance. Plant biotechnology: current and future uses of genetically modified crops. Wiley, UK, pp 206–224CrossRefGoogle Scholar
  23. Bohmert K, Camus I, Bellini C, Bouchez D, Caboche M, Benning C (1998) AGO1 defines a novel locus of Arabidopsis controlling leaf development. EMBO J 17(1):170–180PubMedPubMedCentralCrossRefGoogle Scholar
  24. Boualem A, Laporte P, Jovanovic M, Laffont C, Plet J, Combier JP, Niebel A, Crespi M, Frugier F (2008) MicroRNA166 controls root and nodule development in Medicago truncatula. Plant J 54(5):876–887PubMedCrossRefPubMedCentralGoogle Scholar
  25. Boutet S, Vazquez F, Liu J, Béclin C, Fagard M, Gratias A, Morel J-B, Crété P, Chen X, Vaucheret H (2003) Arabidopsis HEN1: a genetic link between endogenous miRNA controlling development and siRNA controlling transgene silencing and virus resistance. Curr Biol 13(10):843–848PubMedPubMedCentralCrossRefGoogle Scholar
  26. Bozcuk S (1981) Effects of kinetin and salinity on germination of tomato, barley and cotton seeds. Ann Bot 48(1):81–84CrossRefGoogle Scholar
  27. Bressan RA, Hasegawa PM, Pardo JM (1998) Plants use calcium to resolve salt stress. Trends Plant Sci 3(11):411–412CrossRefGoogle Scholar
  28. 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(5880):1185–1190PubMedCrossRefPubMedCentralGoogle Scholar
  29. Brodersen P, Sakvarelidze-Achard L, Schaller H, Khafif M, Schott G, Bendahmane A, Voinnet O (2012) Isoprenoid biosynthesis is required for miRNA function and affects membrane association of Argonaute 1 in Arabidopsis. Proc Natl Acad Sci 109(5):1778–1783PubMedPubMedCentralCrossRefGoogle Scholar
  30. Burklew CE, Ashlock J, Winfrey WB, Zhang B (2012) Effects of aluminum oxide nanoparticles on the growth, development, and microRNA expression of tobacco (Nicotiana tabacum). PLoS One 7(5):34783CrossRefGoogle Scholar
  31. Bushati N, Cohen SM (2007) microRNA functions. Annu Rev Cell Dev Biol 23:175–205PubMedCrossRefPubMedCentralGoogle Scholar
  32. Cabot C, Sibole JV, Barceló J, Poschenrieder C (2009) Abscisic acid decreases leaf Na+ exclusion in salt-treated Phaseolus vulgaris L. J Plant Growth Regul 28(2):187–192CrossRefGoogle Scholar
  33. Cai X, Davis EJ, Ballif J, Liang M, Bushman E, Haroldsen V, Torabinejad J, Wu Y (2006) Mutant identification and characterization of the laccase gene family in Arabidopsis. J Exp Bot 57(11):2563–2569PubMedCrossRefPubMedCentralGoogle Scholar
  34. Campo S, Peris-Peris C, Siré C, Moreno AB, Donaire L, Zytnicki M, Notredame C, Llave C, San Segundo B (2013) Identification of a novel microRNA (miRNA) from rice that targets an alternatively spliced transcript of the Nramp6 (Natural resistance-associated macrophage protein 6) gene involved in pathogen resistance. New Phytol 199(1):212–227PubMedCrossRefPubMedCentralGoogle Scholar
  35. Cao W-H, Liu J, He X-J, Mu R-L, Zhou H-L, Chen S-Y, Zhang J-S (2007) Modulation of ethylene responses affects plant salt-stress responses. Plant Physiol 143(2):707–719PubMedPubMedCentralCrossRefGoogle Scholar
  36. Capell T, Bassie L, Christou P (2004) Modulation of the polyamine biosynthetic pathway in transgenic rice confers tolerance to drought stress. Proc Natl Acad Sci U S A 101(26):9909–9914PubMedPubMedCentralCrossRefGoogle Scholar
  37. Carillo P, Annunziata MG, Pontecorvo G, Fuggi A, Woodrow P (2011) Salinity stress and salt tolerance. In: Abiotic stress in plants-mechanisms and adaptations. InTechGoogle Scholar
  38. Carrington JC, Ambros V (2003) Role of microRNAs in plant and animal development. Science 301(5631):336–338PubMedCrossRefPubMedCentralGoogle Scholar
  39. Cerutti L, Mian N, Bateman A (2000) Domains in gene silencing and cell differentiation proteins: the novel PAZ domain and redefinition of the Piwi domain. Trends Biochem Sci 25(10):481–482PubMedCrossRefPubMedCentralGoogle Scholar
  40. Chakrabarti N, Mukherji S (2003) Alleviation of NaCl stress by pretreatment with phytohormones in Vigna radiata. Biol Plant 46(4):589–594CrossRefGoogle Scholar
  41. Chandran V, Stollar EJ, Lindorff-Larsen K, Harper JF, Chazin WJ, Dobson CM, Luisi BF, Christodoulou J (2006) Structure of the regulatory apparatus of a calcium-dependent protein kinase (CDPK): a novel mode of calmodulin-target recognition. J Mol Biol 357(2):400–410PubMedCrossRefPubMedCentralGoogle Scholar
  42. Chaudhuri S, Seal A, Gupta MD (1999) Autophosphorylation-dependent activation of a calcium-dependent protein kinase from groundnut. Plant Physiol 120(3):859–866PubMedPubMedCentralCrossRefGoogle Scholar
  43. Chauhan N, Kumar VH (2016) Gender responsive climate change strategies for sustainable development. Productivity 57(2):182Google Scholar
  44. Chen X (2004) A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303(5666):2022–2025PubMedCrossRefPubMedCentralGoogle Scholar
  45. Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR (2005) Real-time quantification of microRNAs by stem–loop RT–PCR. Nucleic Acids Res 33(20):e179–e179PubMedPubMedCentralCrossRefGoogle Scholar
  46. Chen L, Zhang Y, Ren Y, Xu J, Zhang Z, Wang Y (2012) Genome-wide identification of cold-responsive and new microRNAs in Populus tomentosa by high-throughput sequencing. Biochem Biophys Res Commun 417(2):892–896PubMedCrossRefPubMedCentralGoogle Scholar
  47. Cheng S, Long JS (2007) Testing for IIA in the multinomial logit model. Sociol Methods Res 35(4):583–600CrossRefGoogle Scholar
  48. Cheng L, Zou Y, Ding S, Zhang J, Yu X, Cao J, Lu G (2009) Polyamine accumulation in transgenic tomato enhances the tolerance to high temperature stress. J Integr Plant Biol 51(5):489–499PubMedCrossRefPubMedCentralGoogle Scholar
  49. Cheng HY, Wang Y, Tao X, Fan YF, Dai Y, Yang H, Ma XR (2016) Genomic profiling of exogenous abscisic acid-responsive microRNAs in tomato (Solanum lycopersicum). BMC Genomics 17(1):423PubMedPubMedCentralCrossRefGoogle Scholar
  50. Chinnusamy V, Jagendorf A, Zhu J-K (2005) Understanding and improving salt tolerance in plants. Crop Sci 45(2):437–448CrossRefGoogle Scholar
  51. Christodoulou J, Malmendal A, Harper JF, Chazin WJ (2004) Evidence for differing roles for each lobe of the calmodulin-like domain in a calcium-dependent protein kinase. J Biol Chem 279(28):29092–29100PubMedCrossRefPubMedCentralGoogle Scholar
  52. Chuck G, Candela H, Hake S (2009) Big impacts by small RNAs in plant development. Curr Opin Plant Biol 12(1):81–86PubMedCrossRefPubMedCentralGoogle Scholar
  53. Chuck GS, Tobias C, Sun L, Kraemer F, Li C, Dibble D, Arora R, Bragg JN, Vogel JP, Singh S (2011) Overexpression of the maize Corngrass1 microRNA prevents flowering, improves digestibility, and increases starch content of switchgrass. Proc Natl Acad Sci 108(42):17550–17555PubMedPubMedCentralCrossRefGoogle Scholar
  54. Cominelli E, Sala T, Calvi D, Gusmaroli G, Tonelli C (2008) Over-expression of the Arabidopsis AtMYB41 gene alters cell expansion and leaf surface permeability. Plant J 53(1):53–64PubMedCrossRefPubMedCentralGoogle Scholar
  55. Contreras-Cubas C, Palomar M, Arteaga-Vázquez M, Reyes JL, Covarrubias AA (2012) Non-coding RNAs in the plant response to abiotic stress. Planta 236(4):943–958PubMedCrossRefPubMedCentralGoogle Scholar
  56. Cramer GR, Lynch J, Läuchli A, Epstein E (1987) Influx of Na+, K+, and Ca2+ into roots of salt-stressed cotton seedlings effects of supplemental Ca2+. Plant Physiol 83(3):510–516PubMedPubMedCentralCrossRefGoogle Scholar
  57. Crowe JH, Hoekstra FA, Crowe LM (1992) Anhydrobiosis. Annu Rev Physiol 54(1):579–599PubMedCrossRefPubMedCentralGoogle Scholar
  58. Cuevas J, Lopez-Cobollo R, Alcazar R et al (2008) Putrescine is involved in Arabidopsis freezing tolerance and cold acclimation by regulating abscisic acid levels in response to low temperature. Plant Physiol 148(2):1094–1105PubMedPubMedCentralCrossRefGoogle Scholar
  59. 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(11):214CrossRefGoogle Scholar
  60. Davies P (2004) Plant hormones: biosynthesis, signal transduction. Action Kluwer Academic Publishers, LondonGoogle Scholar
  61. Davies WJ, Tardieu F, Trejo CL (1994) How do chemical signals work in plants that grow in drying soil? Plant Physiol 104(2):309PubMedPubMedCentralCrossRefGoogle Scholar
  62. 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(1):41PubMedPubMedCentralCrossRefGoogle Scholar
  63. Debez A, Chaibi W, Bouzid S (2001) Effet du NaCl et de régulateurs de croissance sur la germination d’Atriplex halimus L. Cah Agric 10(2):135–138Google Scholar
  64. Deinlein U, Stephan AB, Horie T, Luo W, Xu G, Schroeder JI (2014) Plant salt-tolerance mechanisms. Trends Plant Sci 19(6):371–379PubMedPubMedCentralCrossRefGoogle Scholar
  65. Delauney AJ, Verma DPS (1993) Proline biosynthesis and osmoregulation in plants. Plant J 4(2):215–223CrossRefGoogle Scholar
  66. Deng P, Wang L, Cui L, Feng K, Liu F, Du X, Tong W, Nie X, Ji W, Weining S (2015) Global identification of microRNAs and their targets in barley under salinity stress. PLoS One 10(9):e0137990PubMedPubMedCentralCrossRefGoogle Scholar
  67. DeWald DB, Torabinejad J, Jones CA, Shope JC, Cangelosi AR, Thompson JE, Prestwich GD, Hama H (2001) Rapid accumulation of phosphatidylinositol 4, 5-bisphosphate and inositol 1, 4, 5-trisphosphate correlates with calcium mobilization in salt-stressed Arabidopsis. Plant Physiol 126(2):759–769PubMedPubMedCentralCrossRefGoogle Scholar
  68. Diédhiou CJ, Golldack D, Dietz K-J, Popova OV (2008) The SNF1-type serine-threonine protein kinase SAPK4 regulates stress-responsive gene expression in rice. BMC Plant Biol 8(1):49PubMedPubMedCentralCrossRefGoogle Scholar
  69. Ding Y-F, Zhu C (2009) The role of microRNAs in copper and cadmium homeostasis. Biochem Biophys Res Commun 386(1):6–10PubMedCrossRefPubMedCentralGoogle Scholar
  70. Ding Y, Chen Z, Zhu C (2011) Microarray-based analysis of cadmium-responsive microRNAs in rice (Oryza sativa). J Exp Bot 62(10):3563–3573PubMedPubMedCentralCrossRefGoogle Scholar
  71. 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):3077–3086PubMedCrossRefPubMedCentralGoogle Scholar
  72. Djami-Tchatchou AT, Sanan-Mishra N, Ntushelo K, Dubery IA (2017) Functional roles of microRNAs in agronomically important plants—potential as targets for crop improvement and protection. Front Plant Sci 8:378PubMedPubMedCentralCrossRefGoogle Scholar
  73. Dodd AN, Kudla J, Sanders D (2010) The language of calcium signaling. Annu Rev Plant Biol 61:593–62074PubMedCrossRefPubMedCentralGoogle Scholar
  74. Dong Z, Han M-H, Fedoroff N (2008) The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1. Proc Natl Acad Sci 105(29):9970–9975PubMedPubMedCentralCrossRefGoogle Scholar
  75. Drøbak BK, Watkins PA (2000) Inositol (1, 4, 5) trisphosphate production in plant cells: an early response to salinity and hyperosmotic stress. FEBS Lett 481(3):240–244PubMedCrossRefPubMedCentralGoogle Scholar
  76. Edreva A (1996) Polyamines in plants. Bulg J Plant Physiol 22(1–2):73–101Google Scholar
  77. Egamberdieva D (2009) Alleviation of salt stress by plant growth regulators and IAA producing bacteria in wheat. Acta Physiol Plant 31(4):861–864CrossRefGoogle Scholar
  78. Eldem V, Akçay UÇ, Ozhuner E, Bakır Y, Uranbey S, Unver T (2012) Genome-wide identification of miRNAs responsive to drought in peach (Prunus persica) by high-throughput deep sequencing. PLoS One 7(12):e50298PubMedPubMedCentralCrossRefGoogle Scholar
  79. Ellouzi H, Hamed KB, Hernández I, Cela J, Müller M, Magné C, Abdelly C, Munné-Bosch S (2014) A comparative study of the early osmotic, ionic, redox and hormonal signaling response in leaves and roots of two halophytes and a glycophyte to salinity. Planta 240(6):1299–1317PubMedPubMedCentralCrossRefGoogle Scholar
  80. Esmaeili F, Shiran B, Fallahi H, Mirakhorli N, Budak H, Martínez-Gómez P (2017) In silico search and biological validation of microRNAs related to drought response in peach and almond. Funct Integr Genom 17(2–3):189–201CrossRefGoogle Scholar
  81. Everard JD, Gucci R, Kann SC, Flore JA, Loescher WH (1994) Gas exchange and carbon partitioning in the leaves of celery (Apium graveolens L.) at various levels of root zone salinity. Plant Physiol 106(1):281–292PubMedPubMedCentralCrossRefGoogle Scholar
  82. Ezaki B, Gardner RC, Ezaki Y, Matsumoto H (2000) Expression of aluminum-induced genes in transgenic Arabidopsis plants can ameliorate aluminum stress and/or oxidative stress. Plant Physiol 122(3):657–666PubMedPubMedCentralCrossRefGoogle Scholar
  83. Faller M, Guo F (2008) MicroRNA biogenesis: there’s more than one way to skin a cat. BBA-Gene Regul Mech 1779(11):663–667Google Scholar
  84. Fang J, Grzymala-Busse JW (2006) Mining of microRNA expression data-a rough set approach. In: Rough sets and knowledge technology, pp 758–765CrossRefGoogle Scholar
  85. Fang Y, Spector DL (2007) Identification of nuclear dicing bodies containing proteins for microRNA biogenesis in living Arabidopsis plants. Curr Biol 17(9):818–823PubMedPubMedCentralCrossRefGoogle Scholar
  86. Fang Y, Xie K, Xiong L (2014) Conserved miR164-targeted NAC genes negatively regulate drought resistance in rice. J Exp Bot 65(8):2119–2135PubMedPubMedCentralCrossRefGoogle Scholar
  87. Fariduddin Q, Varshney P, Yusuf M, Ahmad A (2013) Polyamines: potent modulators of plant responses to stress. J Plant Interact 8(1):1–16CrossRefGoogle Scholar
  88. Farooq M, Hussain M, Wakeel A, Siddique KH (2015) Salt stress in maize: effects, resistance mechanisms, and management. A review. Agron Sustain Dev 35(2):461–481CrossRefGoogle Scholar
  89. Filipowicz W, Bhattacharyya SN, Sonenberg N (2008) Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet 9(2):102–114PubMedCrossRefPubMedCentralGoogle Scholar
  90. Flowers T, Yeo A (1995) Breeding for salinity resistance in crop plants: where next? Funct Plant Biol 22(6):875–884Google Scholar
  91. Flowers TJ, Garcia A, Koyama M, Yeo AR (1997) Breeding for salt tolerance in crop plants—the role of molecular biology. Acta Physiol Plant 19(4):427–433CrossRefGoogle Scholar
  92. Flowers TJ, Galal HK, Bromham L (2010) Evolution of halophytes: multiple origins of salt tolerance in land plants. Funct Plant Biol 37(7):604–612CrossRefGoogle Scholar
  93. Ford CW (1984) Accumulation of low molecular weight solutes in water-stressed tropical legumes. Phytochemistry 23(5):1007–1015CrossRefGoogle Scholar
  94. Franz S, Ehlert B, Liese A, Kurth J, Cazalé A-C, Romeis T (2011) Calcium-dependent protein kinase CPK21 functions in abiotic stress response in Arabidopsis thaliana. Mol Plant 4(1):83–96PubMedCrossRefPubMedCentralGoogle Scholar
  95. Frazier TP, Sun G, Burklew CE, Zhang B (2011) Salt and drought stresses induce the aberrant expression of microRNA genes in tobacco. Mol Biotechnol 49(2):159–165PubMedCrossRefPubMedCentralGoogle Scholar
  96. Frugier F, Poirier S, Satiat-Jeunemaître B, Kondorosi A, Crespi M (2000) A Krüppel-like zinc finger protein is involved in nitrogen-fixing root nodule organogenesis. Genes Dev 14(4):475–482PubMedPubMedCentralGoogle Scholar
  97. Fu C, Sunkar R, Zhou C, Shen H, Zhang JY, Matts J, Wolf J, Mann DG, Stewart CN, Tang Y (2012) Overexpression of miR156 in switchgrass (Panicum virgatum L.) results in various morphological alterations and leads to improved biomass production. Plant Biotechnol J 10(4):443–452PubMedPubMedCentralCrossRefGoogle Scholar
  98. Fujii H, Chiou T-J, Lin S-I, Aung K, Zhu J-K (2005) A miRNA involved in phosphate-starvation response in Arabidopsis. Curr Biol 15(22):2038–2043PubMedCrossRefPubMedCentralGoogle Scholar
  99. Fujioka Y, Utsumi M, Ohba Y, Watanabe Y (2007) Location of a possible miRNA processing site in SmD3/SmB nuclear bodies in Arabidopsis. Plant Cell Physiol 48(9):1243–1253PubMedCrossRefPubMedCentralGoogle Scholar
  100. Fukuda A, Tanaka Y (2006) Effects of ABA, auxin, and gibberellin on the expression of genes for vacuolar H+-inorganic pyrophosphatase, H+-ATPase subunit A, and Na+/H+ antiporter in barley. Plant Physiol Biochem 44(5):351–358PubMedCrossRefPubMedCentralGoogle Scholar
  101. Galli V, Guzman F, de Oliveira LF, Loss-Morais G, Körbes AP, Silva SD, Margis-Pinheiro MM, Margis R (2014) Identifying microRNAs and transcript targets in Jatropha seeds. PLoS One 9(2):e83727PubMedPubMedCentralCrossRefGoogle Scholar
  102. Gandikota M, Birkenbihl RP, Höhmann S, Cardon GH, Saedler H, Huijser P (2007) The miRNA156/157 recognition element in the 3′ UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlings. Plant J 49(4):683–693PubMedCrossRefPubMedCentralGoogle Scholar
  103. 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(5):991–1001PubMedCrossRefPubMedCentralGoogle Scholar
  104. Gao C, Wang Y, Jiang B, Liu G, Yu L, Wei Z, Yang C (2011a) A novel vacuolar membrane H+-ATPase c subunit gene (ThVHAc1) from Tamarix hispida confers tolerance to several abiotic stresses in Saccharomyces cerevisiae. Mol Biol Rep 38(2):957–963PubMedPubMedCentralCrossRefGoogle Scholar
  105. Gao P, Bai X, Yang L, Lv D, Pan X, Li Y, Cai H, Ji W, Chen Q, Zhu Y (2011b) osa-MIR393: a salinity-and alkaline stress-related microRNA gene. Mol Biol Rep 38(1):237–242PubMedCrossRefPubMedCentralGoogle Scholar
  106. 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 Report 34(5):931–946CrossRefGoogle Scholar
  107. Garcia AB, Engler JDA, Iyer S, Gerats T, Van Montagu M, Caplan AB (1997) Effects of osmoprotectants upon NaCl stress in rice. Plant Physiol 115(1):159–169PubMedPubMedCentralCrossRefGoogle Scholar
  108. Garg AK, Kim J-K, Owens TG, Ranwala AP, Do Choi Y, Kochian LV, Wu RJ (2002) Trehalose accumulation in rice plants confers high tolerance levels to different abiotic stresses. Proc Natl Acad Sci 99(25):15898–15903PubMedPubMedCentralCrossRefGoogle Scholar
  109. Gaude N, Nakamura Y, Scheible WR, Ohta H, Dörmann P (2008) Phospholipase C5 (NPC5) is involved in galactolipid accumulation during phosphate limitation in leaves of Arabidopsis. Plant J 56(1):28–39PubMedCrossRefPubMedCentralGoogle Scholar
  110. Giacomelli JI, Weigel D, Chan RL, Manavella PA (2012) Role of recently evolved miRNA regulation of sunflower HaWRKY6 in response to temperature damage. New Phytol 195(4):766–773PubMedCrossRefPubMedCentralGoogle Scholar
  111. Gill SS, Tuteja N (2010) Polyamines and abiotic stress tolerance in plants. Plant Signal Behav 5(1):26–33PubMedPubMedCentralCrossRefGoogle Scholar
  112. Goddijn O, Smeekens S (1998) Sensing trehalose biosynthesis in plants. Plant J 14(2):143–146PubMedCrossRefPubMedCentralGoogle Scholar
  113. 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(8):1383–1391PubMedCrossRefPubMedCentralGoogle Scholar
  114. Gómez-Cadenas A, Arbona V, Jacas J, Primo-Millo E, Talon M (2002) Abscisic acid reduces leaf abscission and increases salt tolerance in citrus plants. J Plant Growth Regul 21(3):234–240CrossRefGoogle Scholar
  115. Gonai T, Kawahara S, Tougou M, Satoh S, Hashiba T, Hirai N, Kawaide H, Kamiya Y, Yoshioka T (2004) Abscisic acid in the thermoinhibition of lettuce seed germination and enhancement of its catabolism by gibberellin. J Exp Bot 55(394):111–118PubMedCrossRefPubMedCentralGoogle Scholar
  116. Goswami K, Tripathi A, Sanan-Mishra N (2017) Comparative miRomics of salt-tolerant and salt-sensitive rice. J Integr Bioinform 14(1)Google Scholar
  117. Greenway H, Munns R (1980) Mechanisms of salt tolerance in nonhalophytes. Annu Rev Plant Physiol 31(1):149–190CrossRefGoogle Scholar
  118. Groppa M, Benavides M (2008) Polyamines and abiotic stress: recent advances. Amino Acids 34(1):35–45PubMedCrossRefPubMedCentralGoogle Scholar
  119. 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):840–851PubMedCrossRefPubMedCentralGoogle Scholar
  120. Gul B, Khan MA, Weber DJ (2000) Alleviation of salinity and dark-enforced dormancy in Allenrolfea occidentalis seeds under various thermoperiods. Aust J Bot 48(6):745–752CrossRefGoogle Scholar
  121. Guo Y, Qiu Q-S, Quintero FJ, Pardo JM, Ohta M, Zhang C, Schumaker KS, Zhu J-K (2004) Transgenic evaluation of activated mutant alleles of SOS2 reveals a critical requirement for its kinase activity and C-terminal regulatory domain for salt tolerance in Arabidopsis thaliana. Plant Cell 16(2):435–449PubMedPubMedCentralCrossRefGoogle Scholar
  122. Guo S, Xu Y, Liu H, Mao Z, Zhang C, Ma Y, Zhang Q, Meng Z, Chong K (2013) The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14. Nat Commun 4:1566PubMedPubMedCentralCrossRefGoogle Scholar
  123. Gupta O, Sharma P, Gupta R, Sharma I (2014) MicroRNA mediated regulation of metal toxicity in plants: present status and future perspectives. Plant Mol Biol 84(1–2):1–18PubMedCrossRefPubMedCentralGoogle Scholar
  124. Hajyzadeh M, Turktas M, Khawar KM, Unver T (2015) miR408 overexpression causes increased drought tolerance in chickpea. Gene 555(2):186–193PubMedCrossRefGoogle Scholar
  125. Halfter U, Ishitani M, Zhu J-K (2000) The Arabidopsis SOS2 protein kinase physically interacts with and is activated by the calcium-binding protein SOS3. Proc Natl Acad Sci 97(7):3735–3740PubMedPubMedCentralCrossRefGoogle Scholar
  126. Han M-H, Goud S, Song L, Fedoroff N (2004) The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation. Proc Natl Acad Sci U S A 101(4):1093–1098PubMedPubMedCentralCrossRefGoogle Scholar
  127. Hasanuzzaman M, Nahar K, Fujita M, Ahmad P, Chandna R, Prasad M, Ozturk M (2013) Enhancing plant productivity under salt stress: relevance of poly-omics. In: Salt stress in plants. Springer, New York, pp 113–156CrossRefGoogle Scholar
  128. Hasegawa PM, Bressan RA, Zhu J-K, Bohnert HJ (2000) Plant cellular and molecular responses to high salinity. Annu Rev Plant Biol 51(1):463–499CrossRefGoogle Scholar
  129. He L, Ban Y, Inoue H, Matsuda N, Liu J, Moriguchi T (2008) Enhancement of spermidine content and antioxidant capacity in transgenic pear shoots overexpressing apple spermidine synthase in response to salinity and hyperosmosis. Phytochemistry 69(11):2133–2141PubMedCrossRefPubMedCentralGoogle Scholar
  130. Hernandez Y, Sanan-Mishra N (2017) miRNA mediated regulation of NAC transcription factors in plant development and environment stress response. Plant Gene 11:190–198CrossRefGoogle Scholar
  131. Hirayama T, Ohto C, Mizoguchi T, Shinozaki K (1995) A gene encoding a phosphatidylinositol-specific phospholipase C is induced by dehydration and salt stress in Arabidopsis thaliana. Proc Natl Acad Sci 92(9):3903–3907PubMedPubMedCentralCrossRefGoogle Scholar
  132. Hivrale V, Zheng Y, Puli COR, Jagadeeswaran G, Gowdu K, Kakani VG, Barakat A, Sunkar R (2016) Characterization of drought-and heat-responsive microRNAs in switchgrass. Plant Sci 242:214–223PubMedCrossRefPubMedCentralGoogle Scholar
  133. Holmstrom K-o, Mantyla E, Wellin B, Mandal A (1996) Drought tolerance in tobacco. Nature 379(6567):683CrossRefGoogle Scholar
  134. Holmström KO, Somersalo S, Mandal A, Palva TE, Welin B (2000) Improved tolerance to salinity and low temperature in transgenic tobacco producing glycine betaine. J Exp Bot 51(343):177–185PubMedCrossRefGoogle Scholar
  135. Hrabak EM, Chan CW, Gribskov M, Harper JF, Choi JH, Halford N, Kudla J, Luan S, Nimmo HG, Sussman MR (2003) The Arabidopsis CDPK-SnRK superfamily of protein kinases. Plant Physiol 132(2):666–680PubMedPubMedCentralCrossRefGoogle Scholar
  136. Hua X-J, Van de Cotte B, Van Montagu M, Verbruggen N (1997) Developmental regulation of pyrroline-5-carboxylate reductase gene expression in Arabidopsis. Plant Physiol 114(4):1215–1224PubMedPubMedCentralCrossRefGoogle Scholar
  137. Huang DW, Sherman BT, Zheng X, Yang J, Imamichi T, Stephens R, Lempicki RA (2009) Extracting biological meaning from large gene lists with DAVID. Curr Protoc Bioinformatics 27:13.11:13.11.1–13.1113.11.13CrossRefGoogle Scholar
  138. Huang SQ, Xiang AL, Che LL, Chen S, Li H, Song JB, Yang ZM (2010) A set of miRNAs from Brassica napus in response to sulphate deficiency and cadmium stress. Plant Biotechnol J 8(8):887–899PubMedCrossRefPubMedCentralGoogle Scholar
  139. Hugouvieux V, Kwak JM, Schroeder JI (2001) An mRNA cap binding protein, ABH1, modulates early abscisic acid signal transduction in Arabidopsis. Cell 106(4):477–487PubMedCrossRefPubMedCentralGoogle Scholar
  140. Hunt L, Mills LN, Pical C, Leckie CP, Aitken FL, Kopka J, Mueller-Roeber B, McAinsh MR, Hetherington AM, Gray JE (2003) Phospholipase C is required for the control of stomatal aperture by ABA. Plant J 34(1):47–55PubMedCrossRefPubMedCentralGoogle Scholar
  141. Hwang J-U, Lee Y (2001) Abscisic acid-induced actin reorganization in guard cells of dayflower is mediated by cytosolic calcium levels and by protein kinase and protein phosphatase activities. Plant Physiol 125(4):2120–2128PubMedPubMedCentralCrossRefGoogle Scholar
  142. Iqbal M, Ashraf M (2010) Changes in hormonal balance: a possible mechanism of pre-sowing chilling-induced salt tolerance in spring wheat. J Agron Crop Sci 196(6):440–454CrossRefGoogle Scholar
  143. Jackson M (1997) Hormones from roots as signals for the shoots of stressed plants. Trends Plant Sci 2(1):22–28CrossRefGoogle Scholar
  144. Jagadeeswaran G, Saini A, Sunkar R (2009) Biotic and abiotic stress down-regulate miR398 expression in Arabidopsis. Planta 229(4):1009–1014PubMedCrossRefPubMedCentralGoogle Scholar
  145. Jammes F, Song C, Shin D, Munemasa S, Takeda K, Gu D, Cho D, Lee S, Giordo R, Sritubtim S (2009) MAP kinases MPK9 and MPK12 are preferentially expressed in guard cells and positively regulate ROS-mediated ABA signaling. Proc Natl Acad Sci 106(48):20520–20525PubMedPubMedCentralCrossRefGoogle Scholar
  146. Jeong JS, Kim YS, Baek KH, Jung H, Ha S-H, Do Choi Y, Kim M, Reuzeau C, Kim J-K (2010) Root-specific expression of OsNAC10 improves drought tolerance and grain yield in rice under field drought conditions. Plant Physiol 153(1):185–197PubMedPubMedCentralCrossRefGoogle Scholar
  147. Jeong JS, Kim YS, Redillas MC, Jang G, Jung H, Bang SW, Choi YD, Ha SH, Reuzeau C, Kim JK (2013) OsNAC5 overexpression enlarges root diameter in rice plants leading to enhanced drought tolerance and increased grain yield in the field. Plant Biotechnol J 11(1):101–114PubMedCrossRefPubMedCentralGoogle Scholar
  148. Jia W, Wang Y, Zhang S, Zhang J (2002) Salt-stress-induced ABA accumulation is more sensitively triggered in roots than in shoots. J Exp Bot 53(378):2201–2206PubMedCrossRefGoogle Scholar
  149. Jia X, Wang W-X, Ren L, Chen Q-J, 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(1–2):51–59PubMedCrossRefPubMedCentralGoogle Scholar
  150. Jiang Y, Deyholos MK (2009) Functional characterization of Arabidopsis NaCl-inducible WRKY25 and WRKY33 transcription factors in abiotic stresses. Plant Mol Biol 69(1–2):91–105PubMedCrossRefPubMedCentralGoogle Scholar
  151. Jiao Y, Wang Y, Xue D, Wang J, Yan M, Liu G, Dong G, Zeng D, Lu Z, Zhu X (2010) Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat Genet 42(6):541–544PubMedCrossRefPubMedCentralGoogle Scholar
  152. Johnson JM, Reichelt M, Vadassery J, Gershenzon J, Oelmüller R (2014) An Arabidopsis mutant impaired in intracellular calcium elevation is sensitive to biotic and abiotic stress. BMC Plant Biol 14(1):162CrossRefGoogle Scholar
  153. Jonak C, Páy A, Börge L, Hirt H, Heberle-Bors E (1993) The plant homologue of MAP kinase is expressed in a cell cycle-dependent and organ-specific manner. Plant J 3(4):611–617PubMedCrossRefPubMedCentralGoogle Scholar
  154. Jones-Rhoades MW, Bartel DP (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14(6):787–799PubMedCrossRefPubMedCentralGoogle Scholar
  155. Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 57:19–53PubMedCrossRefPubMedCentralGoogle Scholar
  156. Jung J-H, Seo PJ, Park C-M (2009) MicroRNA biogenesis and function in higher plants. Mol Biol Rep 3(2):111–126Google Scholar
  157. Kang DJ, Seo YJ, Lee JD, Ishii R, Kim K, Shin D, Park S, Jang S, Lee IJ (2005) Jasmonic acid differentially affects growth, ion uptake and abscisic acid concentration in salt-tolerant and salt-sensitive rice cultivars. J Agron Crop Sci 191(4):273–282CrossRefGoogle Scholar
  158. Kansal S, Devi RM, Balyan SC, Arora MK, Singh AK, Mathur S, Raghuvanshi S (2015) Unique miRNome during anthesis in drought-tolerant indica rice var. Nagina 22. Planta 241(6):1543–1559PubMedCrossRefPubMedCentralGoogle Scholar
  159. Kantar M, Lucas SJ, Budak H (2011) miRNA expression patterns of Triticum dicoccoides in response to shock drought stress. Planta 233(3):471–484PubMedCrossRefPubMedCentralGoogle Scholar
  160. Kaouthar F, Ameny F-K, Yosra K, Walid S, Ali G, Faical B (2016) Responses of transgenic Arabidopsis plants and recombinant yeast cells expressing a novel durum wheat manganese superoxide dismutase TdMnSOD to various abiotic stresses. J Plant Physiol 198:56–68PubMedCrossRefPubMedCentralGoogle Scholar
  161. Karakas B, Ozias-Akins P, Stushnoff C, Suefferheld M, Rieger M (1997) Salinity and drought tolerance of mannitol-accumulating transgenic tobacco. Plant Cell Environ 20(5):609–616CrossRefGoogle Scholar
  162. Karan R, Subudhi PK (2012) A stress inducible SUMO conjugating enzyme gene (SaSce9) from a grass halophyte Spartina alterniflora enhances salinity and drought stress tolerance in Arabidopsis. BMC Plant Biol 12(1):187PubMedPubMedCentralCrossRefGoogle Scholar
  163. Kasuga M, Liu Q, Miura S, Yamaguchi-Shinozaki K, Shinozaki K (1999) Improving plant drought, salt, and freezing tolerance by gene transfer of a single stress-inducible transcription factor. Nat Biotechnol 17(3)PubMedCrossRefPubMedCentralGoogle Scholar
  164. Keskin BC, Yuksel B, Memon AR, Topal-Sarıkaya A (2010) Abscisic acid regulated gene expression in bread wheat (Triticum aestivum L.). Aust J Crop Sci 4(8):617Google Scholar
  165. Khaksefidi RE, Mirlohi S, Khalaji F, Fakhari Z, Shiran B, Fallahi H, Rafiei F, Budak H, Ebrahimie E (2015) Differential expression of seven conserved microRNAs in response to abiotic stress and their regulatory network in Helianthus annuus. Front Plant Sci 6:741Google Scholar
  166. Khan M, Hamid A, Salahuddin A, Quasem A, Karim M (1997) Effect of sodium chloride on growth, photosynthesis and mineral ions accumulation of different types of rice (Oryza sativa L.). J Agron Crop Sci 179(3):149–161CrossRefGoogle Scholar
  167. Khan NA, Syeed S, Masood A, Nazar R, Iqbal N (2010) Application of salicylic acid increases contents of nutrients and antioxidative metabolism in mungbean and alleviates adverse effects of salinity stress. Int J Plant Biol 1(1):e1CrossRefGoogle Scholar
  168. Khan Y, Yadav A, Bonthala VS, Muthamilarasan M, Yadav CB, Prasad M (2014) Comprehensive genome-wide identification and expression profiling of foxtail millet (Setaria italica L.) miRNAs in response to abiotic stress and development of miRNA database. Plant Cell Tissue Organ Cult 118(2):279–292CrossRefGoogle Scholar
  169. Khatib F, Makris A, Yamaguchi-Shinozaki K, Kumar S, Sarker A, Erskine W, Baum M (2011) Expression of the DREB1A gene in lentil (Lens culinaris Medik. subsp. culinaris) transformed with the Agrobacterium system. Crop Pasture Sci 62(6):488–495CrossRefGoogle Scholar
  170. Khokon M, Okuma E, Hossain MA, Munemasa S, Uraji M, Nakamura Y, Mori IC, Murata Y (2011) Involvement of extracellular oxidative burst in salicylic acid-induced stomatal closure in Arabidopsis. Plant Cell Environ 34(3):434–443PubMedCrossRefPubMedCentralGoogle Scholar
  171. Khraiwesh B, Zhu J-K, Zhu J (2012) Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants. BBA-Gene Regul Mech 1819(2):137–148Google Scholar
  172. Kidner CA, Martienssen RA (2005) The developmental role of microRNA in plants. Curr Opin Plant Biol 8(1):38–44PubMedCrossRefPubMedCentralGoogle Scholar
  173. Kim BG, Waadt R, Cheong YH, Pandey GK, Dominguez-Solis JR, Schültke S, Lee SC, Kudla J, Luan S (2007) The calcium sensor CBL10 mediates salt tolerance by regulating ion homeostasis in Arabidopsis. Plant J 52(3):473–484PubMedCrossRefPubMedCentralGoogle Scholar
  174. Kim S, Yang J-Y, Xu J, Jang I-C, Prigge MJ, Chua N-H (2008) Two cap-binding proteins CBP20 and CBP80 are involved in processing primary MicroRNAs. Plant Cell Physiol 49(11):1634–1644PubMedPubMedCentralCrossRefGoogle Scholar
  175. Kishor PK, Hong Z, Miao G-H, Hu C-AA, Verma DPS (1995) Overexpression of [delta]-pyrroline-5-carboxylate synthetase increases proline production and confers osmotolerance in transgenic plants. Plant Physiol 108(4):1387–1394PubMedPubMedCentralCrossRefGoogle Scholar
  176. Knight H, Knight MR (2001) Abiotic stress signalling pathways: specificity and cross-talk. Trends Plant Sci 6(6):262–267PubMedCrossRefPubMedCentralGoogle Scholar
  177. Knight H, Trewavas AJ, Knight MR (1997) Calcium signalling in Arabidopsis thaliana responding to drought and salinity. Plant J 12(5):1067–1078PubMedCrossRefPubMedCentralGoogle Scholar
  178. Knight H, Veale EL, Warren GJ, Knight MR (1999) The sfr6 mutation in Arabidopsis suppresses low-temperature induction of genes dependent on the CRT/DRE sequence motif. Plant Cell 11(5):875–886PubMedPubMedCentralGoogle Scholar
  179. Kohl DH, Schubert KR, Carter MB, Hagedorn CH, Shearer G (1988) Proline metabolism in N2-fixing root nodules: energy transfer and regulation of purine synthesis. Proc Natl Acad Sci 85(7):2036–2040PubMedPubMedCentralCrossRefGoogle Scholar
  180. Kong X, Zhang M, Xu X, Li X, Li C, Ding Z (2014) System analysis of microRNAs in the development and aluminium stress responses of the maize root system. Plant Biotechnol J 12(8):1108–1121PubMedCrossRefPubMedCentralGoogle Scholar
  181. Kopka J, Pical C, Hetherington AM, Müller-Röber B (1998) Ca 2+/phospholipid-binding (C 2) domain in multiple plant proteins: novel components of the calcium-sensing apparatus. Plant Mol Biol 36(5):627–637PubMedCrossRefPubMedCentralGoogle Scholar
  182. Kruszka K, Pacak A, Swida-Barteczka A, Nuc P, Alaba S, Wroblewska Z, Karlowski W, Jarmolowski A, Szweykowska-Kulinska Z (2014) Transcriptionally and post-transcriptionally regulated microRNAs in heat stress response in barley. J Exp Bot 65(20):6123–6135PubMedPubMedCentralCrossRefGoogle Scholar
  183. Kudla J, Batistič O, Hashimoto K (2010) Calcium signals: the lead currency of plant information processing. Plant Cell 22(3):541–563PubMedPubMedCentralCrossRefGoogle Scholar
  184. Kumar R (2014) Role of microRNAs in biotic and abiotic stress responses in crop plants. Appl Biochem Biotechnol 174(1):93–115PubMedCrossRefPubMedCentralGoogle Scholar
  185. Kumar B, Singh B (1996) Effect of plant hormones on growth and yield of wheat irrigated with saline water. Ann Agric Res 17:209–212Google Scholar
  186. Kurihara Y, Watanabe Y (2004) Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc Natl Acad Sci U S A 101(34):12753–12758PubMedPubMedCentralCrossRefGoogle Scholar
  187. Kurihara Y, Takashi Y, Watanabe Y (2006) The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis. RNA 12(2):206–212PubMedPubMedCentralCrossRefGoogle Scholar
  188. Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T (2001) Identification of novel genes coding for small expressed RNAs. Science 294(5543):853–858PubMedCrossRefPubMedCentralGoogle Scholar
  189. Landouar-Arsivaud L, Juchaux-Cachau M, Jeauffre J, Biolley J-P, Maurousset L, Lemoine R (2011) The promoters of 3 celery salt-induced phloem-specific genes as new tools for monitoring salt stress responses. Plant Physiol Biochem 49(1):2–8PubMedCrossRefPubMedCentralGoogle Scholar
  190. Lanet E, Delannoy E, Sormani R, Floris M, Brodersen P, Crété P, Voinnet O, Robaglia C (2009) Biochemical evidence for translational repression by Arabidopsis microRNAs. Plant Cell 21(6):1762–1768PubMedPubMedCentralCrossRefGoogle Scholar
  191. Lau NC, Lim LP, Weinstein EG, Bartel DP (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294(5543):858–862PubMedCrossRefPubMedCentralGoogle Scholar
  192. Lauchli A, Schubert S (1989) The role of calcium in the regulation of membrane and cellular growth processes under salt stress. In: Environmental stress in plants. Springer, New York, pp 131–138CrossRefGoogle Scholar
  193. 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):843–854PubMedCrossRefPubMedCentralGoogle Scholar
  194. Lehmann J, Atzorn R, Brückner C, Reinbothe S, Leopold J, Wasternack C, Parthier B (1995) Accumulation of jasmonate, abscisic acid, specific transcripts and proteins in osmotically stressed barley leaf segments. Planta 197(1):156–162CrossRefGoogle Scholar
  195. Leung AK, Sharp PA (2010) MicroRNA functions in stress responses. Mol Cell 40(2):205–215PubMedPubMedCentralCrossRefGoogle Scholar
  196. Lewis D, Smith D (1967) Sugar alcohols (polyols) in fungi and green plants. New Phytol 66(2):143–184CrossRefGoogle Scholar
  197. Li J, Yang H, Peer WA, Richter G, Blakeslee J, Bandyopadhyay A, Titapiwantakun B, Undurraga S, Khodakovskaya M, Richards EL (2005) Arabidopsis H+-PPase AVP1 regulates auxin-mediated organ development. Science 310(5745):121–125PubMedCrossRefPubMedCentralGoogle Scholar
  198. Li W-X, Oono Y, Zhu J, He X-J, Wu J-M, Iida K, Lu X-Y, Cui X, Jin H, Zhu J-K (2008) The Arabidopsis NFYA5 transcription factor is regulated transcriptionally and post transcriptionally to promote drought resistance. Plant Cell 20(8):2238–2251PubMedPubMedCentralCrossRefGoogle Scholar
  199. Li H, Jiang H, Bu Q, Zhao Q, Sun J, Xie Q, Li C (2011) The Arabidopsis RING finger E3 ligase RHA2b acts additively with RHA2a in regulating ABA signaling and drought response. Plant Physiol 156:550. 111.176214PubMedPubMedCentralCrossRefGoogle Scholar
  200. Li Z-Y, Xu Z-S, He G-Y, Yang G-X, Chen M, Li L-C, Ma Y-Z (2012) Overexpression of soybean GmCBL1 enhances abiotic stress tolerance and promotes hypocotyl elongation in Arabidopsis. Biochem Biophys Res Commun 427(4):731–736PubMedCrossRefPubMedCentralGoogle Scholar
  201. Li M-Y, Wang F, Xu Z-S, Jiang Q, Ma J, Tan G-F, Xiong A-S (2014) High throughput sequencing of two celery varieties small RNAs identifies microRNAs involved in temperature stress response. BMC Genomics 15(1):242PubMedPubMedCentralCrossRefGoogle Scholar
  202. Li SB, Xie ZZ, Hu CG, Zhang JZ (2016) A review of auxin response factors (ARFs) in plants. Front Plant Sci 7:46Google Scholar
  203. Liang M, Haroldsen V, Cai X, Wu Y (2006) Expression of a putative laccase gene, ZmLAC1, in maize primary roots under stress. Plant Cell Environ 29(5):746–753PubMedCrossRefPubMedCentralGoogle Scholar
  204. Lima J, Arenhart R, Margis-Pinheiro M, Margis R (2011) Aluminum triggers broad changes in microRNA expression in rice roots. Genet Mol Res 10(4):2817–2832PubMedCrossRefPubMedCentralGoogle Scholar
  205. Lin H, Yang Y, Quan R, Mendoza I, Wu Y, Du W, Zhao S, Schumaker KS, Pardo JM, Guo Y (2009) Phosphorylation of SOS3-like calcium binding Protein8 by SOS2 protein kinase stabilizes their protein complex and regulates salt tolerance in Arabidopsis. Plant Cell 21(5):1607–1619PubMedPubMedCentralCrossRefGoogle Scholar
  206. Lin JS, Lin CC, Lin HH, Chen YC, Jeng ST (2012) MicroR828 regulates lignin and H2O2 accumulation in sweet potato on wounding. New Phytol 196(2):427–440PubMedCrossRefPubMedCentralGoogle Scholar
  207. Lippold F, Sanchez DH, Musialak M, Schlereth A, Scheible W-R, Hincha DK, Udvardi MK (2009) AtMyb41 regulates transcriptional and metabolic responses to osmotic stress in Arabidopsis. Plant Physiol 149(4):1761–1772PubMedPubMedCentralCrossRefGoogle Scholar
  208. Liu Q, Zhang H (2012) Molecular identification and analysis of arsenite stress-responsive miRNAs in rice. J Agric Food Chem 60(26):6524–6536PubMedCrossRefPubMedCentralGoogle Scholar
  209. Liu J, Zhu J-K (1998) A calcium sensor homolog required for plant salt tolerance. Science 280(5371):1943–1945PubMedPubMedCentralCrossRefGoogle Scholar
  210. Liu S, Calderwood DA, Ginsberg MH (2000) Integrin cytoplasmic domain-binding proteins. J Cell Sci 113(20):3563–3571PubMedPubMedCentralGoogle Scholar
  211. Liu J-H, Kitashiba H, Wang J, Ban Y, Moriguchi T (2007) Polyamines and their ability to provide environmental stress tolerance to plants. Plant Biotechnol 24(1):117–126CrossRefGoogle Scholar
  212. Liu H-H, Tian X, Li Y-J, Wu C-A, Zheng C-C (2008) Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana. RNA 14(5):836–843PubMedPubMedCentralCrossRefGoogle Scholar
  213. Liu D, Song Y, Chen Z, Yu D (2009) Ectopic expression of miR396 suppresses GRF target gene expression and alters leaf growth in Arabidopsis. Physiol Plant 136(2):223–236PubMedCrossRefPubMedCentralGoogle Scholar
  214. Liu Y-Q, Zhang M, Yin B-C, Ye B-C (2012) Attomolar ultrasensitive microRNA detection by DNA-scaffolded silver-nanocluster probe based on isothermal amplification. Anal Chem 84(12):5165–5169PubMedCrossRefPubMedCentralGoogle Scholar
  215. Liu N, Yang J, Guo S, Xu Y, Zhang M (2013) Genome-wide identification and comparative analysis of conserved and novel microRNAs in grafted watermelon by high-throughput sequencing. PLoS One 8(2):e57359PubMedPubMedCentralCrossRefGoogle Scholar
  216. Llave C, Xie Z, Kasschau KD, Carrington JC (2002) Cleavage of scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297(5589):2053–2056PubMedCrossRefPubMedCentralGoogle Scholar
  217. Lopez C, Takahashi H, Yamazaki S (2002) Plant–water relations of kidney bean plants treated with NaCl and foliarly applied glycinebetaine. J Agron Crop Sci 188(2):73–80CrossRefGoogle Scholar
  218. Louis P, Galinski EA (1997) Characterization of genes for the biosynthesis of the compatible solute ectoine from Marinococcus halophilus and osmoregulated expression in Escherichia coli. Microbiology 143(4):1141–1149PubMedCrossRefPubMedCentralGoogle Scholar
  219. Lu C, Fedoroff N (2000) A mutation in the Arabidopsis HYL1 gene encoding a dsRNA binding protein affects responses to abscisic acid, auxin, and cytokinin. Plant Cell 12(12):2351–2365PubMedPubMedCentralCrossRefGoogle Scholar
  220. Lu S, Sun Y-H, Shi R, Clark C, Li L, Chiang VL (2005) Novel and mechanical stress–responsive microRNAs in Populus trichocarpa that are absent from Arabidopsis. Plant Cell 17(8):2186–2203PubMedPubMedCentralCrossRefGoogle Scholar
  221. Lu S, Sun YH, Chiang VL (2008) Stress-responsive microRNAs in Populus. Plant J 55(1):131–151PubMedCrossRefPubMedCentralGoogle Scholar
  222. Lu Y, Feng Z, Bian L, Xie H, Liang J (2011) miR398 regulation in rice of the responses to abiotic and biotic stresses depends on CSD1 and CSD2 expression. Funct Plant Biol 38(1):44–53CrossRefGoogle Scholar
  223. Lv D-K, Bai X, Li Y, Ding X-D, Ge Y, Cai H, Ji W, Wu N, Zhu Y-M (2010) Profiling of cold-stress-responsive miRNAs in rice by microarrays. Gene 459(1):39–47PubMedCrossRefPubMedCentralGoogle Scholar
  224. Ma NN, Zuo YQ, Liang XQ, Yin B, Wang GD, Meng QW (2013) The multiple stress-responsive transcription factor SlNAC1 improves the chilling tolerance of tomato. Physiol Plant 149(4):474–486PubMedCrossRefPubMedCentralGoogle Scholar
  225. Ma X, Xin Z, Wang Z, Yang Q, Guo S, Guo X, Cao L, Lin T (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(1):21PubMedPubMedCentralCrossRefGoogle Scholar
  226. Maeda T, Wurgler-Murphy SM, Saito H (1994) A two-component system that regulates an osmosensing MAP kinase cascade in yeast. Nature 369(6477):242–245PubMedCrossRefPubMedCentralGoogle Scholar
  227. Magome H, Yamaguchi S, Hanada A, Kamiya Y, Oda K (2004) Dwarf and delayed-flowering 1, a novel Arabidopsis mutant deficient in gibberellin biosynthesis because of overexpression of a putative AP2 transcription factor. Plant J 37(5):720–729PubMedCrossRefPubMedCentralGoogle Scholar
  228. Mahajan S, Tuteja N (2005) Cold, salinity and drought stresses: an overview. Arch Biochem Biophys 444(2):139–158CrossRefPubMedGoogle Scholar
  229. Mahajan S, Sopory SK, Tuteja N (2006) CBL-CIPK paradigm: role in calcium and stress signaling in plants. Proc Indian Natl Sci Acad 72(2):63Google Scholar
  230. Mahale BM, Fakrudin B, Ghosh S, Krishnaraj P (2014) LNA mediated in situ hybridization of miR171 and miR397a in leaf and ambient root tissues revealed expressional homogeneity in response to shoot heat shock in Arabidopsis thaliana. J Plant Biochem Biotechnol 23(1):93–103CrossRefGoogle Scholar
  231. Manavella PA, Hagmann J, Ott F, Laubinger S, Franz M, Macek B, Weigel D (2012) Fast-forward genetics identifies plant CPL phosphatases as regulators of miRNA processing factor HYL1. Cell 151(4):859–870PubMedCrossRefPubMedCentralGoogle Scholar
  232. Margis R, Fusaro AF, Smith NA, Curtin SJ, Watson JM, Finnegan EJ, Waterhouse PM (2006) The evolution and diversification of Dicers in plants. FEBS Lett 580(10):2442–2450PubMedCrossRefPubMedCentralGoogle Scholar
  233. May P, Liao W, Wu Y, Shuai B, McCombie WR, Zhang MQ, Liu QA (2013) The effects of carbon dioxide and temperature on microRNA expression in Arabidopsis development. Nat Commun 4:2145PubMedCrossRefPubMedCentralGoogle Scholar
  234. McAinsh MR, Hetherington AM (1998) Encoding specificity in Ca2+ signalling systems. Trends Plant Sci 3(1):32–36CrossRefGoogle Scholar
  235. McConn M, Creelman RA, Bell E, Mullet JE (1997) Jasmonate is essential for insect defense in Arabidopsis. Proc Natl Acad Sci 94(10):5473–5477PubMedPubMedCentralCrossRefGoogle Scholar
  236. McCue KF, Hanson AD (1990) Drought and salt tolerance: towards understanding and application. Trends Biotechnol 8:358–362CrossRefGoogle Scholar
  237. Mehrpooyan F, Othman R, Harikrishna J (2012) Tissue and temporal expression of miR172 paralogs and the AP2-like target in oil palm (Elaeis guineensis Jacq.). Tree Genet Genomes 8(6):1331–1343CrossRefGoogle Scholar
  238. Meng Y, Shao C, Wang H, Chen M (2011) The regulatory activities of plant microRNAs: a more dynamic perspective. Plant Physiol 157(4):1583–1595PubMedPubMedCentralCrossRefGoogle Scholar
  239. Merchan F, Lorenzo LD, Rizzo SG, Niebel A, Manyani H, Frugier F, Sousa C, Crespi M (2007) Identification of regulatory pathways involved in the reacquisition of root growth after salt stress in Medicago truncatula. Plant J 51(1):1–17PubMedCrossRefGoogle Scholar
  240. Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, Bowman JL, Cao X, Carrington JC, Chen X, Green PJ (2008) Criteria for annotation of plant MicroRNAs. Plant Cell 20(12):3186–3190PubMedPubMedCentralCrossRefGoogle Scholar
  241. Mikami K, Katagiri T, Iuchi S, Yamaguchi-Shinozaki K, Shinozaki K (1998) A gene encoding phosphatidylinositol-4-phosphate 5-kinase is induced by water stress and abscisic acid in Arabidopsis thaliana. Plant J 15(4):563–568PubMedCrossRefGoogle Scholar
  242. Mittal D, Sharma N, Sharma V, Sopory S, Sanan-Mishra N (2016) Role of microRNAs in rice plant under salt stress. Ann Appl Biol 168(1):2–18CrossRefGoogle Scholar
  243. Mok DW, Mok MC (2001) Cytokinin metabolism and action. Annu Rev Plant Biol 52(1):89–118CrossRefGoogle Scholar
  244. Morgan PW, Drew MC (1997) Ethylene and plant responses to stress. Physiol Plant 100(3):620–630CrossRefGoogle Scholar
  245. Munnik T, Testerink C (2009) Plant phospholipid signaling: “in a nutshell”. J Lipid Res 50(Supplement):S260–S265PubMedPubMedCentralCrossRefGoogle Scholar
  246. Munns R, Tester M (2008) Mechanisms of salinity tolerance. Annu Rev Plant Biol 59:651–681PubMedPubMedCentralCrossRefGoogle Scholar
  247. 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 signaling. Science 312(5772):436–439PubMedCrossRefPubMedCentralGoogle Scholar
  248. Nayyar H, Walia D (2003) Water stress induced proline accumulation in contrasting wheat genotypes as affected by calcium and abscisic acid. Biol Plant 46(2):275–279CrossRefGoogle Scholar
  249. Nelson PT, Baldwin DA, Scearce LM, Oberholtzer JC, Tobias JW, Mourelatos Z (2004) Microarray-based, high-throughput gene expression profiling of microRNAs. Nat Methods 1(2)PubMedCrossRefPubMedCentralGoogle Scholar
  250. Ni Z, Hu Z, Jiang Q, Zhang H (2013) GmNFYA3, a target gene of miR169, is a positive regulator of plant tolerance to drought stress. Plant Mol Biol 82(1–2):113–129PubMedCrossRefGoogle Scholar
  251. Nilsen E, Orcutt D (1996) The physiology of plants under deficit, Abiotic Factors. Willey, New York, p 689Google Scholar
  252. Niu X, Bressan RA, Hasegawa PM, Pardo JM (1995) Ion homeostasis in NaCl stress environments. Plant Physiol 109(3):735PubMedPubMedCentralCrossRefGoogle Scholar
  253. Olszewski N, T-p S, Gubler F (2002) Gibberellin signaling biosynthesis, catabolism, and response pathways. Plant Cell 14(suppl 1):S61–S80PubMedPubMedCentralCrossRefGoogle Scholar
  254. Parashar A, Varma S (1988) Effect of presowing seed soaking in gibberellic acid, duration of soaking, different temperatures and their interaction on seed germination and early seedling growth of wheat under saline conditions. Plant Physiol Biochem 15:189Google Scholar
  255. Pareek A, Singla S, Grover A (1997) Salt responsive proteins/genes in crop plantsGoogle Scholar
  256. Parihar P, Singh S, Singh R, Singh VP, Prasad SM (2015) Effect of salinity stress on plants and its tolerance strategies: a review. Environ Sci Pollut Res Int 22(6):4056–4075PubMedCrossRefPubMedCentralGoogle Scholar
  257. Park W, Li J, Song R, Messing J, Chen X (2002) Carpel factory, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr Biol 12(17):1484–1495PubMedPubMedCentralCrossRefGoogle Scholar
  258. Park MY, Wu G, Gonzalez-Sulser A, Vaucheret H, Poethig RS (2005) Nuclear processing and export of microRNAs in Arabidopsis. Proc Natl Acad Sci U S A 102(10):3691–3696PubMedPubMedCentralCrossRefGoogle Scholar
  259. Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, Hayward DC, Ball EE, Degnan B, Müller P (2000) Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408(6808):86–89PubMedCrossRefPubMedCentralGoogle Scholar
  260. Peng Z, Lu Q, Verma D (1996) Reciprocal regulation of Δ 1-pyrroline-5-carboxylate synthetase and proline dehydrogenase genes controls proline levels during and after osmotic stress in plants. Mol Gen Genet 253(3):334–341PubMedPubMedCentralGoogle Scholar
  261. Pérez-Quintero ÁL, Zapata A, López C, Neme R (2010) Plant microRNAs and their role in defense against viruses: a bioinformatics approach. BMC Plant Biol 10(1):138PubMedPubMedCentralCrossRefGoogle Scholar
  262. Peters C, Li M, Narasimhan R, Roth M, Welti R, Wang X (2010) Nonspecific phospholipase C NPC4 promotes responses to abscisic acid and tolerance to hyperosmotic stress in Arabidopsis. Plant Cell 22(8):2642–2659PubMedPubMedCentralCrossRefGoogle Scholar
  263. Pfeffer S, Zavolan M, Grässer FA, Chien M, Russo JJ, Ju J, John B, Enright AJ, Marks D, Sander C (2004) Identification of virus-encoded microRNAs. Science 304(5671):734–736PubMedCrossRefPubMedCentralGoogle Scholar
  264. Pharr D, Stoop J, Williamson J, Feusi MS, Massel M, Conkling M (1995) The dual role of mannitol as osmoprotectant and photoassimilate in celery. Hort Sci 30:1182Google Scholar
  265. Phillips JR, Dalmay T, Bartels D (2007) The role of small RNAs in abiotic stress. FEBS Lett 581(19):3592–3597PubMedCrossRefGoogle Scholar
  266. Pillai RS, Artus CG, Filipowicz W (2004) Tethering of human ago proteins to mRNA mimics the miRNA-mediated repression of protein synthesis. RNA 10(10):1518–1525PubMedPubMedCentralCrossRefGoogle Scholar
  267. Pilon-Smits EA, Terry N, Sears T, Kim H, Zayed A, Hwang S, van Dun K, Voogd E, Verwoerd TC, Krutwagen RW (1998) Trehalose-producing transgenic tobacco plants show improved growth performance under drought stress. J Plant Physiol 152(4–5):525–532CrossRefGoogle Scholar
  268. Pokotylo I, Kolesnikov Y, Kravets V, Zachowski A, Ruelland E (2014) Plant phosphoinositide-dependent phospholipases C: variations around a canonical theme. Biochimie 96:144–157PubMedCrossRefPubMedCentralGoogle Scholar
  269. Pospíšilová J (2003) Interaction of cytokinins and abscisic acid during regulation of stomatal opening in bean leaves. Photosynthetica 41(1):49–56CrossRefGoogle Scholar
  270. Prakash L, Prathapasenan G (1990) NaCl-and gibberellic acid-induced changes in the content of auxin and the activities of cellulase and pectin lyase during leaf growth in rice (Oryza sativa). Ann Bot 65(3):251–257CrossRefGoogle Scholar
  271. Pruthvi V, Narasimhan R, Nataraja KN (2014) Simultaneous expression of abiotic stress responsive transcription factors, AtDREB2A, AtHB7 and AtABF3 improves salinity and drought tolerance in peanut (Arachis hypogaea L.). PLoS One 9(12):e111152PubMedPubMedCentralCrossRefGoogle Scholar
  272. Qiu Q-S, Guo Y, Dietrich MA, Schumaker KS, Zhu J-K (2002) Regulation of SOS1, a plasma membrane Na+/H+ exchanger in Arabidopsis thaliana, by SOS2 and SOS3. Proc Natl Acad Sci 99(12):8436–8441PubMedPubMedCentralCrossRefGoogle Scholar
  273. Qiu Q-S, Barkla BJ, Vera-Estrella R, Zhu J-K, Schumaker KS (2003) Na+/H+ exchange activity in the plasma membrane of Arabidopsis. Plant Physiol 132(2):1041–1052PubMedPubMedCentralCrossRefGoogle Scholar
  274. Qiu Z, Hai B, Guo J, Li Y, Zhang L (2016) Characterization of wheat miRNAs and their target genes responsive to cadmium stress. Plant Physiol Biochem 101:60–67PubMedCrossRefPubMedCentralGoogle Scholar
  275. Quan R, Lin H, Mendoza I, Zhang Y, Cao W, Yang Y, Shang M, Chen S, Pardo JM, Guo Y (2007) SCABP8/CBL10, a putative calcium sensor, interacts with the protein kinase SOS2 to protect Arabidopsis shoots from salt stress. Plant Cell 19(4):1415–1431PubMedPubMedCentralCrossRefGoogle Scholar
  276. Quintero FJ, Ohta M, Shi H, Zhu J-K, Pardo JM (2002) Reconstitution in yeast of the Arabidopsis SOS signaling pathway for Na+ homeostasis. Proc Natl Acad Sci 99(13):9061–9066PubMedPubMedCentralCrossRefGoogle Scholar
  277. Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP (2002) MicroRNAs in plants. Genes Dev 16(13):1616–1626PubMedPubMedCentralCrossRefGoogle Scholar
  278. Rejeb KB, Abdelly C, Savouré A (2014) How reactive oxygen species and proline face stress together. Plant Physiol Biochem 80:278–284PubMedCrossRefPubMedCentralGoogle Scholar
  279. Ren G, Yu B (2012) Critical roles of RNA-binding proteins in miRNA biogenesis in Arabidopsis. RNA Biol 9(12):1424–1428PubMedCrossRefPubMedCentralGoogle Scholar
  280. Ren X, Chen Z, Liu Y, Zhang H, Zhang M, Liu Q, Hong X, Zhu JK, Gong Z (2010) ABO3, a WRKY transcription factor, mediates plant responses to abscisic acid and drought tolerance in Arabidopsis. Plant J 63(3):417–429PubMedPubMedCentralCrossRefGoogle Scholar
  281. Ren G, Xie M, Dou Y, Zhang S, Zhang C, Yu B (2012) Regulation of miRNA abundance by RNA binding protein TOUGH in Arabidopsis. Proc Natl Acad Sci 109(31):12817–12821PubMedPubMedCentralCrossRefGoogle Scholar
  282. Reyes JL, Chua NH (2007) ABA induction of miR159 controls transcript levels of two MYB factors during Arabidopsis seed germination. Plant J 49(4):592–606PubMedCrossRefPubMedCentralGoogle Scholar
  283. Rhodes D, Hanson A (1993) Quaternary ammonium and tertiary sulfonium compounds in higher plants. Annu Rev Plant Biol 44(1):357–384CrossRefGoogle Scholar
  284. Ribaut J, Pilet P (1994) Water stress and indol-3yl-acetic acid content of maize roots. Planta 193(4):502–507CrossRefGoogle Scholar
  285. Roy S (2016) Function of MYB domain transcription factors in abiotic stress and epigenetic control of stress response in plant genome. Plant Signal Behav 11(1):e1117723PubMedCrossRefPubMedCentralGoogle Scholar
  286. Roy M, Wu R (2002) Overexpression of S-adenosylmethionine decarboxylase gene in rice increases polyamine level and enhances sodium chloride-stress tolerance. Plant Sci 163(5):987–992CrossRefGoogle Scholar
  287. Rubinelli PM, Chuck G, Li X, Meilan R (2013) Constitutive expression of the Corngrass1 microRNA in poplar affects plant architecture and stem lignin content and composition. Biomass Bioenergy 54:312–321CrossRefGoogle Scholar
  288. Ruiz-Ferrer V, Voinnet O (2009) Roles of plant small RNAs in biotic stress responses. Annu Rev Plant Biol 60:485–510PubMedCrossRefPubMedCentralGoogle Scholar
  289. Rutschmann F, Stalder U, Piotrowski M, Oecking C, Schaller A (2002) LeCPK1, a calcium-dependent protein kinase from tomato. Plasma membrane targeting and biochemical characterization. Plant Physiol 129(1):156–168PubMedPubMedCentralCrossRefGoogle Scholar
  290. Saijo Y, Hata S, Kyozuka J, Shimamoto K, Izui K (2000) Over-expression of a single Ca2+-dependent protein kinase confers both cold and salt/drought tolerance on rice plants. Plant J 23(3):319–327PubMedCrossRefPubMedCentralGoogle Scholar
  291. Sailaja B, Anjum N, Prasanth VV, Sarla N, Subrahmanyam D, Voleti S, Viraktamath B, Mangrauthia SK (2014) Comparative study of susceptible and tolerant genotype reveals efficient recovery and root system contributes to heat stress tolerance in rice. Plant Mol Biol Report 32(6):1228–1240CrossRefGoogle Scholar
  292. Sakhabutdinova A, Fatkhutdinova D, Bezrukova M, Shakirova F (2003) Salicylic acid prevents the damaging action of stress factors on wheat plants. Bulg J Plant Physiol 21:314–319Google Scholar
  293. 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 Gen Genomics 282(5):463CrossRefGoogle Scholar
  294. Sanders D, Brownlee C, Harper JF (1999) Communicating with calcium. Plant Cell 11(4):691–706PubMedPubMedCentralCrossRefGoogle Scholar
  295. Sanders D, Pelloux J, Brownlee C, Harper JF (2002) Calcium at the crossroads of signaling. Plant Cell 14(suppl 1):S401–S417PubMedPubMedCentralCrossRefGoogle Scholar
  296. Saradhi PP, Mohanty P (1993) Proline in relation to free radical production in seedlings of Brassica juncea raised under sodium chloride stress. Plant Soil 155(1):497–500Google Scholar
  297. Sarkar T, Thankappan R, Kumar A, Mishra GP, Dobaria JR (2014) Heterologous expression of the AtDREB1A gene in transgenic peanut-conferred tolerance to drought and salinity stresses. PLoS One 9(12):e110507PubMedPubMedCentralCrossRefGoogle Scholar
  298. Schmidt R, Schippers JH, Mieulet D, Obata T, Fernie AR, Guiderdoni E, Mueller-Roeber B (2013) Multipass, a rice R2R3-type MYB transcription factor, regulates adaptive growth by integrating multiple hormonal pathways. Plant J 76(2):258–273PubMedPubMedCentralGoogle Scholar
  299. Schommer C, Palatnik JF, Aggarwal P, Chételat A, Cubas P, Farmer EE, Nath U, Weigel D (2008) Control of jasmonate biosynthesis and senescence by miR319 targets. PLoS Biol 6(9):230CrossRefGoogle Scholar
  300. Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, Weigel D (2005) Specific effects of microRNAs on the plant transcriptome. Dev Cell 8(4):517–527PubMedCrossRefPubMedCentralGoogle Scholar
  301. Seki M, Narusaka M, Ishida J, Nanjo T, Fujita M, Oono Y, Kamiya A, Nakajima M, Enju A, Sakurai T (2002) Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J 31(3):279–292CrossRefPubMedGoogle Scholar
  302. Serrano R, Mulet JM, Rios G, Marquez JA, De Larrinoa IF, Leube MP, Mendizabal I, Pascual-Ahuir A, Proft M, Ros R (1999) A glimpse of the mechanisms of ion homeostasis during salt stress. J Exp Bot 50:1023–1036CrossRefGoogle Scholar
  303. Sharma D, Tiwari M, Lakhwani D, Tripathi RD, Trivedi PK (2015a) Differential expression of microRNAs by arsenate and arsenite stress in natural accessions of rice. Metallomics 7(1):174–187PubMedCrossRefPubMedCentralGoogle Scholar
  304. Sharma N, Tripathi A, Sanan-Mishra N (2015b) Profiling the expression domains of a rice-specific microRNA under stress. Front Plant Sci 6:333PubMedPubMedCentralCrossRefGoogle Scholar
  305. Sharma N, Mittal D, Mishra NS (2017) Micro-regulators of hormones and Stress. In: Mechanism of plant hormone signaling under stress. Wiley, New York, pp 319–351CrossRefGoogle Scholar
  306. Shen J, Xie K, Xiong L (2010) Global expression profiling of rice microRNAs by one-tube stem-loop reverse transcription quantitative PCR revealed important roles of microRNAs in abiotic stress responses. Mol Gen Genomics 284(6):477–488CrossRefGoogle Scholar
  307. Shi H, Zhu J-K (2002) Regulation of expression of the vacuolar Na+/H+ antiporter gene AtNHX1 by salt stress and abscisic acid. Plant Mol Biol 50(3):543–550PubMedCrossRefPubMedCentralGoogle Scholar
  308. Shi H, Ishitani M, Kim C, Zhu J-K (2000) The Arabidopsis thaliana salt tolerance gene SOS1 encodes a putative Na+/H+ antiporter. Proc Natl Acad Sci 97(12):6896–6901PubMedPubMedCentralCrossRefGoogle Scholar
  309. Sickler CM, Edwards GE, Kiirats O, Gao Z, Loescher W (2007) Response of mannitol-producing Arabidopsis thaliana to abiotic stress. Funct Plant Biol 34(4):382–391CrossRefGoogle Scholar
  310. Siomi H, Siomi MC (2010) Posttranscriptional regulation of microRNA biogenesis in animals. Mol Cell 38(3):323–332PubMedCrossRefPubMedCentralGoogle Scholar
  311. Sivakumar P, Sharmila P, Saradhi PP (1998) Proline suppresses Rubisco activity in higher plants. Biochem Biophys Res Commun 252(2):428–432PubMedCrossRefPubMedCentralGoogle Scholar
  312. Smirnoff N (1993) The role of active oxygen in the response of plants to water deficit and desiccation. New Phytol 125(1):27–58CrossRefGoogle Scholar
  313. Smirnoff N (1998) Plant resistance to environmental stress. Curr Opin Biotechnol 9(2):214–219PubMedCrossRefPubMedCentralGoogle Scholar
  314. Smith JL, De Moraes CM, Mescher MC (2009) Jasmonate-and salicylate-mediated plant defense responses to insect herbivores, pathogens and parasitic plants. Pest Manag Sci 65(5):497–503PubMedCrossRefPubMedCentralGoogle Scholar
  315. Song J-J, Smith SK, Hannon GJ, Joshua-Tor L (2004) Crystal structure of Argonaute and its implications for RISC slicer activity. Science 305(5689):1434–1437PubMedCrossRefPubMedCentralGoogle Scholar
  316. Song L, Han M-H, Lesicka J, Fedoroff N (2007) Arabidopsis primary microRNA processing proteins HYL1 and DCL1 define a nuclear body distinct from the Cajal body. Proc Natl Acad Sci 104(13):5437–5442PubMedPubMedCentralCrossRefGoogle Scholar
  317. Song G, Zhang R, Zhang S, Li Y, Gao J, Han X, Chen M, Wang J, Li W, Li G (2017a) Response of microRNAs to cold treatment in the young spikes of common wheat. BMC Genomics 18(1):212PubMedPubMedCentralCrossRefGoogle Scholar
  318. Song Z, Xu Q, Lin C, Tao C, Zhu C, Xing S, Fan Y, Liu W, Yan J, Li J, Sang T (2017b) Transcriptomic characterization of candidate genes responsive to salt tolerance of Miscanthus energy crops. GCB Bioenergy 9(7):1222–1237CrossRefGoogle Scholar
  319. Srivastava S, Srivastava AK, Suprasanna P, D’souza S (2012) Identification and profiling of arsenic stress-induced microRNAs in Brassica juncea. J Exp Bot 64(1):303–315PubMedCrossRefPubMedCentralGoogle Scholar
  320. Stephenson TJ, McIntyre CL, Collet C, Xue G-P (2007) Genome-wide identification and expression analysis of the NF-Y family of transcription factors in Triticum aestivum. Plant Mol Biol 65(1–2):77–92PubMedCrossRefPubMedCentralGoogle Scholar
  321. Stief A, Altmann S, Hoffmann K, Pant BD, Scheible W-R, Bäurle I (2014) Arabidopsis miR156 regulates tolerance to recurring environmental stress through SPL transcription factors. Plant Cell 26(4):1792–1807PubMedPubMedCentralCrossRefGoogle Scholar
  322. Stoop JM, Pharr DM (1994) Mannitol metabolism in celery stressed by excess macronutrients. Plant Physiol 106(2):503–511PubMedPubMedCentralCrossRefGoogle Scholar
  323. Sun G, Stewart CN Jr, Xiao P, Zhang B (2012) MicroRNA expression analysis in the cellulosic biofuel crop switchgrass (Panicum virgatum) under abiotic stress. PLoS One 7(3):e32017PubMedPubMedCentralCrossRefGoogle Scholar
  324. Sun X, Xu L, Wang Y, Yu R, Zhu X, Luo X, Gong Y, Wang R, Limera C, Zhang K (2015) Identification of novel and salt-responsive miRNAs to explore miRNA-mediated regulatory network of salt stress response in radish (Raphanus sativus L.). BMC Genomics 16(1):197PubMedPubMedCentralCrossRefGoogle Scholar
  325. Sunkar R, Zhu J-K (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16(8):2001–2019PubMedPubMedCentralCrossRefGoogle Scholar
  326. Sunkar R, Kapoor A, Zhu J-K (2006) Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance. Plant Cell 18(8):2051–2065PubMedPubMedCentralCrossRefGoogle Scholar
  327. Tähtiharju S, Sangwan V, Monroy AF, Dhindsa RS, Borg M (1997) The induction of kin genes in cold-acclimating Arabidopsis thaliana. Evidence of a role for calcium. Planta 203(4):442–447PubMedCrossRefPubMedCentralGoogle Scholar
  328. Tamura T, Hara K, Yamaguchi Y, Koizumi N, Sano H (2003) Osmotic stress tolerance of transgenic tobacco expressing a gene encoding a membrane-located receptor-like protein from tobacco plants. Plant Physiol 131(2):454–462PubMedPubMedCentralCrossRefGoogle Scholar
  329. Tang Z, Zhang L, Xu C, Yuan S, Zhang F, Zheng Y, Zhao C (2012) Uncovering small RNA-mediated responses to cold stress in a wheat thermosensitive genic male-sterile line by deep sequencing. Plant Physiol 159(2):721–738PubMedPubMedCentralCrossRefGoogle Scholar
  330. Tarczynski MC, Jensen RG, Bohnert HJ (1993) Stress protection of transgenic tobacco by production of the osmolyte mannitol. Sci N Y Then Wash 259:508–508CrossRefGoogle Scholar
  331. Thiebaut F, Grativol C, Carnavale-Bottino M, Rojas CA, Tanurdzic M, Farinelli L, Martienssen RA, Hemerly AS, Ferreira PCG (2012) Computational identification and analysis of novel sugarcane microRNAs. BMC Genomics 13(1):290PubMedPubMedCentralCrossRefGoogle Scholar
  332. Tran L-SP, Urao T, Qin F, Maruyama K, Kakimoto T, Shinozaki K, Yamaguchi-Shinozaki K (2007) Functional analysis of AHK1/ATHK1 and cytokinin receptor histidine kinases in response to abscisic acid, drought, and salt stress in Arabidopsis. Proc Natl Acad Sci 104(51):20623–20628PubMedPubMedCentralCrossRefGoogle Scholar
  333. Trindade I, Capitão C, Dalmay T, Fevereiro MP, Dos Santos DM (2010) miR398 and miR408 are up-regulated in response to water deficit in Medicago truncatula. Planta 231(3):705–716PubMedCrossRefPubMedCentralGoogle Scholar
  334. Tripathi DK, Singh VP, Gangwar S, Prasad SM, Maurya JN, Chauhan DK (2014) Role of silicon in enrichment of plant nutrients and protection from biotic and abiotic stresses. In: Improvement of crops in the era of climatic changes. Springer, p 39–56Google Scholar
  335. Tripathi, A., Chacon, O., Singla-Pareek, S.L., Sopory, S.K., Sanan-Mishra N. (2017) Mapping the microRNA expression profiles in glyoxalase over-expressing salinity tolerant rice. Curr Genomics 18(999):1Google Scholar
  336. Tuli R, Chakrabarty D, Trivedi PK, Tripathi RD (2010) Recent advances in arsenic accumulation and metabolism in rice. Mol Breed 26(2):307–323CrossRefGoogle Scholar
  337. Tuteja N, Sopory SK (2008) Chemical signaling under abiotic stress environment in plants. Plant Signal Behav 3(8):525–536PubMedPubMedCentralCrossRefGoogle Scholar
  338. Tyczewska A, Gracz J, Kuczyński J, Twardowski T (2017) Deciphering soybean molecular stress response via high-throughput approach. Acta Biochim Pol 63 (4):631–643Google Scholar
  339. Urano K, Yoshiba Y, Nanjo T, Igarashi Y, Seki M, Sekiguchi F, Yamaguchi-Shinozaki K, Shinozaki K (2003) Characterization of Arabidopsis genes involved in biosynthesis of polyamines in abiotic stress responses and developmental stages. Plant Cell Environ 26(11):1917–1926CrossRefGoogle Scholar
  340. Urao T, Katagiri T, Mizoguchi T, Yamaguchi-Shinozaki K, Hayashida N, Shinozaki K (1994) Two genes that encode Ca 2+−dependent protein kinases are induced by drought and high-salt stresses in Arabidopsis thaliana. Mol Gen Genet 244(4):331–340PubMedCrossRefPubMedCentralGoogle Scholar
  341. Valdés-López O, Yang SS, Aparicio-Fabre R, Graham PH, Reyes JL, Vance CP, Hernández G (2010) MicroRNA expression profile in common bean (Phaseolus vulgaris) under nutrient deficiency stresses and manganese toxicity. New Phytol 187(3):805–818PubMedCrossRefPubMedCentralGoogle Scholar
  342. Vaucheret H (2006) Post-transcriptional small RNA pathways in plants: mechanisms and regulations. Genes Dev 20(7):759–771PubMedCrossRefPubMedCentralGoogle Scholar
  343. Vaucheret H, Vazquez F, Crété P, Bartel DP (2004) The action of Argonaute1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev 18(10):1187–1197PubMedPubMedCentralCrossRefGoogle Scholar
  344. Vazquez F, Vaucheret H, Rajagopalan R, Lepers C, Gasciolli V, Mallory AC, Hilbert J-L, Bartel DP, Crété P (2004) Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol Cell 16(1):69–79PubMedCrossRefPubMedCentralGoogle Scholar
  345. Voinnet O (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 136(4):669–687PubMedCrossRefPubMedCentralGoogle Scholar
  346. Waditee R, Bhuiyan MNH, Rai V, Aoki K, Tanaka Y, Hibino T, Suzuki S, Takano J, Jagendorf AT, Takabe T (2005) Genes for direct methylation of glycine provide high levels of glycinebetaine and abiotic-stress tolerance in Synechococcus and Arabidopsis. Proc Natl Acad Sci U S A 102(5):1318–1323PubMedPubMedCentralCrossRefGoogle Scholar
  347. Waie B, Rajam MV (2003) Effect of increased polyamine biosynthesis on stress responses in transgenic tobacco by introduction of human S-adenosylmethionine gene. Plant Sci 164(5):727–734CrossRefGoogle Scholar
  348. Walker M, Dumbroff E (1981) Effects of salt stress on abscisic acid and cytokinin levels in tomato. Z Pflanzenphysiol 101(5):461–470CrossRefGoogle Scholar
  349. Wang Y, Mopper S, Hasenstein KH (2001) Effects of salinity on endogenous ABA, IAA, JA, and SA in Iris hexagona. J Chem Ecol 27(2):327–342PubMedCrossRefPubMedCentralGoogle Scholar
  350. Wang W, Vinocur B, Altman A (2003) Plant responses to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance. Planta 218(1):1–14PubMedPubMedCentralCrossRefGoogle Scholar
  351. Wang T, Chen L, Zhao M, Tian Q, Zhang W-H (2011) Identification of drought-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing. BMC Genomics 12(1):367PubMedPubMedCentralCrossRefGoogle Scholar
  352. Wang Y, Sun F, Cao H, Peng H, Ni Z, Sun Q, Yao Y (2012) TamiR159 directed wheat TaGAMYB cleavage and its involvement in anther development and heat response. PLoS One 7(11):e48445. genomics 9 (4):499PubMedPubMedCentralCrossRefGoogle Scholar
  353. Wang B, Sun YF, Song N, Wei JP, Wang XJ, Feng H, Yin ZY, Kang ZS (2014) MicroRNAs involving in cold, wounding and salt stresses in Triticum aestivum L. Plant Physiol Biochem 80:90–96PubMedCrossRefPubMedCentralGoogle Scholar
  354. Wang Q, Liu N, Yang X, Tu L, Zhang X (2016) Small RNA-mediated responses to low-and high-temperature stresses in cotton. Sci Rep 6:35558PubMedPubMedCentralCrossRefGoogle Scholar
  355. Wei J-Z, Tirajoh A, Effendy J, Plant AL (2000) Characterization of salt-induced changes in gene expression in tomato (Lycopersicon esculentum) roots and the role played by abscisic acid. Plant Sci 159(1):135–148PubMedCrossRefGoogle Scholar
  356. Wei L, Zhang D, Xiang F, Zhang Z (2009) Differentially expressed miRNAs potentially involved in the regulation of defense mechanism to drought stress in maize seedlings. Int J Plant Sci 170(8):979–989CrossRefGoogle Scholar
  357. Wen X-P, Pang X-M, Matsuda N, Kita M, Inoue H, Hao Y-J, Honda C, Moriguchi T (2008) Over-expression of the apple spermidine synthase gene in pear confers multiple abiotic stress tolerance by altering polyamine titers. Transgenic Res 17(2):251–263PubMedCrossRefPubMedCentralGoogle Scholar
  358. Wernimont AK, Amani M, Qiu W, Pizarro JC, Artz JD, Lin YH, Lew J, Hutchinson A, Hui R (2011) Structures of parasitic CDPK domains point to a common mechanism of activation. Proteins 79(3):803–820PubMedCrossRefPubMedCentralGoogle Scholar
  359. White PJ, Broadley MR (2003) Calcium in plants. Ann Bot 92(4):487–511PubMedPubMedCentralCrossRefGoogle Scholar
  360. Willmann MR, Poethig RS (2007) Conservation and evolution of miRNA regulatory programs in plant development. Curr Opin Plant Biol 10(5):503–511PubMedPubMedCentralCrossRefGoogle Scholar
  361. Wu G, Poethig RS (2006) Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3. Development 133(18):3539–3547PubMedPubMedCentralCrossRefGoogle Scholar
  362. Wu G, Park MY, Conway SR, Wang J-W, Weigel D, Poethig RS (2009) The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell 138(4):750–759PubMedPubMedCentralCrossRefGoogle Scholar
  363. Wu Y, Vulić M, Keren I, Lewis K (2012) Role of oxidative stress in persister tolerance. Antimicrob Agents Chemother 56(9):4922–4926PubMedPubMedCentralCrossRefGoogle Scholar
  364. Xia Q, Shi T, Liu S, Wang MY (2012) A level set solution to the stress-based structural shape and topology optimization. Comput Struct 90:55–64CrossRefGoogle Scholar
  365. Xie FL, Huang SQ, Guo K, Xiang AL, Zhu YY, Nie L, Yang ZM (2007) Computational identification of novel microRNAs and targets in Brassica napus. FEBS Lett 581(7):1464–1474PubMedCrossRefGoogle Scholar
  366. 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(3):1382–1394PubMedPubMedCentralCrossRefGoogle Scholar
  367. Xie F, Jones DC, Wang Q, Sun R, Zhang B (2015) Small RNA sequencing identifies miRNA roles in ovule and fibre development. Plant Biotechnol J 13(3):355–369PubMedCrossRefGoogle Scholar
  368. 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(1):123PubMedPubMedCentralCrossRefGoogle Scholar
  369. Xing D-H, Lai Z-B, Zheng Z-Y, Vinod K, Fan B-F, Chen Z-X (2008) Stress-and pathogen-induced Arabidopsis WRKY48 is a transcriptional activator that represses plant basal defense. Mol Plant 1(3):459–470PubMedCrossRefGoogle Scholar
  370. Xiong L, Wang R-G, Mao G, Koczan JM (2006) Identification of drought tolerance determinants by genetic analysis of root response to drought stress and abscisic acid. Plant Physiol 142(3):1065–1074PubMedPubMedCentralCrossRefGoogle Scholar
  371. Xu J, Li Y, Wang Y, Liu H, Lei L, Yang H, Liu G, Ren D (2008) Activation of MAPK kinase 9 induces ethylene and camalexin biosynthesis and enhances sensitivity to salt stress in Arabidopsis. J Biol Chem 283(40):26996–27006PubMedCrossRefGoogle Scholar
  372. Yamaguchi S, Kamiya Y (2000) Gibberellin biosynthesis: its regulation by endogenous and environmental signals. Plant Cell Physiol 41:251PubMedCrossRefGoogle Scholar
  373. Yamaguchi-Shinozaki K, Shinozaki K (2005) Organization of cis-acting regulatory elements in osmotic-and cold-stress-responsive promoters. Trends Plant Sci 10(2):88–94PubMedCrossRefPubMedCentralGoogle Scholar
  374. Yamaguchi-Shinozaki K, Shinozaki K (2006) Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Annu Rev Plant Biol 57:781–803PubMedCrossRefPubMedCentralGoogle Scholar
  375. Yan S, Tang Z, Su W, Sun W (2005) Proteomic analysis of salt stress-responsive proteins in rice root. Proteomics 5(1):235–244PubMedPubMedCentralCrossRefGoogle Scholar
  376. Yan Y, Wang H, Hamera S, Chen X, Fang R (2014) miR444a has multiple functions in the rice nitrate-signaling pathway. Plant J 78(1):44–55PubMedCrossRefGoogle Scholar
  377. Yancey PH, Clark ME, Hand SC, Bowlus RD, Somero GN (1982) Living with water stress: evolution of osmolyte systems. Science 217(4566):1214–1222PubMedCrossRefPubMedCentralGoogle Scholar
  378. Yang F, Yu D (2009) Overexpression of Arabidopsis MiR396 enhances drought tolerance in transgenic tobacco plants. Acta Bot Yunnanica 31(5):421–426CrossRefGoogle Scholar
  379. Yang C-W, González-Lamothe R, Ewan RA, Rowland O, Yoshioka H, Shenton M, Ye H, O’Donnell E, Jones JD, Sadanandom A (2006) The E3 ubiquitin ligase activity of Arabidopsis PLANT U-BOX 17 and its functional tobacco homolog ACRE276 are required for cell death and defense. Plant Cell 18(4):1084–1098PubMedPubMedCentralCrossRefGoogle Scholar
  380. Yang J, Kloepper JW, Ryu C-M (2009) Rhizosphere bacteria help plants tolerate abiotic stress. Trends Plant Sci 14(1):1–4PubMedCrossRefPubMedCentralGoogle Scholar
  381. Yang H, Jin X, Lam CWK, Yan S-K (2011) Oxidative stress and diabetes mellitus. Clin Chem Lab Med 49(11):1773–1782PubMedCrossRefPubMedCentralGoogle Scholar
  382. Yang Y, He M, Zhu Z, Li S, Xu Y, Zhang C, Singer SD, Wang Y (2012) Identification of the dehydrin gene family from grapevine species and analysis of their responsiveness to various forms of abiotic and biotic stress. BMC Plant Biol 12(1):140PubMedPubMedCentralCrossRefGoogle Scholar
  383. Yang C, Li D, Mao D, Liu X, Ji C, Li X, Zhao X, Cheng Z, Chen C, Zhu L (2013) Overexpression of microRNA319 impacts leaf morphogenesis and leads to enhanced cold tolerance in rice (Oryza sativa L.). Plant Cell Environ 36(12):2207–2218PubMedCrossRefPubMedCentralGoogle Scholar
  384. Yang C, Ma B, He S-J, Xiong Q, Duan K-X, Yin C-C, Chen H, Lu X, Chen S-Y, Zhang J-S (2015) MHZ6/OsEIL1 and OsEIL2 regulate ethylene response of roots and coleoptiles and negatively affect salt tolerance in rice. Plant Physiol 169:148. pp. 00353.02015PubMedPubMedCentralCrossRefGoogle Scholar
  385. Yeo A (1998) Molecular biology of salt tolerance in the context of whole-plant physiology. J Exp Bot 49(323):915–929Google Scholar
  386. Yin Z, Li Y, Yu J, Liu Y, Li C, Han X, Shen F (2012) Difference in miRNA expression profiles between two cotton cultivars with distinct salt sensitivity. Mol Biol Rep 39(4):4961–4970PubMedCrossRefGoogle Scholar
  387. Yoshida S, Maruyama S, Nozaki H, Shirasu K (2010) Horizontal gene transfer by the parasitic plant Striga hermonthica. Science 328(5982):1128–1128PubMedCrossRefPubMedCentralGoogle Scholar
  388. Yu B, Yang Z, Li J, Minakhina S, Yang M, Padgett RW, Steward R, Chen X (2005) Methylation as a crucial step in plant microRNA biogenesis. Science 307(5711):932–935PubMedPubMedCentralCrossRefGoogle Scholar
  389. Yu S, Wang W, Wang B (2012) Recent progress of salinity tolerance research in plants. Russ J Genet 48(5):497–505CrossRefGoogle Scholar
  390. Yu F, Wu Y, Xie Q (2016) Ubiquitin–proteasome system in ABA signaling: from perception to action. Mol Plant 9(1):21–33PubMedCrossRefPubMedCentralGoogle Scholar
  391. Zeng Q-Y, Yang C-Y, Ma Q-B, Li X-P, Dong W-W, Nian H (2012) Identification of wild soybean miRNAs and their target genes responsive to aluminum stress. BMC Plant Biol 12(1):182PubMedPubMedCentralCrossRefGoogle Scholar
  392. Zhang C-s, Lu Q, Verma DPS (1997) Characterization of Δ 1-pyrroline-5-carboxylate synthetase gene promoter in transgenic Arabidopsis thaliana subjected to water stress. Plant Sci 129(1):81–89. (1):98-109CrossRefGoogle Scholar
  393. Zhang J, Jia W, Yang J, Ismail AM (2006) Role of ABA in integrating plant responses to drought and salt stresses. Field Crop Res 97(1):111–119CrossRefGoogle Scholar
  394. Zhang A, Jiang M, Zhang J, Ding H, Xu S, Hu X, Tan M (2007) Nitric oxide induced by hydrogen peroxide mediates abscisic acid-induced activation of the mitogen-activated protein kinase cascade involved in antioxidant defense in maize leaves. New Phytol 175(1):36–50PubMedCrossRefPubMedCentralGoogle Scholar
  395. 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(1):449PubMedPubMedCentralCrossRefGoogle Scholar
  396. Zhang X, Wang L, Meng H, Wen H, Fan Y, Zhao J (2011) Maize ABP9 enhances tolerance to multiple stresses in transgenic Arabidopsis by modulating ABA signaling and cellular levels of reactive oxygen species. Plant Mol Biol 75(4–5):365–378PubMedPubMedCentralCrossRefGoogle Scholar
  397. Zhang Y-C, Yu Y, Wang C-Y, Li Z-Y, Liu Q, Xu J, Liao J-Y, Wang X-J, Qu L-H, Chen F (2013) Overexpression of microRNA OsmiR397 improves rice yield by increasing grain size and promoting panicle branching. Nat Biotechnol 31(9):848–852PubMedCrossRefPubMedCentralGoogle Scholar
  398. 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(2):585–590PubMedCrossRefPubMedCentralGoogle Scholar
  399. 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(1):29PubMedPubMedCentralCrossRefGoogle Scholar
  400. Zhao M, Ding H, Zhu JK, Zhang F, Li WX (2011) Involvement of miR169 in the nitrogen-starvation responses in Arabidopsis. New Phytol 190(4):906–915PubMedPubMedCentralCrossRefGoogle Scholar
  401. Zheng X-y, Spivey NW, Zeng W, Liu P-P, Fu ZQ, Klessig DF, He SY, Dong X (2012) Coronatine promotes Pseudomonas syringae virulence in plants by activating a signaling cascade that inhibits salicylic acid accumulation. Cell Host Microbe 11(6):587–596PubMedPubMedCentralCrossRefGoogle Scholar
  402. Zheng L, Liu G, Meng X, Liu Y, Ji X, Li Y, Nie X, Wang Y (2013) A WRKY gene from Tamarix hispida, ThWRKY4, mediates abiotic stress responses by modulating reactive oxygen species and expression of stress-responsive genes. Plant Mol Biol 82(4–5):303–320PubMedCrossRefPubMedCentralGoogle Scholar
  403. Zhifang G, Loescher W (2003) Expression of a celery mannose 6-phosphate reductase in Arabidopsis thaliana enhances salt tolerance and induces biosynthesis of both mannitol and a glucosyl-mannitol dimer. Plant Cell Environ 26(2):275–283CrossRefGoogle Scholar
  404. Zholkevich V, Pustovoytova T (1993) The role of Cucumis sativum L leaves and content of phytohormones under soil drought. Russ J Plant Physiol 40:676–680Google Scholar
  405. Zhou X, Wang G, Sutoh K, Zhu J-K, Zhang W (2008a) Identification of cold-inducible microRNAs in plants by transcriptome analysis. BBA-Gene Regul Mech 1779(11):780–788Google Scholar
  406. Zhou ZS, Huang SQ, Yang ZM (2008b) Bioinformatic identification and expression analysis of new microRNAs from Medicago truncatula. Biochem Biophys Res Commun 374(3):538–542PubMedCrossRefPubMedCentralGoogle Scholar
  407. Zhou J, Wang X, He K, Charron J-BF, Elling AA, Deng XW (2010) Genome-wide profiling of histone H3 lysine 9 acetylation and dimethylation in Arabidopsis reveals correlation between multiple histone marks and gene expression. Plant Mol Biol 72(6):585–595PubMedCrossRefPubMedCentralGoogle Scholar
  408. Zhou J, Liu M, Jiang J, Qiao G, Lin S, Li H, Xie L, Zhuo R (2012a) Expression profile of miRNAs in Populus cathayana L. and Salix matsudana Koidz under salt stress. Mol Biol Rep 39(9):8645–8654PubMedCrossRefPubMedCentralGoogle Scholar
  409. Zhou ZS, Song JB, Yang ZM (2012b) Genome-wide identification of Brassica napus microRNAs and their targets in response to cadmium. J Exp Bot 63(12):4597–4613PubMedPubMedCentralCrossRefGoogle Scholar
  410. Zhou M, Li D, Li Z, Hu Q, Yang C, Zhu L, Luo H (2013) Constitutive expression of a miR319 gene alters plant development and enhances salt and drought tolerance in transgenic creeping bentgrass. Plant Physiol 161(3):1375–1391PubMedPubMedCentralCrossRefGoogle Scholar
  411. Zhu J-K (2002) Salt and drought stress signal transduction in plants. Annu Rev Plant Biol 53(1):247–273PubMedPubMedCentralCrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Ratanesh Kumar
    • 1
  • Sudhir Kumar
    • 1
  • Neeti Sanan-Mishra
    • 1
  1. 1.Plant RNAi Biology GroupInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia

Personalised recommendations